Contacts of the helix formed by residues 82 - 111 (chain B) in PDB entry 4U1D
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 SER 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PRO* 4.3 9.9 - - - +
79B ILE* 3.6 4.7 + - - +
81B GLY* 1.3 77.6 - - - +
83B THR* 1.3 63.9 + - - +
84B GLU* 3.3 14.6 + - - -
85B GLY* 2.9 25.6 + - - -
86B LEU* 3.2 27.5 + - - +
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Residues in contact with THR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 1.3 69.6 - - - +
84B GLU* 1.3 75.3 + - - +
85B GLY 3.0 1.3 - - - -
86B LEU* 3.1 4.9 + - - +
87B VAL* 2.9 33.7 + - + +
174B LEU* 3.7 28.0 - - + +
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PRO* 3.7 20.4 - - + +
46B SER* 6.3 1.1 - - - -
82B SER* 3.3 19.8 - - - -
83B THR* 1.3 78.7 + - - +
85B GLY* 1.3 57.1 + - - +
87B VAL* 3.4 11.5 + - - +
88B SER* 2.9 29.1 + - - -
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Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PRO* 3.7 13.9 - - - +
79B ILE* 3.2 31.1 - - - +
82B SER* 2.9 14.4 + - - -
83B THR 3.0 0.4 - - - -
84B GLU* 1.3 76.9 - - - +
86B LEU* 1.3 57.3 + - - +
88B SER* 3.1 6.4 + - - -
89B VAL* 2.9 28.2 + - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS* 6.0 1.1 - - - -
80B GLN* 3.1 42.4 - - + +
82B SER 3.2 21.3 + - - +
83B THR 3.1 6.5 + - - +
85B GLY* 1.3 71.7 - - - +
87B VAL* 1.3 67.6 + - - +
89B VAL* 3.1 11.0 + - + +
90B GLY 2.9 19.4 + - - -
172B ASN* 3.3 40.8 - - - +
174B LEU* 3.5 26.7 - - + -
175B LEU* 3.4 15.2 - - + +
223B ASN* 3.7 19.1 - - - +
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B THR* 2.9 32.4 + - + +
84B GLU* 3.5 11.2 - - - +
85B GLY 3.2 0.2 - - - -
86B LEU* 1.3 75.4 - - + +
88B SER* 1.3 58.4 + - - +
90B GLY* 3.2 4.1 + - - -
91B ALA* 2.9 27.8 + - + +
94B ARG* 3.9 8.9 + - - +
174B LEU* 5.9 2.7 - - + -
175B LEU* 5.5 0.2 - - - -
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PRO* 3.9 12.5 + - - -
46B SER* 5.8 0.2 - - - -
49B GLU* 3.4 27.6 + - - +
75B TYR* 2.7 28.4 + - - -
84B GLU 2.9 13.6 + - - -
85B GLY 3.3 9.0 - - - -
87B VAL* 1.3 74.5 - - - +
89B VAL* 1.3 65.1 + - - +
91B ALA* 3.4 7.6 - - - +
92B VAL* 2.9 27.1 + - - +
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TYR* 4.6 4.0 - - + -
76B LYS* 3.7 44.0 - - + +
79B ILE* 3.6 21.8 - - + -
80B GLN* 5.2 2.2 - - + +
85B GLY 2.9 18.4 + - - +
86B LEU* 3.1 14.8 + - + +
88B SER* 1.3 75.6 - - - +
90B GLY* 1.3 58.7 + - - +
92B VAL* 3.1 12.6 - - + +
93B ALA* 2.9 27.4 + - - +
168B LEU* 4.9 5.8 - - + -
169B LEU* 4.7 9.4 - - + -
175B LEU* 4.2 15.7 - - + -
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU 2.9 13.9 + - - -
87B VAL* 3.2 4.0 + - - -
89B VAL* 1.3 77.1 - - - +
91B ALA* 1.3 56.8 + - - +
93B ALA* 3.3 8.7 - - - +
94B ARG* 2.9 42.0 + - - -
169B LEU* 5.2 0.7 - - - -
175B LEU* 4.0 12.7 - - - +
178B THR* 3.7 13.9 - - - +
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 3.2 25.1 - - - +
53B PHE* 3.9 6.6 - - + -
87B VAL* 2.9 15.5 + - + +
88B SER* 3.1 8.5 + - - +
90B GLY* 1.3 76.5 - - - +
92B VAL* 1.3 60.7 + - - +
94B ARG* 3.2 24.0 + - - +
95B LYS* 2.9 26.9 + - - +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 4.0 10.3 - - + -
52B VAL* 3.5 32.3 - - + -
53B PHE* 3.6 24.0 - - + -
56B LEU* 3.4 10.1 - - + +
72B LEU* 3.8 19.8 - - + +
75B TYR* 4.2 12.8 - - + -
88B SER* 2.9 20.1 + - - +
89B VAL* 3.1 22.4 - - + +
91B ALA* 1.3 72.6 - - - +
93B ALA* 1.3 61.5 + - - +
95B LYS* 3.7 0.9 - - - -
96B PHE* 2.9 26.3 + - - +
168B LEU* 6.1 0.9 - - + -
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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
----------------------------------------------------------
72B LEU* 5.3 4.0 - - - -
89B VAL 2.9 13.5 + - - +
90B GLY* 3.3 10.8 - - - +
92B VAL* 1.3 79.2 - - - +
94B ARG* 1.3 63.5 + - - +
96B PHE* 3.2 6.7 + - - +
97B ILE* 3.0 28.7 + - - +
165B VAL* 4.1 11.9 - - + +
168B LEU* 4.9 4.7 - - + -
169B LEU* 3.7 36.3 - - + -
178B THR* 4.6 0.7 - - + -
182B VAL* 5.9 0.7 - - - -
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Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B VAL* 3.9 11.5 + - - +
90B GLY* 2.9 17.6 + - - +
91B ALA* 3.2 48.2 + - - +
92B VAL 3.3 0.2 - - - -
93B ALA* 1.3 76.2 - - - +
95B LYS* 1.3 55.6 + - - +
97B ILE* 3.3 8.0 + - - +
98B ASP* 2.9 41.4 + - - +
178B THR* 3.8 26.9 + - + +
182B VAL* 5.9 4.3 - - + -
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Residues in contact with LYS 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 3.6 54.0 - - + -
56B LEU* 4.0 9.0 - - + -
57B GLU* 3.8 23.6 + - - -
91B ALA 2.9 18.5 + - - +
92B VAL 3.6 4.9 - - - +
93B ALA 3.2 0.2 - - - -
94B ARG* 1.3 75.7 - - - +
96B PHE* 1.3 63.9 + - - +
98B ASP* 3.1 6.8 + - + -
99B LEU* 2.9 55.8 + - + +
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Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 3.9 22.6 - - + +
60B VAL* 3.9 17.9 - - + -
65B GLY* 5.8 1.6 - - - -
68B LEU* 3.7 35.0 - - + -
69B LYS* 5.6 3.6 - - + -
72B LEU* 3.5 24.5 - - + -
92B VAL 2.9 17.5 + - - +
93B ALA 3.2 4.2 + - - +
95B LYS* 1.3 74.8 - - - +
97B ILE* 1.3 64.2 + - + +
99B LEU* 3.1 6.1 + - - +
100B VAL* 3.0 27.9 + - + +
157B PHE* 4.7 1.8 - + - -
161B SER* 3.3 38.1 - - - -
164B ALA* 5.0 8.1 - - + -
165B VAL* 3.5 23.6 - - + -
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ALA 3.0 15.9 + - - +
94B ARG* 3.7 9.4 - - - +
96B PHE* 1.3 75.9 - - - +
98B ASP* 1.3 59.5 + - - +
100B VAL* 3.1 12.2 - - + +
101B GLU* 2.9 50.2 + - - +
161B SER* 4.3 1.1 - - - +
162B TYR* 3.4 49.1 - - + +
165B VAL* 3.9 25.1 - - + -
182B VAL* 4.0 18.8 - - + -
185B LYS* 3.9 14.1 - - + -
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Residues in contact with ASP 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ARG* 2.9 27.4 + - - +
95B LYS* 3.7 7.8 - - + +
97B ILE* 1.3 76.1 - - - +
99B LEU* 1.3 60.4 + - + +
101B GLU* 3.4 16.1 + - - +
102B SER* 2.9 33.7 + - - -
185B LYS* 4.2 10.9 - - - -
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 3.5 20.0 - - + +
57B GLU* 3.4 45.8 - - + +
60B VAL* 3.9 13.6 - - + +
95B LYS* 2.9 55.0 + - + +
96B PHE* 3.1 8.0 + - - +
98B ASP* 1.3 77.0 - - + +
100B VAL* 1.3 66.8 + - - +
102B SER* 3.2 7.4 + - - -
103B LYS* 3.0 24.6 + - - +
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 4.4 8.2 - - + +
96B PHE* 3.0 24.6 + - + +
97B ILE* 3.1 24.0 - - + +
99B LEU* 1.3 74.1 - - - +
101B GLU* 1.3 57.2 + - - +
103B LYS* 3.2 5.6 + - + +
104B ILE* 3.0 28.2 + - - +
154B TRP* 5.9 0.4 - - + -
157B PHE* 3.9 24.9 - - + -
158B THR* 3.3 40.8 - - + +
161B SER* 4.1 17.0 - - - +
162B TYR* 5.9 1.1 - - + -
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Residues in contact with GLU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 2.9 26.6 + - - +
98B ASP* 3.6 12.1 - - - +
100B VAL* 1.3 80.1 - - - +
102B SER* 1.3 57.5 + - - +
104B ILE* 3.8 9.7 + - + +
105B ALA* 3.6 16.1 + - - +
158B THR* 5.5 2.5 - - + -
162B TYR* 3.1 27.6 + - - +
185B LYS* 3.2 38.9 - - - +
188B HIS* 5.9 3.1 - - - -
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASP* 2.9 18.2 + - - +
99B LEU* 3.2 6.5 + - - -
101B GLU* 1.3 75.0 - - - +
103B LYS* 1.3 66.0 + - - +
104B ILE 3.2 1.6 - - - -
105B ALA* 3.1 10.3 + - - +
106B SER* 3.0 25.4 + - - -
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 3.5 28.0 - - + -
61B GLU* 3.4 32.4 + - - +
99B LEU 3.0 11.1 + - - +
100B VAL* 3.2 8.9 + - - +
102B SER* 1.3 75.7 - - - +
104B ILE* 1.3 64.0 + - - +
106B SER* 3.2 12.7 + - - +
107B GLU* 2.9 51.7 + - - +
154B TRP* 3.5 39.7 - - + -
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B VAL 3.0 10.3 + - - +
101B GLU* 3.8 12.1 - - + +
103B LYS* 1.3 76.7 - - - +
105B ALA* 1.3 63.6 + - - +
107B GLU* 5.0 2.5 - - + -
108B GLN* 2.9 32.4 + - + +
151B ILE* 5.4 1.6 - - + +
154B TRP* 3.7 22.4 - - + +
155B LEU* 3.7 25.4 - - + +
158B THR* 3.0 37.2 - - + +
189B PHE* 5.3 1.3 - - + -
192B LYS* 5.9 0.2 - - - +
193B TYR* 3.2 30.3 - - + +
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLU 3.6 8.0 + - - +
102B SER* 3.1 16.0 + - - +
104B ILE* 1.3 80.5 - - - +
106B SER* 1.3 58.9 + - - +
108B GLN* 4.1 2.4 - - - +
109B THR* 2.9 35.3 + - - +
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B SER* 3.0 14.4 + - - -
103B LYS* 3.2 18.7 + - - +
105B ALA* 1.3 76.4 - - - +
107B GLU* 1.3 65.2 + - - +
109B THR* 3.2 10.3 - - - +
110B ARG* 2.9 43.2 + - - +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LYS* 2.9 47.0 + - - +
104B ILE* 4.3 3.1 - - + +
106B SER* 1.3 74.8 - - - +
108B GLN* 1.3 58.8 + - - +
110B ARG* 3.3 27.8 + - - +
111B ALA* 2.9 33.4 + - - +
151B ILE* 4.5 16.4 - - + +
154B TRP* 3.7 49.6 + - + +
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Residues in contact with GLN 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 2.9 27.2 + - + +
105B ALA* 4.1 3.1 - - - +
107B GLU* 1.3 79.1 - - - +
109B THR* 1.3 62.4 + - - +
110B ARG 3.5 0.2 + - - -
111B ALA* 3.6 16.5 + - - +
151B ILE* 3.9 22.7 - - + +
155B LEU* 4.7 10.3 - - - +
193B TYR* 4.1 35.0 - - + +
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Residues in contact with THR 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ALA 2.9 22.8 + - - +
106B SER* 3.2 11.9 - - - +
108B GLN* 1.3 77.8 - - - +
110B ARG* 1.3 66.6 + - + +
111B ALA 4.7 1.0 - - - -
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B SER* 2.9 28.8 + - - +
107B GLU* 3.3 34.4 + - - +
109B THR* 1.3 80.3 - - + +
111B ALA* 1.3 71.1 + - + +
----------------------------------------------------------
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU 2.9 19.9 + - - +
108B GLN* 3.6 14.6 + - - +
109B THR 3.6 2.3 - - - +
110B ARG* 1.3 84.0 - - + +
151B ILE* 3.6 35.9 - - + -
----------------------------------------------------------
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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