Contacts of the helix formed by residues 70 - 92 (chain A) in PDB entry 2F93
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 ALA 70 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLY* 3.1 14.0 + - - +
61A VAL* 4.4 13.4 - - + +
68A VAL* 4.1 2.0 + - - +
69A PHE* 1.3 71.1 - - - +
71A PRO* 1.3 72.1 - - + +
72A ARG 3.2 0.5 + - - -
73A TYR* 3.2 10.5 + - - +
74A ILE* 3.0 30.3 + - + +
113A PHE* 4.5 14.9 - - + -
117A MET* 5.0 8.1 - - + -
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Residues in contact with PRO 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA* 3.7 20.4 - - + +
53A VAL* 4.1 12.1 - - + -
54A MET* 3.5 29.6 - - + -
58A VAL 3.6 12.8 - - - +
59A GLY* 3.4 18.2 - - - +
69A PHE* 3.4 4.0 - - - -
70A ALA* 1.3 93.0 - - + +
72A ARG* 1.3 60.9 + - - +
74A ILE* 4.0 7.9 - - + +
75A ASP* 2.9 26.7 + - - +
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Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 5.5 1.6 - - - -
54A MET* 3.9 16.1 - - + +
68A VAL* 6.2 0.6 - - - +
69A PHE* 3.1 30.4 + - + +
70A ALA 3.1 1.0 - - - -
71A PRO* 1.3 79.9 - - - +
73A TYR* 1.3 82.8 + - + +
75A ASP* 3.2 6.7 - - - +
76A TRP* 3.0 70.0 + - + +
177A ILE* 5.4 0.6 - - - +
183A PRO* 5.1 4.4 - - - +
193A ASP* 2.8 39.8 + - - -
194A VAL* 3.6 30.1 - - - +
197A ILE* 3.8 24.3 - - + +
201A ASP* 5.6 0.7 - - - +
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Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 4.3 5.8 - - + +
69A PHE 3.2 38.8 + - - -
70A ALA* 3.2 3.6 + - - +
72A ARG* 1.3 92.6 + - - +
74A ILE* 1.3 61.0 + - - +
76A TRP* 3.4 38.0 + + - +
77A ILE* 2.9 35.6 + - - +
109A MET 5.1 1.5 - - - +
112A GLY* 4.0 20.6 - - - -
113A PHE* 3.4 36.8 - + + -
116A ALA* 3.6 19.7 - - + -
117A MET* 5.7 1.6 - - - -
178A TRP* 4.1 9.3 - + - -
183A PRO* 3.2 29.5 - - - +
301A RET 5.4 0.2 - - + -
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 3.0 22.9 + - + +
71A PRO* 4.0 6.7 - - + +
73A TYR* 1.3 72.8 - - - +
75A ASP* 1.3 69.2 + - - +
77A ILE* 3.3 13.2 + - + +
78A LEU* 3.2 39.0 + - + +
113A PHE* 3.7 33.7 - - + -
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 4.7 9.6 - - - -
47A ALA* 3.2 33.0 - - - +
50A ALA* 3.7 15.5 - - + +
51A TYR* 4.7 8.3 - - - -
54A MET* 6.0 0.3 - - - +
71A PRO 2.9 19.8 + - - +
72A ARG* 3.2 8.6 - - - +
74A ILE* 1.3 75.9 - - - +
76A TRP* 1.3 66.8 + - - +
78A LEU* 3.0 4.4 + - - +
79A THR* 2.7 51.0 + - - +
201A ASP* 4.9 2.3 - - - +
205A LYS* 3.6 8.9 + - - -
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Residues in contact with TRP 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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72A ARG* 3.0 47.8 + - + +
73A TYR* 3.6 36.3 - + - +
74A ILE 3.3 0.2 - - - -
75A ASP* 1.3 90.1 - - - +
77A ILE* 1.3 60.2 + - - +
79A THR* 3.9 3.4 - - - -
80A THR* 2.6 36.6 + - + -
109A MET* 4.0 15.5 - - + -
174A TYR* 3.5 34.1 - + - -
178A TRP* 5.8 0.7 - + - -
197A ILE* 4.0 14.1 - - + -
201A ASP* 3.6 20.8 + - - -
205A LYS* 4.3 0.2 - - - -
301A RET 3.7 62.9 - - + +
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Residues in contact with ILE 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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73A TYR 2.9 24.3 + - - +
74A ILE* 3.6 15.7 - - + +
76A TRP* 1.3 75.3 - - - +
78A LEU* 1.3 69.8 + - + +
81A PRO* 3.1 20.3 - - - +
105A ASN* 5.1 0.2 - - - +
106A THR* 5.5 10.7 + - + -
109A MET* 3.7 28.2 - - + +
110A LEU* 3.8 29.4 - - + +
113A PHE* 4.0 28.3 - - + -
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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
----------------------------------------------------------
46A ILE* 4.5 29.0 - - + +
74A ILE* 3.3 34.3 - - + +
75A ASP 3.0 4.0 + - - +
77A ILE* 1.3 89.8 - - + +
79A THR* 1.3 58.3 + - - +
81A PRO* 3.3 15.0 - - - +
82A LEU* 3.5 17.9 - - - +
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Residues in contact with THR 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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43A ILE* 3.5 29.3 - - - +
46A ILE* 3.6 27.4 - - + -
47A ALA 4.2 0.4 - - - +
75A ASP* 2.7 44.2 + - - +
76A TRP* 3.9 1.2 - - - -
78A LEU* 1.3 71.6 - - - +
80A THR* 1.3 67.4 + - - +
81A PRO* 3.2 2.5 - - - -
82A LEU* 2.9 19.5 + - - +
83A ILE* 3.0 15.1 + - - +
205A LYS* 3.2 21.2 + - - -
301A RET 3.8 1.4 - - - +
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Residues in contact with THR 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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76A TRP* 2.6 25.0 + - - +
79A THR* 1.3 72.6 + - - +
81A PRO* 1.3 66.8 - - - +
83A ILE* 3.1 7.6 + - - +
84A VAL* 2.9 25.8 + - - +
105A ASN* 2.9 22.4 + - - -
109A MET* 3.2 21.3 - - + +
171A TRP* 3.6 16.4 - - + -
301A RET 3.7 45.5 - - + -
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Residues in contact with PRO 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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77A ILE 3.1 27.6 - - - +
78A LEU* 3.3 14.8 - - - +
79A THR 3.3 2.2 - - - -
80A THR* 1.3 98.3 - - - +
82A LEU* 1.3 58.3 + - + -
84A VAL* 3.4 1.3 + - + -
85A TYR* 2.9 26.7 + - - +
102A ILE* 3.5 33.3 - - + +
105A ASN* 3.6 14.1 - - - +
106A THR* 5.1 4.3 - - - +
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Residues in contact with LEU 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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39A THR* 3.4 20.3 - - + +
42A GLY* 4.2 27.6 - - - -
43A ILE* 3.5 14.6 - - + +
46A ILE* 4.3 13.0 - - + -
78A LEU 3.5 20.2 - - - +
79A THR* 2.9 9.3 + - - +
81A PRO* 1.3 78.1 - - + +
83A ILE* 1.3 62.0 + - - +
85A TYR* 3.3 16.7 + - + +
86A PHE* 2.9 23.0 + - - +
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Residues in contact with ILE 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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43A ILE* 3.7 22.4 - - + -
79A THR 3.0 16.5 + - - +
80A THR* 3.5 7.4 - - - +
82A LEU* 1.3 77.4 - - - +
84A VAL* 1.3 58.0 + - - +
86A PHE* 3.2 6.0 + - - +
87A LEU* 2.9 34.8 + - + +
167A THR* 4.5 2.7 - - - +
171A TRP* 3.8 30.1 - - + +
204A THR 3.9 19.7 - - - +
205A LYS* 4.3 6.3 - - + -
208A PHE* 3.9 28.5 - - + -
301A RET 4.0 24.7 - - + -
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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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80A THR 2.9 19.4 + - - +
81A PRO* 3.7 4.9 - - + +
83A ILE* 1.3 78.3 - - + +
85A TYR* 1.3 50.4 + - - +
87A LEU* 3.3 11.6 + - + +
88A GLY* 2.7 31.5 + - - -
98A PHE* 4.6 0.7 - - - -
101A VAL* 3.6 38.1 - - + +
102A ILE* 4.1 11.9 - - + -
105A ASN* 3.6 24.7 - - + +
137A LEU* 4.6 11.2 - - + -
141A LEU* 5.3 4.7 - - + -
145A MET* 4.6 6.6 - - + +
171A TRP* 4.0 12.3 - - + -
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Residues in contact with TYR 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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35A ARG* 2.9 40.6 + - - -
39A THR* 3.7 25.4 - - + -
81A PRO 2.9 17.9 + - - +
82A LEU* 3.4 17.0 - - + +
84A VAL* 1.3 75.1 - - - +
86A PHE* 1.3 55.2 + - - +
88A GLY* 3.1 1.2 + - - -
89A LEU* 2.8 70.8 + - + +
98A PHE* 3.7 28.5 - + - -
102A ILE* 4.9 5.4 - - + -
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Residues in contact with PHE 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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36A TYR* 3.5 48.2 - + + -
39A THR* 4.1 12.8 - - + -
40A LEU* 3.6 22.7 - - + -
43A ILE* 4.9 0.9 - - + -
82A LEU 2.9 13.4 + - - +
83A ILE* 3.4 11.4 - - - +
85A TYR* 1.3 78.1 - - - +
87A LEU* 1.3 63.2 + - - +
89A LEU* 3.2 11.7 + - + +
90A LEU* 3.1 36.1 + - + +
159A LEU* 5.3 0.7 - - + -
163A LEU* 3.6 23.6 - - + -
208A PHE* 3.7 18.6 - + + -
212A ALA* 3.8 22.2 - - + -
300A BOG 4.3 7.6 - - + -
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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
----------------------------------------------------------
83A ILE* 2.9 23.6 + - + +
84A VAL* 3.6 12.3 - - + +
86A PHE* 1.3 76.9 - - - +
88A GLY* 1.3 57.3 + - - +
90A LEU* 3.3 4.2 + - + +
91A ALA* 3.0 23.0 + - - +
141A LEU* 3.9 21.1 - - + -
145A MET* 4.0 8.5 - - + -
160A TYR* 3.5 30.7 - - + -
163A LEU* 3.7 38.6 - - + +
164A ARG* 4.2 4.9 - - - +
167A THR* 3.9 28.9 - - + +
208A PHE* 4.0 10.3 - - + -
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Residues in contact with GLY 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 2.7 16.7 + - - -
85A TYR 3.1 0.2 + - - -
87A LEU* 1.3 71.7 - - - +
89A LEU* 1.3 57.7 + - - +
91A ALA* 3.3 0.7 + - - -
92A GLY 3.0 23.0 + - - -
93A LEU* 3.2 30.5 + - - +
98A PHE* 3.4 22.9 - - - -
145A MET* 3.9 3.5 - - - +
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Residues in contact with LEU 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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35A ARG* 4.3 24.5 - - + -
36A TYR* 3.1 34.1 + - + +
39A THR* 4.6 4.0 - - - +
85A TYR* 2.8 65.0 + - + +
86A PHE* 3.5 6.5 - - - +
88A GLY* 1.3 72.7 - - - +
90A LEU* 1.3 63.3 + - - +
92A GLY* 3.2 8.2 + - - -
98A PHE* 3.6 10.3 - - + -
152A ARG* 3.0 15.9 + - - -
300A BOG 4.3 14.2 + - - +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.7 23.1 - - + +
86A PHE* 3.1 20.6 + - + +
87A LEU* 3.6 9.9 - - + +
89A LEU* 1.3 78.6 - - - +
91A ALA* 1.3 59.0 + - - +
149A ALA* 4.7 1.1 - - - -
152A ARG* 3.0 27.9 + - - +
156A ILE* 3.2 26.9 - - + +
159A LEU* 3.9 21.5 - - + -
160A TYR* 4.1 23.1 - - + +
163A LEU* 3.7 29.8 - - + -
219A LEU* 5.3 0.2 - - + -
300A BOG 4.1 19.3 - - + -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU 3.0 17.3 + - - +
88A GLY* 3.8 5.4 - - - +
89A LEU 3.3 0.4 - - - -
90A LEU* 1.3 76.0 - - - +
92A GLY* 1.3 55.5 + - - +
93A LEU* 4.2 15.0 - - + -
145A MET* 3.4 25.4 - - + +
148A SER* 2.6 37.6 + - - +
149A ALA* 3.8 10.8 - - + -
152A ARG* 4.1 3.0 - - - +
160A TYR* 4.0 10.9 - - + -
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Residues in contact with GLY 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 GLY 3.0 5.7 + - - -
89A LEU* 3.2 8.4 + - - -
90A LEU 3.2 4.4 - - - -
91A ALA* 1.3 79.2 - - - +
93A LEU* 1.3 66.4 + - - +
94A ASP 3.9 0.5 + - - -
97A GLU* 4.4 1.2 - - - +
148A SER* 3.7 6.8 + - - -
152A ARG* 4.3 13.0 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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