Contacts of the helix formed by residues 82 - 105 (chain A) in PDB entry 4B8Z
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 TYR 82 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A MET* 4.5 4.0 - - + -
78A ARG* 3.0 50.6 + - + +
79A ASN 3.5 0.6 + - - -
81A LYS* 1.4 105.4 - - + +
83A ASN* 1.3 56.9 + - - +
84A LEU 3.3 2.9 - - - -
85A ASP* 3.3 22.7 + - + +
86A PHE* 3.0 36.3 + + + -
184A ASP* 4.8 5.1 + - - -
160C GLN* 3.3 16.4 - - - -
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Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASN* 3.2 15.8 + - - +
80A ILE* 4.5 6.5 + - - +
81A LYS 3.9 1.2 - - - -
82A TYR* 1.3 75.0 - - - +
84A LEU* 1.4 56.2 + - - +
86A PHE* 3.9 3.7 - - - +
87A TRP* 3.1 28.1 + - - +
138A ASN 3.8 2.0 + - - -
139A SER 2.9 21.4 + - - -
140A ASN* 3.4 14.2 - - - -
141A PHE* 3.5 40.5 - - + -
142A GLY* 3.1 24.3 + - - +
143A TYR 4.2 1.9 + - - -
156C ALA* 4.5 4.3 - - + +
159C GLN* 5.2 0.8 + - - -
160C GLN* 3.1 4.1 + - - +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASN* 1.4 70.1 - - - +
85A ASP* 1.4 59.8 + - - +
87A TRP* 3.3 9.1 + - + +
88A ARG* 2.8 59.0 + - + +
99C HIS* 4.7 7.0 - - + -
102C PHE* 5.6 0.7 - - + -
153C GLN* 4.6 0.9 - - - +
156C ALA* 3.7 33.6 + - + +
157C TYR* 3.9 46.9 - - + -
160C GLN* 2.8 24.1 + - - +
161C TYR* 4.1 18.2 - - + +
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Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A MET* 3.6 22.0 - - + -
82A TYR* 3.3 16.5 + - + +
84A LEU* 1.4 78.7 - - - +
86A PHE* 1.4 58.0 + - - +
88A ARG* 4.8 2.5 - - - -
89A LYS* 3.0 45.6 + - + +
160C GLN* 2.9 29.1 + - - -
161C TYR* 4.2 7.4 + - - -
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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
----------------------------------------------------------
72A MET* 3.3 54.3 - - + -
73A VAL* 4.0 1.1 - - - -
74A GLY 3.5 18.2 - - - -
78A ARG* 3.6 39.3 - - + -
79A ASN* 3.3 39.5 - - - +
82A TYR* 3.0 30.9 + - + +
83A ASN* 4.0 5.4 - - - +
85A ASP* 1.4 75.2 - - - +
87A TRP* 1.3 55.9 + - - +
90A ASN* 2.7 35.0 + - - +
142A GLY 4.2 2.2 - - - -
143A TYR* 3.7 25.7 - + + +
146A ALA* 4.0 1.9 - - - +
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Residues in contact with TRP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASN 3.1 19.1 + - - +
84A LEU* 3.6 13.9 - - + +
85A ASP 3.2 0.2 - - - -
86A PHE* 1.3 76.7 - - - +
88A ARG* 1.4 83.6 + - + +
91A VAL* 3.1 67.5 + - + +
142A GLY* 3.6 19.9 - - - +
145A TYR* 3.7 13.2 - - + -
146A ALA* 3.6 29.0 - - - +
149A MET* 4.2 5.2 - - + -
87C TRP* 5.2 2.5 - + - -
91C VAL* 5.9 4.0 - - + -
95C ASP* 5.3 2.8 + - - -
149C MET* 3.4 51.6 - - + -
152C VAL* 4.3 10.3 - - + -
153C GLN* 4.2 19.8 - - + +
156C ALA* 5.3 2.5 - - + -
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Residues in contact with ARG 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 LEU* 2.8 32.5 + - + +
85A ASP* 4.4 2.7 - - - +
87A TRP* 1.4 84.8 - - + +
89A LYS* 1.4 64.1 + - + +
91A VAL* 3.4 2.8 + - - +
92A HIS* 2.7 50.0 + - + -
95C ASP* 2.8 43.6 + - - +
99C HIS* 3.3 57.3 + - - +
157C TYR* 3.7 10.1 - - + -
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 3.7 16.9 - - + +
72A MET* 4.4 15.0 - - + -
85A ASP* 3.0 35.5 + - + +
88A ARG* 1.4 73.8 - - + +
90A ASN* 1.4 59.5 + - - +
92A HIS* 3.7 2.8 + - - +
93A MET* 3.2 41.0 + - + +
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Residues in contact with ASN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 3.5 11.9 - - - +
72A MET* 2.6 48.7 + - - +
86A PHE* 2.7 25.2 + - - +
87A TRP 3.7 0.8 + - - -
88A ARG 3.3 0.8 - - - -
89A LYS* 1.4 73.7 - - - +
91A VAL* 1.4 55.2 + - - +
93A MET* 3.2 5.8 + - - +
94A ASN* 2.8 47.3 + - - +
143A TYR* 3.5 23.2 - - - +
146A ALA* 3.7 12.9 - - + +
147A LYS* 4.7 4.1 - - - +
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TRP* 3.1 65.0 + - + +
88A ARG* 3.9 3.6 - - - +
90A ASN* 1.4 74.4 - - - +
92A HIS* 1.3 63.2 + - + +
94A ASN* 3.9 6.0 - - - +
95A ASP* 3.0 33.4 + - + +
146A ALA* 4.0 11.7 - - + +
149A MET* 5.3 4.7 - - + -
87C TRP* 5.8 4.7 - - + -
91C VAL* 4.2 25.1 - - + -
95C ASP* 6.2 3.8 - - + -
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Residues in contact with HIS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 4.0 29.1 - - - +
88A ARG* 2.7 56.3 + - + +
89A LYS* 3.8 6.5 + - - +
91A VAL* 1.3 79.1 - - + +
93A MET* 1.4 57.2 + - - +
95A ASP* 3.5 3.3 + - - +
96A ASN* 3.0 39.5 + - - -
51C THR* 6.4 0.2 - - - +
92C HIS* 6.3 2.9 - + - -
95C ASP* 2.9 33.5 + - - +
96C ASN* 5.7 0.8 + - - -
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Residues in contact with MET 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.4 30.7 - - + -
49A THR* 3.8 6.1 - - + -
68A HIS* 4.3 2.5 - - + -
70A ALA* 3.9 27.4 - - - +
71A ALA* 3.9 1.1 - - - -
72A MET* 3.7 26.2 - - + +
89A LYS* 3.2 37.5 + - + +
90A ASN* 3.6 6.7 - - - +
92A HIS* 1.4 77.1 - - - +
94A ASN* 1.3 58.6 + - - +
96A ASN* 3.6 0.7 + - - +
97A VAL* 3.1 35.7 + - - +
900A NAP 3.6 38.6 - - - +
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Residues in contact with ASN 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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68A HIS* 2.8 31.4 + - + +
70A ALA 4.4 4.0 - - - +
71A ALA* 5.6 0.9 - - - +
90A ASN* 2.8 34.6 + - - +
91A VAL* 3.9 5.4 - - - +
93A MET* 1.3 71.4 - - - +
95A ASP* 1.3 57.9 + - - +
97A VAL* 4.0 0.7 - - - +
98A LEU* 2.9 41.4 + - + +
146A ALA 3.4 25.1 + - - -
147A LYS* 4.9 5.5 + - - +
150A ILE* 3.5 32.1 - - + +
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Residues in contact with ASP 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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91A VAL* 3.0 22.1 + - + +
92A HIS* 4.0 4.0 - - - +
94A ASN* 1.3 76.7 - - - +
96A ASN* 1.3 64.1 + - - +
98A LEU* 4.3 4.4 - - - +
99A HIS* 3.0 30.5 + - - +
157A TYR* 4.9 1.4 + - - -
87C TRP* 5.2 3.9 + - - +
88C ARG* 2.9 45.2 + - - +
91C VAL* 6.2 3.8 - - + -
92C HIS* 3.0 24.3 + - - -
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Residues in contact with ASN 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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48A LEU 2.9 26.6 + - - +
49A THR 3.1 23.8 + - - -
50A ASP 3.7 0.2 - - - -
51A THR* 3.4 31.8 - - - +
54A THR* 3.4 15.3 - - + +
92A HIS* 3.0 21.8 + - - +
93A MET 4.0 0.7 - - - +
95A ASP* 1.3 80.1 - - - +
97A VAL* 1.3 57.4 + - - +
99A HIS* 5.2 0.9 - - - -
100A SER* 2.7 36.6 + - - +
92C HIS* 5.7 1.0 + - - -
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Residues in contact with VAL 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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13A THR* 4.2 15.5 - - + -
48A LEU* 4.5 12.8 - - + -
54A THR* 4.3 12.3 - - + -
58A PHE* 3.6 22.8 - - + -
66A VAL* 4.2 7.6 - - + -
68A HIS* 3.5 44.4 - - + +
93A MET 3.1 22.3 + - - +
94A ASN 4.1 1.1 - - - +
96A ASN* 1.3 74.5 - - - +
98A LEU* 1.3 61.4 + - + +
100A SER 3.5 0.2 + - - -
101A ALA* 3.1 29.8 + - - +
109A VAL* 5.2 2.5 - - + -
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Residues in contact with LEU 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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68A HIS* 5.5 2.0 - - + -
94A ASN* 2.9 28.7 + - + +
95A ASP* 4.3 3.6 - - - +
97A VAL* 1.3 77.9 - - + +
99A HIS* 1.3 59.2 + - - +
101A ALA* 3.7 1.7 - - - +
102A PHE* 3.2 17.2 + - - +
109A VAL* 3.7 20.6 - - + -
111A SER* 3.7 21.1 - - - +
150A ILE* 4.5 15.9 - - + +
153A GLN* 3.8 28.7 - - + -
154A ASN* 3.9 11.9 - - - +
157A TYR* 3.9 14.4 - - + +
165A PHE* 3.3 30.4 - - + -
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Residues in contact with HIS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASP* 3.0 19.7 + - - +
96A ASN* 4.8 1.1 - - - +
98A LEU* 1.3 73.7 - - - +
100A SER* 1.4 59.3 + - - +
102A PHE* 3.3 23.7 + + - +
103A GLU* 3.1 44.3 + - + +
157A TYR* 2.7 28.7 + + - +
84C LEU* 4.6 6.5 - - + -
88C ARG* 3.3 47.6 + - - +
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Residues in contact with SER 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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51A THR 5.0 0.7 + - - -
54A THR* 3.7 9.1 - - - +
55A ARG* 3.9 16.3 + - - +
58A PHE* 3.6 31.0 - - - -
96A ASN* 2.7 25.4 + - - -
97A VAL 3.9 0.4 - - - -
99A HIS* 1.4 74.5 - - - +
101A ALA* 1.3 58.8 + - - +
103A GLU* 3.6 5.4 + - - +
104A VAL* 3.2 35.7 + - - +
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Residues in contact with ALA 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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58A PHE* 3.7 19.9 - - + -
66A VAL* 4.2 2.0 - - + -
97A VAL 3.1 18.9 + - - +
98A LEU 3.7 4.9 - - - +
100A SER* 1.3 75.0 - - - +
102A PHE* 1.3 56.1 + - - +
104A VAL* 4.0 2.1 - - - +
105A GLY 3.2 6.1 + - - -
106A ALA* 2.8 39.6 + - + +
109A VAL* 3.6 30.7 - - + -
165A PHE* 4.3 1.6 - - + -
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Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU 3.2 14.5 + - - +
99A HIS* 3.4 32.8 - + - +
100A SER 3.3 0.2 - - - -
101A ALA* 1.3 76.1 - - - +
103A GLU* 1.4 64.9 + - + +
105A GLY* 3.1 18.6 + - - -
106A ALA 5.0 0.2 - - - +
157A TYR* 3.6 23.3 - + + -
161A TYR* 3.5 63.5 - + + -
163A CYS* 3.7 15.7 - - - -
165A PHE* 4.0 7.2 - - + -
84C LEU* 5.6 0.7 - - + -
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Residues in contact with GLU 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 HIS* 3.1 38.3 + - + +
100A SER* 3.6 5.6 + - - +
102A PHE* 1.4 82.3 - - + +
104A VAL* 1.4 60.8 + - + +
105A GLY 3.6 0.3 + - - -
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG 5.4 0.9 - - - +
58A PHE* 3.4 39.5 - - + +
59A GLU* 4.4 5.4 - - + +
62A GLN* 4.2 13.2 - - + -
63A PRO* 3.8 25.6 - - + +
100A SER* 3.2 19.7 + - - +
101A ALA* 4.3 4.5 - - - +
103A GLU* 1.4 78.4 - - + +
105A GLY* 1.3 60.7 + - - +
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Residues in contact with GLY 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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63A PRO 4.6 3.1 - - - +
64A THR* 5.3 1.6 - - - +
101A ALA 3.2 0.8 + - - -
102A PHE 3.1 15.9 + - - -
103A GLU 3.3 0.8 - - - -
104A VAL* 1.3 81.5 - - - +
106A ALA* 1.4 64.4 + - - +
107A ARG* 3.6 2.4 + - - +
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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