Contacts of the helix formed by residues 87 - 114 (chain B) in PDB entry 4QYL
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 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ASN* 3.5 12.6 - - + +
84B ALA* 2.7 40.6 + - + +
85B LYS 3.2 0.2 - - - -
86B ASP* 1.3 84.8 - - - +
88B ILE* 1.3 65.6 + - - +
89B PHE* 3.2 10.3 + - + -
90B TYR* 3.2 15.4 + - - +
91B ARG* 3.1 23.4 + - - +
8F GLY* 3.4 14.6 - - - +
10F ALA* 5.2 0.2 - - - -
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 4.7 10.0 - - + +
87B THR* 1.3 72.6 - - - +
89B PHE* 1.3 79.7 + - + +
91B ARG* 3.4 8.0 + - - +
92B ALA* 2.8 31.2 + - - +
7F GLY 3.1 24.2 - - - +
8F GLY* 2.9 24.4 + - - +
9F LYS 4.0 3.4 - - - +
10F ALA* 3.9 24.2 - - + -
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 3.9 25.8 - - + -
28B PHE* 4.3 0.2 - - - -
79B CYS* 3.2 16.4 - - - -
83B ASN* 3.8 24.7 - - - +
87B THR* 3.1 7.5 - - + +
88B ILE* 1.3 88.1 - - + +
90B TYR* 1.4 65.3 + - - +
92B ALA* 3.3 6.9 + - - +
93B ALA 3.0 18.2 + - - -
5F ALY 3.5 50.0 - - + +
6F GLN 3.6 15.5 - - - -
7F GLY* 3.9 10.1 - - - -
8F GLY* 3.5 26.7 - - - -
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Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B CYS* 4.5 4.3 - - - -
80B LEU* 3.4 43.4 - - + +
83B ASN* 3.4 23.1 - - + +
84B ALA 3.1 18.8 - - - +
85B LYS* 3.6 56.1 + - + +
87B THR* 3.2 8.3 + - - +
89B PHE* 1.4 75.1 - - - +
91B ARG* 1.4 66.0 + - + +
93B ALA* 3.1 4.5 + - - +
94B VAL* 3.0 39.3 + - + +
97B ARG* 6.0 0.3 + - - -
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Residues in contact with ARG 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LYS 4.1 11.9 - - - +
86B ASP* 4.3 10.9 + - - +
87B THR 3.1 19.2 + - - +
88B ILE* 3.8 7.0 - - - +
90B TYR* 1.4 78.9 - - + +
92B ALA* 1.3 61.4 + - - +
94B VAL* 3.3 8.1 + - - +
95B ARG* 3.1 34.5 + - - +
201B SO4 2.8 47.4 + - - +
10F ALA* 3.9 23.2 - - - +
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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
----------------------------------------------------------
23B ASP* 5.7 0.7 - - - +
27B ILE* 3.5 27.8 - - + -
28B PHE* 4.1 12.9 - - + -
88B ILE 2.8 19.1 + - - +
89B PHE 3.5 6.1 - - - +
91B ARG* 1.3 77.2 - - - +
93B ALA* 1.3 57.2 + - - +
95B ARG* 3.4 11.9 + - - +
96B LEU* 2.9 28.6 + - - +
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Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE* 3.8 10.3 - - + -
76B VAL* 4.0 11.2 - - - +
79B CYS* 3.7 24.7 - - + -
80B LEU* 3.6 21.1 - - + -
89B PHE 3.0 12.5 + - - +
90B TYR 3.1 8.5 + - - +
92B ALA* 1.3 73.2 - - - +
94B VAL* 1.3 61.8 + - - +
96B LEU* 3.7 3.9 - - - +
97B ARG* 2.8 30.5 + - - +
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 3.8 9.2 - - + -
90B TYR* 3.0 40.7 + - + +
91B ARG* 3.6 10.1 - - - +
93B ALA* 1.3 75.7 - - - +
95B ARG* 1.3 63.1 + - + +
97B ARG* 3.3 28.3 + - - +
98B GLU* 3.0 38.5 + - - +
201B SO4 5.9 3.4 - - - +
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Residues in contact with ARG 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS 5.9 0.9 - - - +
24B THR* 5.3 6.1 + - - -
91B ARG* 3.1 21.8 + - - +
92B ALA* 3.6 11.9 - - - +
94B VAL* 1.3 75.4 - - + +
96B LEU* 1.4 65.5 + - - +
98B GLU* 3.4 15.7 + - - +
99B GLN* 3.0 47.8 + - - +
201B SO4 2.9 43.1 + - - +
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU 3.9 11.4 - - - +
22B LYS* 3.8 27.3 + - + +
23B ASP* 4.2 13.0 - - + +
28B PHE* 3.6 33.0 - - + -
50B PHE* 4.2 9.6 - - + -
72B PHE* 3.6 28.0 - - + -
75B ILE* 4.3 5.6 - - + -
76B VAL* 4.1 12.1 - - + -
92B ALA 2.9 17.8 + - - +
93B ALA* 3.7 5.8 - - - +
95B ARG* 1.4 72.6 - - - +
97B ARG* 1.3 62.7 + - - +
99B GLN* 4.9 2.5 - - - +
100B GLY* 2.8 29.1 + - - +
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Residues in contact with ARG 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 4.6 5.8 - - + -
76B VAL* 3.8 27.3 - - + +
80B LEU* 3.4 25.0 - - - +
90B TYR* 6.0 0.2 + - - -
93B ALA 2.8 17.8 + - - +
94B VAL* 3.6 27.7 + - - +
96B LEU* 1.3 76.6 - - - +
98B GLU* 1.3 64.3 + - - +
101B GLY* 3.0 22.5 + - - -
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL* 3.0 30.0 + - - +
95B ARG* 3.5 23.6 + - - +
97B ARG* 1.3 82.7 - - + +
99B GLN* 1.3 69.6 + - + +
101B GLY* 3.7 5.9 + - - -
102B ALA* 4.0 8.8 + - - +
201B SO4 5.2 2.4 + - - -
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 3.5 54.0 + - + +
24B THR* 5.8 2.9 - - - +
95B ARG* 3.0 41.7 + - - +
98B GLU* 1.3 82.6 + - + +
100B GLY* 1.3 65.2 + - - +
102B ALA* 3.4 15.0 + - - +
103B VAL* 3.5 13.9 + - - +
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Residues in contact with GLY 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.7 21.1 - - - -
22B LYS* 4.6 4.4 - - - +
72B PHE* 3.9 7.2 - - - -
96B LEU* 2.8 24.2 + - - -
99B GLN* 1.3 70.4 - - - +
101B GLY* 1.3 64.2 + - - +
103B VAL* 3.1 5.8 + - - +
104B LEU* 2.9 33.3 + - - +
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B PHE* 4.8 0.8 - - - -
97B ARG 3.0 16.8 + - - -
98B GLU 4.1 3.1 - - - -
99B GLN 3.3 0.6 - - - -
100B GLY* 1.3 76.2 - - - +
102B ALA* 1.3 60.3 + - - +
104B LEU* 3.4 8.7 + - - +
105B ARG* 3.0 33.9 + - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU 4.0 7.4 + - - +
99B GLN* 3.4 11.5 + - - +
100B GLY 3.2 0.4 - - - -
101B GLY* 1.3 76.1 - - - +
103B VAL* 1.3 62.5 + - + +
105B ARG* 3.4 10.3 + - - +
106B GLN* 3.2 23.4 + - - +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 4.0 8.3 - - + +
18B GLN* 3.6 43.7 - - + +
19B LEU* 3.7 22.2 - - + -
22B LYS* 3.8 21.5 - - + -
99B GLN 3.5 13.6 + - - +
100B GLY* 3.1 10.2 + - - +
102B ALA* 1.3 77.7 - - + +
104B LEU* 1.3 58.1 + - - +
106B GLN* 3.5 5.8 + - - +
107B ALA* 3.0 27.4 + - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B THR* 4.5 2.9 - - + -
19B LEU* 4.2 13.2 - - + -
65B PHE* 3.9 25.2 - - + -
68B PHE* 4.2 20.2 - - + -
69B GLU* 4.0 36.0 - - + +
72B PHE* 3.4 34.1 - - + -
73B ASN* 4.6 2.2 - - - +
100B GLY 2.9 20.0 + - - +
101B GLY* 3.9 7.0 - - - +
103B VAL* 1.3 73.4 - - - +
105B ARG* 1.3 61.4 + - - +
107B ALA* 4.5 2.9 - - - -
108B ARG* 2.8 33.1 + - - +
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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
----------------------------------------------------------
101B GLY* 3.0 25.4 + - - +
102B ALA* 3.7 8.7 - - - +
103B VAL 3.3 0.2 - - - -
104B LEU* 1.3 77.2 - - + +
106B GLN* 1.3 61.3 + - - +
108B ARG* 3.6 5.4 + - - +
109B ARG* 3.2 27.5 + - - +
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Residues in contact with GLN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 5.7 0.9 - - - +
18B GLN* 4.7 11.3 + - - +
102B ALA 3.2 14.0 + - - +
103B VAL* 3.7 6.1 - - - +
105B ARG* 1.3 79.6 - - - +
107B ALA* 1.3 70.1 + - - +
109B ARG* 3.3 25.7 + - - +
110B GLN* 3.1 53.3 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.8 8.5 - - + +
15B THR* 3.3 36.1 - - + +
18B GLN* 5.2 2.5 - - - +
65B PHE* 3.6 11.9 - - + -
103B VAL 3.0 18.0 + - - +
104B LEU 4.0 0.2 - - - +
106B GLN* 1.3 81.5 + - - +
108B ARG* 1.3 68.1 + - - +
110B GLN* 3.1 8.4 + - - +
111B ALA* 2.9 21.8 + - - +
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 3.6 36.3 - - + +
66B ASP* 2.8 35.3 + - - +
69B GLU* 2.8 31.5 + - - +
104B LEU 2.8 19.3 + - - +
105B ARG* 4.0 5.4 - - - +
107B ALA* 1.3 78.6 - - - +
109B ARG* 1.3 58.0 + - - +
111B ALA* 3.0 4.5 + - - +
112B GLU* 2.9 48.9 + - + +
117B ASP* 4.8 13.6 + - + +
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Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ARG* 3.2 18.7 + - - +
106B GLN* 3.5 31.8 - - - +
107B ALA 3.2 0.2 - - - -
108B ARG* 1.3 79.1 - - - +
110B GLN* 1.3 70.5 + - - +
112B GLU* 3.3 16.4 + - - +
113B LYS* 3.0 41.8 + - + +
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Residues in contact with GLN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.2 13.5 - - + -
106B GLN* 3.1 47.4 + - - +
107B ALA* 3.1 7.3 + - - +
109B ARG* 1.3 93.9 - - - +
111B ALA* 1.3 66.2 + - - +
113B LYS* 3.3 28.2 + - - +
114B MET* 3.1 50.5 + - + +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 5.2 1.3 - - + -
11B LEU* 3.6 22.1 - - + +
65B PHE* 4.1 14.6 - - + -
107B ALA 2.9 8.9 + - - +
108B ARG* 3.0 8.9 + - - +
110B GLN* 1.3 75.6 - - - +
112B GLU* 1.3 61.1 + - - +
114B MET 3.5 0.2 + - - -
115B GLY 3.3 2.6 + - - -
116B ILE* 2.9 38.5 + - + +
117B ASP* 3.0 25.4 + - + +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG* 2.9 37.6 + - + +
109B ARG* 3.6 19.7 + - - +
111B ALA* 1.3 78.1 - - - +
113B LYS* 1.3 62.3 + - + +
115B GLY* 3.1 13.0 + - - -
117B ASP* 3.5 31.9 - - + +
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ARG* 3.0 37.0 + - + +
110B GLN* 3.3 30.3 + - - +
112B GLU* 1.3 76.3 - - + +
114B MET* 1.3 64.1 + - + +
115B GLY 3.4 0.6 + - - -
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Residues in contact with MET 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 5.0 12.1 - - + +
11B LEU* 5.2 8.7 - - + -
110B GLN* 3.1 42.6 + - + +
112B GLU 3.2 0.4 - - - -
113B LYS* 1.3 83.4 - - + +
115B GLY* 1.3 61.7 + - - +
116B ILE* 3.3 40.2 + - + +
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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