Contacts of the helix formed by residues 74 - 108 (chain A) in PDB entry 5IU4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ALA 3.3 2.2 + - - -
73A ALA* 1.3 71.2 - - - +
75A HIS* 1.3 60.3 + - - +
77A CYS* 3.3 3.4 + - - +
78A LEU* 2.9 25.1 + - - +
145A ASN 4.9 0.4 - - - -
146A CYS* 2.0 58.1 - - + +
162A GLY 4.0 8.6 + - - +
164A VAL* 4.0 27.6 - - + -
171A VAL* 3.8 23.3 - - - -
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Residues in contact with HIS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ALA* 3.2 1.4 - - - +
74A CYS* 1.3 76.3 + - + +
76A GLY* 1.3 65.4 + - - +
78A LEU* 3.3 24.1 + - + +
79A PHE 3.1 16.6 + - - -
140A MET* 3.6 25.8 - - + +
144A ASN* 3.9 15.8 + - - -
146A CYS* 3.9 19.2 - - + +
2402A CLR 3.7 19.5 - - + +
2420A OLA 5.3 6.8 + - - -
2421A OLA 4.9 8.7 - - - +
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ALA 3.1 8.0 + - - -
75A HIS* 1.3 73.3 - - - +
77A CYS* 1.3 64.2 + - - +
79A PHE* 3.1 12.2 + - - +
80A ILE* 3.1 18.5 + - - +
2402A CLR 3.3 25.8 + - - +
2403A CLR 3.6 28.1 - - - +
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Residues in contact with CYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ILE* 4.3 2.0 - - - -
72A ALA* 4.1 6.5 - - + +
73A ALA 3.0 12.0 + - - +
74A CYS* 3.4 13.5 - - - +
76A GLY* 1.3 74.4 - - - +
78A LEU* 1.3 63.2 + - - +
80A ILE* 3.2 7.0 + - - +
81A ALA* 2.8 21.7 + - - +
164A VAL* 4.8 1.1 - - + -
166A CYS* 2.0 62.3 - - + -
167A LEU 4.1 0.2 - - - -
171A VAL* 3.9 26.0 - - + -
2403A CLR 4.2 2.5 - - - +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A CYS 2.9 12.9 + - - +
75A HIS* 3.5 20.2 - - + +
76A GLY 3.2 0.2 - - - -
77A CYS* 1.3 76.7 - - - +
79A PHE* 1.3 58.1 + - - +
81A ALA* 3.2 3.5 + - - -
82A CYS* 2.9 35.5 + - - +
139A PRO* 3.9 23.1 - - + +
140A MET* 4.3 11.0 - - + -
144A ASN* 3.5 39.0 - - + +
146A CYS* 3.7 12.6 - - - -
171A VAL* 3.5 38.8 - - + +
172A VAL* 4.3 6.5 - - + -
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Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 4.0 17.0 - + - -
75A HIS 3.1 7.1 + - - +
76A GLY* 3.1 10.5 + - - +
78A LEU* 1.3 76.3 - - - +
80A ILE* 1.3 61.9 + - - +
82A CYS* 4.9 0.9 - - - -
83A PHE* 3.0 50.5 + + - +
133A PHE* 5.4 1.6 - + - -
137A LEU* 4.0 21.5 - - + -
140A MET* 3.7 34.3 - - + -
2402A CLR 3.6 57.7 - - + -
2403A CLR 3.8 33.2 - - + -
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 3.5 71.2 - - + +
65A THR* 4.8 5.4 - - + -
66A ILE* 4.2 17.8 - - + +
70A PHE* 5.2 3.6 - - + -
76A GLY 3.1 12.7 + - - +
77A CYS* 3.5 10.5 - - - +
79A PHE* 1.3 76.3 - - - +
81A ALA* 1.3 63.5 + - - +
83A PHE* 4.0 2.1 + - - +
84A VAL* 5.0 2.4 + - - +
166A CYS* 5.0 2.7 - - - -
2403A CLR 3.5 44.4 - - + -
2429A OLC 4.5 10.1 - - + -
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ILE* 3.5 26.2 - - + -
77A CYS 2.8 16.5 + - - +
78A LEU* 3.6 5.6 - - - +
80A ILE* 1.3 77.4 - - - +
82A CYS* 1.3 61.8 + - - +
84A VAL* 3.7 14.9 - - - +
85A LEU* 4.7 0.5 - - - +
168A PHE* 3.6 22.9 - - + -
171A VAL* 4.4 3.6 - - + -
172A VAL* 3.8 24.7 - - + -
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Residues in contact with CYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 2.9 23.8 + - - +
81A ALA* 1.3 77.5 - - - +
83A PHE* 1.3 66.1 + - - +
84A VAL 3.1 3.1 - - - -
85A LEU* 2.8 32.3 + - + +
86A VAL* 3.5 3.5 + - - +
136A GLY 3.3 16.9 - - - +
137A LEU* 3.8 13.5 - - + -
139A PRO* 3.8 35.7 - - - -
140A MET* 5.4 1.6 - - + -
172A VAL* 4.1 17.0 - - - -
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Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.8 7.2 - - + -
58A LEU* 3.7 35.2 - - + -
59A ALA* 4.7 2.7 - - - -
62A PHE* 3.8 30.3 - + + -
79A PHE* 3.0 40.1 + + + +
80A ILE 4.0 0.2 + - - -
81A ALA 3.6 1.2 - - - -
82A CYS* 1.3 76.6 - - - +
84A VAL* 1.3 65.3 + - - +
86A VAL* 3.0 28.1 + - + +
87A LEU* 3.4 39.0 + - + +
133A PHE* 3.8 32.8 - + - -
137A LEU* 4.3 2.7 - - - +
2402A CLR 6.0 1.1 - - + -
2430A OLC 5.1 4.0 - - + -
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A VAL* 5.2 4.3 - - + -
59A ALA* 4.0 30.0 - - + +
62A PHE* 5.7 0.4 - - - -
80A ILE 5.0 2.1 + - - +
81A ALA 3.7 18.8 + - - +
83A PHE* 1.3 78.2 - - - +
85A LEU* 1.3 71.2 + - + +
87A LEU* 3.2 7.1 + - + +
88A ALA* 2.9 27.9 + - - +
168A PHE* 5.6 1.6 - - + -
246A TRP* 3.9 25.4 - - + -
278A HIS* 4.7 14.6 - - + +
2401A ZMA 4.7 11.0 - - + +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ALA 4.7 1.3 - - - +
82A CYS* 2.8 29.2 + - - +
84A VAL* 1.3 80.0 - - + +
86A VAL* 1.3 59.2 + - - +
88A ALA* 3.9 7.1 - - + +
89A GLN* 3.0 30.7 + - - +
136A GLY* 3.8 21.5 - - - +
168A PHE* 5.1 3.8 - - + -
172A VAL* 5.2 0.2 - - + -
176A TYR* 3.8 32.8 - - + +
177A MET* 4.0 15.5 - - + -
181A ASN* 4.1 16.9 + - - +
246A TRP* 5.8 0.2 - - + -
2401A ZMA 3.5 38.8 - - + -
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A CYS 4.0 0.7 - - - +
83A PHE* 3.0 19.5 + - + +
85A LEU* 1.3 77.9 - - - +
87A LEU* 1.3 58.0 + - + +
89A GLN 3.3 0.5 + - - -
90A SER* 2.9 26.0 + - - -
129A TRP* 4.6 7.6 - - + -
132A SER* 3.5 32.0 - - - +
133A PHE* 3.7 42.6 - - + +
136A GLY* 3.9 5.8 - - - -
137A LEU* 3.8 33.7 - - + -
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 3.8 8.2 - - + +
54A LEU* 3.6 30.3 - - + +
55A VAL* 3.5 46.9 - - + +
59A ALA* 4.0 10.8 - - + -
83A PHE* 3.8 31.4 - - + +
84A VAL* 3.2 7.0 + - + +
86A VAL* 1.3 72.8 - - + +
88A ALA* 1.3 67.0 + - - +
90A SER* 3.4 5.6 + - - -
91A SER* 3.0 27.2 + - - -
129A TRP* 4.0 25.1 - - + -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL* 2.9 17.2 + - - +
85A LEU* 4.0 9.2 - - + +
87A LEU* 1.3 76.3 - - - +
89A GLN* 1.3 57.7 + - - +
91A SER* 3.2 9.3 + - - -
92A ILE* 3.0 31.8 + - + +
186A VAL* 6.0 5.8 - - + -
242A PHE* 3.8 11.9 - - + -
246A TRP* 4.1 30.5 - - + -
2401A ZMA 6.0 0.7 - - + -
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Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU 3.0 18.5 + - - +
86A VAL 3.7 4.7 - - - +
87A LEU 3.2 0.2 - - - -
88A ALA* 1.3 74.5 - - - +
90A SER* 1.3 65.1 + - - +
92A ILE* 3.1 21.5 + - - +
93A PHE* 3.0 51.5 + - + -
132A SER* 3.5 12.3 - - - +
135A ILE* 3.7 26.3 - - + +
181A ASN* 4.5 4.9 + - - -
185A CYS* 2.9 48.6 + - - +
186A VAL* 4.4 7.3 - - - +
189A PRO* 4.9 1.4 - - - +
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER* 4.2 4.5 + - - -
48A LEU* 6.2 0.2 - - - -
51A ALA* 4.6 2.5 - - - +
86A VAL 2.9 17.6 + - - -
87A LEU 3.7 4.9 - - - -
89A GLN* 1.3 76.0 - - - +
91A SER* 1.3 56.7 + - - +
93A PHE* 3.3 5.4 + - - +
94A SER* 2.9 30.5 + - - -
128A CYS* 5.1 2.0 - - - +
129A TRP* 3.1 51.1 + - - -
132A SER* 3.1 16.6 + - - -
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Residues in contact with SER 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.6 20.0 - - - +
51A ALA* 3.8 9.1 - - - +
87A LEU 3.0 16.0 + - - -
88A ALA* 3.2 9.8 + - - -
90A SER* 1.3 77.6 - - - +
92A ILE* 1.3 56.2 + - - +
94A SER* 3.2 2.9 + - - -
95A LEU* 2.9 36.9 + - - +
242A PHE* 3.6 14.8 - - - -
2400A NA 2.5 29.6 - - - -
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA 3.0 18.3 + - - +
89A GLN* 3.1 25.5 + - - +
91A SER* 1.3 74.9 - - - +
93A PHE* 1.3 63.1 + - + +
95A LEU* 3.3 1.7 + - - -
96A LEU* 2.9 29.4 + - + +
185A CYS 4.0 5.6 - - - +
186A VAL* 4.2 18.4 - - + +
189A PRO* 3.5 27.4 - - + -
190A LEU* 3.9 28.7 - - + -
193A MET* 3.5 9.8 - - + +
242A PHE* 3.5 28.9 - - + -
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Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 6.2 0.2 - - - -
89A GLN* 3.0 34.4 + - + -
90A SER 3.7 6.1 - - - +
92A ILE* 1.3 80.0 - - + +
94A SER* 1.3 62.6 + - - +
96A LEU* 4.5 7.2 - - + -
97A ALA* 3.0 24.4 + - - +
128A CYS* 3.6 38.3 - - + -
131A LEU* 3.9 25.6 - - + -
132A SER* 3.3 27.6 - - - -
135A ILE* 4.0 19.5 - - + -
189A PRO* 6.0 3.4 - - + -
2409A OLA 3.8 22.5 - - + +
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Residues in contact with SER 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 3.8 25.1 - - - +
47A SER* 3.4 26.3 + - - -
48A LEU* 3.9 16.5 + - - -
90A SER* 2.9 15.0 + - - -
91A SER 3.6 6.7 - - - -
93A PHE* 1.3 76.4 - - - +
95A LEU* 1.3 57.1 + - - +
97A ALA* 3.3 6.7 + - - +
98A ILE* 2.9 35.4 + - - +
128A CYS* 5.8 0.2 - - - +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.9 16.4 - - + -
91A SER* 2.9 22.2 + - - +
92A ILE* 3.3 3.6 + - - -
94A SER* 1.3 75.6 - - - +
96A LEU* 1.3 61.6 + - - +
98A ILE* 3.4 11.2 + - + +
99A ALA* 3.1 22.0 + - - +
190A LEU* 5.3 0.4 - - + -
193A MET* 3.7 24.1 - - + +
197A TYR* 4.6 2.9 + - - -
235A ALA 5.1 2.2 - - - +
238A ILE* 3.8 28.9 - - + -
239A ALA* 4.0 19.6 - - + +
242A PHE* 3.7 43.1 - - + -
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 2.9 17.5 + - + +
93A PHE* 3.8 11.2 - - + +
95A LEU* 1.3 78.0 - - - +
97A ALA* 1.3 56.6 + - - +
99A ALA* 3.2 3.3 + - + +
100A ILE* 2.9 52.2 + - + +
189A PRO* 4.5 15.9 - - + +
192A LEU* 4.5 18.8 - - + -
193A MET* 3.8 37.8 - - + +
196A VAL* 4.8 4.5 - - + -
2409A OLA 4.1 17.5 - - + -
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 3.5 37.9 - - + -
93A PHE 3.0 17.6 + - - +
94A SER 3.6 1.1 - - - +
96A LEU* 1.3 77.4 - - - +
98A ILE* 1.3 57.5 + - - +
100A ILE 3.2 0.7 + - - -
101A ASP* 2.8 27.4 + - - +
128A CYS* 6.2 0.2 - - - -
2409A OLA 3.1 37.9 - - + +
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 4.1 20.9 - - + +
44A PHE* 3.6 24.7 - - + +
45A VAL* 4.0 28.3 - - + +
48A LEU* 4.4 14.4 - - + -
94A SER 2.9 24.8 + - - +
95A LEU* 3.7 11.2 - - + +
96A LEU 3.3 0.2 - - - -
97A ALA* 1.3 75.5 - - - +
99A ALA* 1.3 63.5 + - - +
101A ASP* 3.3 6.0 + - - +
102A ARG* 3.0 24.8 + - + +
197A TYR* 4.2 1.8 - - - +
235A ALA* 3.8 29.4 - - + +
238A ILE* 6.4 0.2 - - + -
288A TYR* 5.3 0.7 - - - +
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU 3.1 11.7 + - - +
96A LEU* 3.2 11.2 + - + +
98A ILE* 1.3 77.0 - - - +
100A ILE* 1.3 62.1 + - - +
102A ARG* 3.3 2.1 + - - -
103A TYR 3.0 18.0 + - - -
193A MET* 4.7 5.6 - - + -
196A VAL* 3.5 22.1 - - + +
197A TYR* 3.6 39.2 + - + -
200A ILE* 3.5 9.9 - - - +
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 2.9 44.2 + - + +
97A ALA 3.8 3.4 - - - +
99A ALA* 1.3 77.5 - - - +
101A ASP* 1.3 64.2 + - - +
103A TYR* 3.1 6.2 + - + +
104A ILE* 3.0 40.7 + - + +
196A VAL* 4.3 17.9 - - + -
2409A OLA 4.0 32.8 - - + -
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.8 4.6 - - + +
41A THR* 2.7 34.0 + - + +
44A PHE* 5.3 1.1 - - + -
97A ALA 2.8 17.4 + - - +
98A ILE* 3.6 7.4 - - - +
100A ILE* 1.3 78.0 - - - +
102A ARG* 1.3 81.8 + - - +
104A ILE* 3.4 5.0 + - - +
105A ALA* 3.1 18.5 + - - +
112A TYR* 2.6 34.4 + - - -
116A VAL* 3.4 13.7 - - - +
2409A OLA 3.8 14.8 + - - +
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Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 3.4 24.0 + - + +
98A ILE* 3.0 27.5 + - + +
99A ALA* 3.7 4.5 - - - +
101A ASP* 1.3 103.1 + - - +
103A TYR* 1.3 61.3 + - - +
105A ALA* 3.4 30.1 + - - +
106A ILE* 3.1 24.8 + - - +
112A TYR* 3.6 11.7 + - - -
197A TYR* 5.4 0.9 - - + +
200A ILE* 3.9 14.7 - - + +
228A GLU* 4.8 16.1 + - - +
231A ALA* 5.0 20.6 - - - +
232A ALA* 4.9 13.9 - - + +
235A ALA* 4.9 9.4 - - + -
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Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA 3.0 14.2 + - - +
100A ILE* 3.1 10.5 + - + +
102A ARG* 1.3 74.3 - - - +
104A ILE* 1.3 69.9 + - + +
106A ILE* 3.3 2.8 + - + +
107A ALA* 2.9 54.7 + - + +
108A ILE* 6.4 0.4 - - + -
196A VAL* 4.0 11.4 - - + -
199A ARG* 3.8 47.2 + - + -
200A ILE* 3.6 27.3 - - + +
203A ALA* 5.0 3.6 - - + -
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Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ILE* 3.0 32.3 + - + +
101A ASP* 3.8 6.1 - - - +
103A TYR* 1.3 83.3 - - + +
105A ALA* 1.3 63.4 + - - +
108A ILE* 3.0 53.0 + - + +
112A TYR* 3.7 22.2 - - + -
115A LEU* 3.9 20.6 - - + -
116A VAL* 3.9 19.1 - - + -
2409A OLA 4.4 9.9 - - + +
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASP 3.1 10.0 + - - +
102A ARG* 3.5 41.1 - - - +
103A TYR 3.2 0.4 - - - -
104A ILE* 1.3 77.0 - - - +
106A ILE* 1.3 60.2 + - - +
109A PRO* 3.3 24.6 - - - +
112A TYR* 3.7 21.7 - - + -
228A GLU* 3.2 13.4 - - - +
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Residues in contact with ILE 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG 3.1 16.1 + - - +
103A TYR* 3.4 15.7 - - + +
105A ALA* 1.3 78.0 - - - +
107A ALA* 1.3 63.3 + - + +
109A PRO* 3.8 6.0 - - - +
200A ILE* 3.9 24.9 - - + +
203A ALA* 4.3 12.6 - - + -
204A ALA* 3.5 35.9 - - + +
207A GLN* 2.6 42.2 + - - +
225A LEU* 4.0 15.0 - - + -
228A GLU* 3.3 27.8 + - + +
229A VAL* 5.0 2.2 - - + -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 2.9 51.6 + - + +
106A ILE* 1.3 80.5 - - + +
108A ILE* 1.3 73.8 + - + +
109A PRO* 3.5 4.5 - - - +
203A ALA* 5.1 5.6 - - + -
207A GLN* 4.3 6.5 + - - +
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 6.4 0.4 - - + -
104A ILE* 3.0 37.1 + - + +
107A ALA* 1.3 88.3 - - + +
109A PRO* 1.3 65.3 - - - +
110A LEU* 3.1 5.6 + - - -
111A ARG* 3.2 62.6 + - + +
112A TYR 3.2 7.3 + - - -
115A LEU* 4.2 12.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il