Contacts of the helix formed by residues 82 - 112 (chain B) in PDB entry 3GVY
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 THR 82 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TRP* 3.6 11.2 - - - -
80B GLY 3.6 0.4 - - - -
81B GLN* 1.3 87.1 - - + +
83B LEU* 1.3 65.9 + - - +
84B ARG* 3.5 9.5 + - - +
85B GLU* 3.0 38.2 + - - +
86B THR* 2.9 23.6 + - - -
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN* 5.3 2.9 - - + -
35B TRP* 3.6 13.2 - - + -
37B PHE* 3.5 57.4 - - + -
40B ILE* 4.3 22.4 - - + -
82B THR* 1.3 71.1 - - - +
84B ARG* 1.3 65.1 + - - +
86B THR* 3.0 23.4 + - + -
87B LEU* 3.4 10.9 + - + +
141B MET* 4.7 0.9 - - + -
149B TYR* 3.6 29.6 - - + -
150B GLY* 4.0 14.4 - - - +
153B ASN* 5.2 1.1 - - + -
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B THR* 3.3 8.6 + - - +
83B LEU* 1.3 77.8 - - - +
85B GLU* 1.3 62.9 + - + +
87B LEU* 3.6 4.2 + - - +
88B ASP* 3.0 53.2 + - - +
138B ILE* 4.4 11.0 - - - +
141B MET* 3.8 36.9 - - - +
146B GLU* 3.0 32.3 + - + +
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ILE 5.2 0.7 - - - +
80B GLY* 3.9 4.6 - - - -
81B GLN* 3.3 34.9 + - - +
82B THR* 3.0 34.7 + - - +
84B ARG* 1.3 76.5 - - + +
86B THR* 1.3 59.3 + - - +
88B ASP* 3.6 12.5 - - + +
89B ALA* 2.8 33.3 + - - +
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 3.1 41.4 + - - +
32B GLN* 2.8 31.2 + - + +
35B TRP* 4.4 9.5 - - - -
80B GLY* 4.0 5.2 - - - -
82B THR 2.9 11.2 + - - -
83B LEU* 3.0 15.5 + - + +
85B GLU* 1.3 76.5 - - - +
87B LEU* 1.3 71.2 + - + +
89B ALA 3.4 0.5 + - - -
90B ASP* 2.8 35.2 + - - +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN* 5.3 0.2 - - - +
40B ILE* 3.6 26.5 - - + -
83B LEU* 3.4 9.9 + - + +
84B ARG 3.9 4.7 - - - +
85B GLU 3.4 0.2 - - - -
86B THR* 1.3 83.8 - - + +
88B ASP* 1.3 66.6 + - - +
90B ASP* 3.3 2.3 + - - +
91B LEU* 2.9 24.1 + - - +
133B TYR* 5.1 2.5 - - + -
134B LEU* 3.7 31.0 - - + +
137B GLN* 3.9 19.5 - - + +
138B ILE* 4.2 15.7 - - + -
141B MET* 3.2 30.7 - - + -
149B TYR* 3.8 17.5 - - + +
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 3.0 49.2 + - - +
85B GLU* 3.6 15.1 - - + +
87B LEU* 1.3 75.5 - - - +
89B ALA* 1.3 58.1 + - - +
91B LEU* 2.7 32.2 + - - +
92B ALA* 3.2 11.5 + - - +
138B ILE* 3.8 13.4 - - - +
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 3.4 11.7 + - - -
28B HIS* 4.6 1.3 - - + -
78B ARG* 3.6 45.1 - - + +
79B ILE 4.8 0.7 - - - -
80B GLY* 4.4 8.7 - - - +
85B GLU 2.8 19.7 + - - +
86B THR 3.9 2.9 - - - +
88B ASP* 1.3 77.0 - - + +
90B ASP* 1.3 61.0 + - - +
92B ALA* 3.7 1.3 + - - +
93B ALA 3.5 13.2 + - - -
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 2.3 40.9 + - - +
25B TYR* 3.5 25.3 + - + -
28B HIS* 2.7 28.2 + - - +
44B SER* 4.7 4.3 + - - -
86B THR* 2.8 16.6 + - - +
87B LEU 3.9 3.8 - - - +
88B ASP 3.1 0.2 - - - -
89B ALA* 1.3 77.4 - - - +
91B LEU* 1.3 61.8 + - - +
92B ALA 3.4 0.2 - - - -
93B ALA* 3.7 2.3 + - - +
94B GLU* 3.2 28.2 + - - +
130B HIS* 5.1 1.9 - - + -
134B LEU* 3.7 18.5 - - + +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.7 2.5 - - + -
87B LEU 2.9 12.1 + - - +
88B ASP* 2.7 23.0 + - - +
90B ASP* 1.3 71.2 - - - +
92B ALA* 1.3 56.8 + - - -
94B GLU* 3.6 1.0 + - - +
95B HIS* 3.0 40.5 + - + +
131B ILE* 4.1 33.9 - - + -
134B LEU* 3.7 24.0 - - + +
135B GLU* 4.4 20.0 - - + +
138B ILE* 5.0 11.7 - - + -
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 3.6 29.6 - - - +
88B ASP 3.2 9.6 + - - +
89B ALA* 3.7 1.8 + - - +
90B ASP 3.4 0.2 - - - -
91B LEU* 1.3 74.9 - - - +
93B ALA* 1.3 67.2 + - - +
94B GLU 3.0 1.3 - - - -
95B HIS* 3.1 7.8 + - - +
96B ASP* 2.8 30.9 + - - +
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Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR* 5.9 2.9 - - - +
21B ALA* 5.9 4.5 - - + -
24B GLN* 3.6 30.1 - - - +
25B TYR* 4.8 9.6 - - + +
78B ARG* 3.6 18.2 - - - +
89B ALA 3.5 5.1 + - - +
90B ASP 3.8 5.6 - - - +
92B ALA* 1.3 79.2 - - - +
94B GLU* 1.3 62.5 + - - +
96B ASP* 3.3 5.0 + - - +
97B ALA* 3.2 21.9 + - - +
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 2.5 24.1 + - - +
51B GLU* 3.6 2.6 - - - +
90B ASP 3.2 18.3 + - - +
91B LEU* 3.6 7.0 - - - +
92B ALA 3.0 0.4 - - - -
93B ALA* 1.3 73.1 - - - +
95B HIS* 1.3 66.7 + - - +
96B ASP 2.9 2.7 + - - -
97B ALA* 3.1 2.9 + - - -
98B ARG* 3.0 23.7 + - - +
127B GLU* 2.5 49.6 - - - +
130B HIS* 2.7 30.2 + - + +
131B ILE* 3.8 18.6 - - + -
134B LEU* 4.2 5.6 - - + -
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Residues in contact with HIS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.1 55.8 - - + +
91B LEU* 3.0 40.6 + - + +
92B ALA* 3.1 7.4 + - - +
94B GLU* 1.3 72.6 - - - +
96B ASP* 1.3 64.8 + - - +
98B ARG* 4.1 15.0 + - - +
99B THR* 2.8 27.5 + - - -
131B ILE* 4.3 19.8 - - + +
135B GLU* 4.5 2.2 + - - -
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 2.6 37.4 + - - +
92B ALA* 2.8 15.2 + - - +
93B ALA* 3.5 6.7 - - - +
95B HIS* 1.3 78.7 - - - +
97B ALA* 1.3 52.1 - - - +
99B THR* 2.5 30.9 + - - -
100B LEU* 2.8 16.1 + - - +
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER* 3.9 26.7 - - - +
93B ALA 3.2 11.5 + - - +
94B GLU* 3.1 4.3 + - - +
96B ASP* 1.3 76.9 - - - +
98B ARG* 1.3 53.1 + - - +
100B LEU* 3.0 9.5 + - - -
101B TYR* 2.7 48.6 + - + +
127B GLU* 3.7 22.4 - - - +
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 6.2 3.3 - - - +
112A ARG 4.8 11.3 + - - -
113A ASP* 5.5 6.7 + - - +
94B GLU 3.0 15.7 + - - +
95B HIS* 4.1 15.2 + - - +
97B ALA* 1.3 75.4 - - - +
99B THR* 1.3 74.3 + - - +
101B TYR* 3.5 12.1 + - - +
102B ILE* 2.8 42.5 + - + +
124B ILE* 4.3 15.1 - - + +
127B GLU* 4.6 9.7 - - + +
128B GLU* 2.8 29.0 + - + +
131B ILE* 4.1 22.4 - - + -
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Residues in contact with THR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B HIS 2.8 17.1 + - - -
96B ASP* 2.5 18.4 + - - -
98B ARG* 1.3 86.7 + - - +
100B LEU* 1.3 60.3 + - - +
102B ILE* 3.3 17.5 + - + +
103B GLU* 3.5 13.0 + - + +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 4.7 18.2 - - + +
13B ALA* 3.6 44.6 - - + +
14B ALA* 3.9 8.1 - - + +
17B SER* 3.8 17.5 - - - +
96B ASP 2.8 10.3 + - - +
97B ALA* 3.3 9.4 - - - +
99B THR* 1.3 77.6 - - - +
101B TYR* 1.3 70.9 + - + +
103B GLU* 3.0 20.2 + - - +
104B ALA* 3.1 12.2 + - + +
120B PHE* 6.0 0.2 - - + -
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA* 3.6 26.5 - - + -
17B SER* 3.9 6.9 + - - -
18B GLU* 2.5 37.6 + - - +
97B ALA* 2.7 29.7 + - + +
98B ARG* 3.7 7.2 - - - +
100B LEU* 1.3 81.4 - - + +
102B ILE* 1.3 62.9 + - - +
104B ALA* 3.8 0.6 - - - -
105B ARG* 2.8 30.0 + - - +
120B PHE* 3.8 23.8 - + + +
123B LEU* 3.5 38.5 - - + +
124B ILE* 4.2 14.6 - - + -
127B GLU* 3.5 30.3 + - + -
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 3.3 60.3 - - + +
114A TYR* 4.3 7.8 - - + -
98B ARG* 2.8 39.2 + - + +
99B THR* 3.3 10.5 + - + +
100B LEU 3.2 1.2 - - - -
101B TYR* 1.3 77.3 - - - +
103B GLU* 1.3 57.7 + - + +
105B ARG* 2.9 15.4 + - - +
106B ASP* 2.4 28.6 + - - +
124B ILE* 4.1 18.2 - - + -
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Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 3.6 17.0 + - - +
10B TYR* 2.6 46.6 + - - -
99B THR* 3.5 10.0 + - + +
100B LEU* 3.0 14.1 + - + +
102B ILE* 1.3 79.9 - - + +
104B ALA* 1.3 56.8 + - - +
106B ASP* 3.3 9.7 - - - +
107B HIS* 3.6 12.3 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 3.4 44.6 - - + +
100B LEU* 3.1 12.5 + - + +
101B TYR 3.9 0.4 - - - +
102B ILE 3.0 0.2 - - - -
103B GLU* 1.3 76.3 - - - +
105B ARG* 1.3 64.4 + - - +
106B ASP 3.1 2.7 + - - -
107B HIS* 3.2 10.4 + - - +
108B CYS* 3.2 20.1 + - - -
120B PHE* 3.7 23.1 - - + -
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 5.9 1.2 - - - +
109A GLU* 5.0 3.0 - - - +
114A TYR* 3.3 55.2 + - + -
117A LYS* 3.9 10.1 - - - +
101B TYR 2.8 19.5 + - - +
102B ILE* 2.9 7.8 + - - +
104B ALA* 1.3 78.1 - - - +
106B ASP* 1.3 74.7 + - - +
108B CYS* 3.7 5.9 - - - +
109B GLU* 3.4 34.1 + - - +
110B LYS* 4.5 1.8 - - - +
117B LYS* 3.9 25.8 - - - +
120B PHE* 3.7 18.4 - - + -
121B GLU* 3.2 48.9 + - + +
124B ILE* 4.8 3.1 - - + -
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Residues in contact with ASP 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 2.1 39.2 + - - +
114A TYR* 3.9 2.5 - - - +
102B ILE 2.4 20.1 + - - +
103B GLU 3.3 8.3 - - - +
105B ARG* 1.3 88.3 - - - +
107B HIS* 1.3 65.3 + - - +
108B CYS 3.1 0.4 - - - -
109B GLU* 3.6 4.0 - - - -
110B LYS* 2.8 54.8 + - - +
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Residues in contact with HIS 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASP* 2.8 28.6 + - - -
6B LYS* 2.9 22.9 - - + +
7B VAL* 3.6 20.2 - - + -
10B TYR* 3.3 36.6 - + + -
103B GLU 3.6 8.4 + - - +
104B ALA 3.2 6.6 + - - +
106B ASP* 1.3 74.7 - - - +
108B CYS* 1.3 54.9 + - - +
110B LYS* 2.8 31.3 + - + +
111B VAL* 3.1 24.3 + - + +
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Residues in contact with CYS 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 3.8 21.5 - - - -
10B TYR* 5.7 1.1 - - - -
104B ALA* 3.2 14.1 + - - -
105B ARG 3.7 9.0 - - - +
106B ASP 3.1 0.2 - - - -
107B HIS* 1.3 76.5 - - - +
109B GLU* 1.3 65.2 + - - +
111B VAL* 3.3 8.9 + - - -
112B ARG 2.8 4.5 + - - -
113B ASP 2.8 43.4 + - - +
116B SER* 3.5 25.8 - - - -
117B LYS* 3.7 10.1 - - - +
120B PHE* 4.2 12.6 - - - -
----------------------------------------------------------
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 3.4 20.7 + - - +
106B ASP* 3.4 18.5 + - - +
108B CYS* 1.3 77.7 - - - +
110B LYS* 1.3 80.4 + - + +
112B ARG* 3.3 12.8 + - - +
114B TYR* 3.4 24.5 + - - -
117B LYS* 3.1 36.3 - - + +
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 5.3 0.2 - - - +
114A TYR* 5.3 1.0 + - - -
105B ARG* 4.5 2.0 - - - +
106B ASP* 2.8 47.6 + - - +
107B HIS* 2.8 23.0 + - - +
109B GLU* 1.3 90.5 - - + +
111B VAL* 1.3 60.5 + - + +
112B ARG* 3.2 12.0 + - - -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASP* 3.5 33.0 - - + +
7B VAL* 3.4 30.3 - - + -
107B HIS* 3.1 22.1 + - + +
108B CYS* 3.6 9.0 - - - +
110B LYS* 1.3 77.1 - - + +
112B ARG* 1.3 73.6 + - - +
113B ASP* 3.9 8.2 - - + +
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Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B CYS 2.8 6.5 + - - -
109B GLU 3.3 6.8 + - - -
110B LYS 3.2 17.7 - - - -
111B VAL* 1.3 82.8 - - - +
113B ASP* 1.3 60.7 + - - +
114B TYR* 3.1 53.8 + - + +
115B PRO* 5.4 0.2 - - - +
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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