Contacts of the helix formed by residues 96 - 118 (chain B) in PDB entry 3MQT
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 GLY 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ARG* 1.3 70.7 - - - +
97B LEU* 1.3 67.5 + - - -
98B GLY 3.2 2.9 - - - -
99B LEU* 2.8 17.3 + - - +
100B PHE* 3.2 21.1 - - - -
262B THR* 2.9 22.4 + - - -
93G GLY 4.8 5.8 - - - -
95G ARG* 3.5 15.5 - - - +
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Residues in contact with LEU 97 (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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46B PRO* 4.4 10.8 - - + -
49B CYS* 4.4 9.9 - - - -
50B MET* 3.5 33.6 - - + +
53B PHE* 3.9 24.5 - - + -
95B ARG 3.8 1.2 + - - -
96B GLY* 1.3 70.9 - - - -
98B GLY* 1.3 63.9 + - - +
100B PHE* 3.0 36.2 + - + +
101B ALA 3.5 2.9 + - - -
53G PHE* 4.0 31.0 - - + -
92G ILE* 3.9 18.6 + - + +
95G ARG 4.3 4.2 + - - -
97G LEU* 4.4 23.5 - - + +
98G GLY 5.0 0.2 - - - +
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Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 3.7 29.3 - - - -
89B THR* 5.5 1.1 + - - -
92B ILE 4.2 5.6 + - - -
93B GLY* 4.1 16.8 - - - -
95B ARG 4.4 2.2 + - - -
96B GLY 3.1 1.2 + - - -
97B LEU* 1.3 78.2 - - - +
99B LEU* 1.3 64.6 + - - +
101B ALA* 3.3 13.0 + - - +
102B ILE* 3.4 17.2 + - - +
97G LEU* 5.1 1.4 - - - +
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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
----------------------------------------------------------
82B TYR* 3.6 24.2 - - - +
86B TYR* 4.4 4.5 - - + -
93B GLY* 4.1 0.4 - - - -
94B MET* 3.3 43.1 - - - +
95B ARG* 3.5 3.8 - - - +
96B GLY 2.8 11.2 + - - +
98B GLY* 1.3 73.8 - - - +
100B PHE* 1.3 66.1 + - - +
101B ALA 3.1 1.6 - - - -
102B ILE* 3.2 20.4 + - + +
103B SER* 2.8 27.7 + - - -
262B THR* 3.9 9.6 - - - +
263B THR* 3.9 17.9 - - + -
285B ARG 3.4 14.1 - - - +
286B CYS 3.8 13.7 - - - +
287B GLY* 3.9 7.0 + - - -
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ALA* 3.4 8.4 - - - +
44B ASP* 3.4 35.2 - - + +
45B GLY* 4.0 11.4 - - - -
50B MET* 3.7 2.9 - - + -
96B GLY* 3.2 20.9 - - - -
97B LEU* 3.0 30.0 + - + +
99B LEU* 1.3 76.6 - - - +
101B ALA* 1.3 62.1 + - - +
103B SER* 3.2 11.4 + - - -
104B GLY 3.2 10.6 + - - -
262B THR* 4.0 11.7 - - + -
284B ASN 3.6 12.2 - - - +
285B ARG* 3.5 51.8 - - + -
91G TRP 3.6 11.7 - - - -
92G ILE* 4.1 15.0 - - + -
93G GLY 5.9 0.4 - - - -
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Residues in contact with ALA 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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12B PHE* 3.7 29.3 - - + -
43B ALA* 4.4 0.9 - - - -
50B MET* 4.1 8.3 - - + -
53B PHE* 3.7 32.3 - - + -
66B ILE* 3.9 7.2 - - + -
97B LEU 3.5 1.0 + - - -
98B GLY 3.3 8.1 + - - +
99B LEU 3.1 0.8 - - - -
100B PHE* 1.3 80.3 - - - +
102B ILE* 1.3 61.4 + - - +
104B GLY 3.5 0.7 + - - -
105B ILE* 3.4 27.4 + - - +
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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
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66B ILE* 3.5 22.7 - - + -
82B TYR* 3.6 35.0 - - + +
85B MET* 4.2 21.0 - - + +
86B TYR* 3.9 32.3 - - + +
89B THR* 4.2 9.6 - - - +
94B MET 5.8 0.9 - - - +
98B GLY 3.4 12.3 + - - +
99B LEU* 3.2 26.8 + - + +
101B ALA* 1.3 76.2 - - - +
103B SER* 1.3 54.1 + - - +
105B ILE* 3.2 1.9 + - - +
106B ASP* 2.8 33.4 + - - +
287B GLY* 3.9 2.7 - - - +
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Residues in contact with SER 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU 4.3 1.8 - - - -
99B LEU 2.8 11.3 + - - -
100B PHE 3.2 9.6 + - - -
102B ILE* 1.3 77.6 - - - +
104B GLY* 1.3 61.9 + - - +
106B ASP* 3.8 1.6 - - - +
107B MET* 3.0 25.1 + - - +
283B TYR 3.6 11.0 - - - +
284B ASN* 3.4 21.5 - - - -
285B ARG 3.1 7.1 - - - -
287B GLY 2.6 40.0 + - - -
288B GLY* 3.8 3.8 - - - +
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Residues in contact with GLY 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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29B VAL* 3.6 23.3 - - - +
41B GLY* 3.8 2.4 - - - -
42B GLU 3.2 30.2 + - - -
43B ALA* 4.1 2.2 - - - -
100B PHE 3.2 8.1 + - - -
101B ALA 3.5 1.8 + - - -
102B ILE 3.3 0.4 - - - -
103B SER* 1.3 79.9 - - - +
105B ILE* 1.3 60.9 + - - +
107B MET* 3.5 3.3 + - - +
108B ALA* 3.2 18.0 + - - +
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 4.1 10.1 - - + -
12B PHE* 3.9 25.1 - - + -
29B VAL* 3.7 11.2 - - + -
31B VAL* 4.2 12.6 - - + -
66B ILE* 3.9 26.0 - - + -
67B LYS* 5.0 2.2 - - - +
70B VAL* 4.3 12.1 - - + -
85B MET* 3.7 35.2 - - + -
101B ALA 3.4 14.7 + - - +
102B ILE 3.2 1.5 + - - +
104B GLY* 1.3 72.3 - - - +
106B ASP* 1.3 67.5 + - - +
108B ALA* 3.0 5.2 + - - +
109B LEU* 2.9 37.1 + - + +
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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
----------------------------------------------------------
78B PHE* 4.6 5.4 - - - +
82B TYR* 4.4 8.5 + - + +
85B MET* 4.4 9.3 - - + +
102B ILE 2.8 17.3 + - - +
103B SER 3.8 2.0 - - - +
105B ILE* 1.3 77.5 - - - +
107B MET* 1.3 60.6 + - - +
109B LEU* 3.2 20.2 + - - +
110B TYR* 3.1 26.7 + - - -
287B GLY 3.7 12.8 - - - +
288B GLY 3.4 0.9 - - - -
289B VAL* 2.9 15.1 + - - -
290B THR* 2.4 52.8 + - - -
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Residues in contact with MET 107 (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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40B LEU 4.1 0.2 - - - -
41B GLY* 3.7 9.9 - - - -
42B GLU 3.6 30.3 - - - +
103B SER 3.0 13.2 + - - +
104B GLY 3.6 5.8 - - - +
105B ILE 3.2 0.2 - - - -
106B ASP* 1.3 76.2 - - - +
108B ALA* 1.3 62.0 + - - +
110B TYR* 3.2 20.6 + - - +
111B ASP 3.3 7.8 + - - -
283B TYR* 3.8 39.3 - - + +
284B ASN* 4.3 0.2 - - + -
289B VAL* 5.1 11.4 - - + +
315B ILE* 3.8 15.5 - - - +
316B THR* 4.1 12.8 - - - +
319B ALA* 3.9 19.5 - - + -
369B LEU* 3.8 19.5 - - + +
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Residues in contact with ALA 108 (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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29B VAL* 3.7 4.9 - - + +
31B VAL* 3.6 22.9 - - + -
39B GLY* 3.4 11.3 - - - +
40B LEU 3.5 27.8 + - - -
41B GLY 3.6 3.8 - - - +
104B GLY 3.2 8.0 + - - +
105B ILE 3.0 8.4 + - - +
107B MET* 1.3 78.5 - - - +
109B LEU* 1.3 58.8 + - - +
111B ASP* 3.3 0.7 + - - -
112B LEU* 2.8 30.3 + - - +
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Residues in contact with LEU 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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7B ILE* 3.8 25.6 - - + -
31B VAL* 3.8 21.8 - - + -
70B VAL* 4.4 10.8 - - + -
75B PRO* 4.1 16.6 - - + +
78B PHE* 3.8 10.8 - - + -
81B ASN* 4.0 34.1 - - + +
85B MET* 4.4 6.3 - - + -
105B ILE* 2.9 27.5 + - + +
106B ASP* 3.5 13.0 - - - +
107B MET 3.2 0.4 - - - -
108B ALA* 1.3 75.7 - - - +
110B TYR* 1.3 60.2 + - - +
112B LEU* 3.9 2.8 - - + +
113B ALA* 2.8 33.4 + - - +
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Residues in contact with TYR 110 (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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78B PHE* 3.4 51.1 - + - +
106B ASP* 3.1 31.0 - - - -
107B MET* 3.2 9.2 + - - +
109B LEU* 1.3 74.1 - - - +
111B ASP* 1.3 64.0 + - - +
114B GLY* 3.1 19.4 + - - -
121B ALA* 4.0 15.0 - - + +
124B LEU* 4.0 22.8 - - + +
125B MET* 4.1 22.2 - - + -
289B VAL* 3.7 29.2 - - + -
290B THR* 2.8 37.7 + - - +
293B LEU* 4.0 8.8 - - + +
368B GLY* 4.0 3.8 - - - -
369B LEU* 4.7 3.6 - - + -
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Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLY* 3.2 5.1 - - - -
40B LEU* 2.6 46.0 + - - +
107B MET 3.3 2.6 + - - +
108B ALA 3.3 8.0 + - - +
109B LEU 3.3 0.2 - - - -
110B TYR* 1.3 74.7 - - - +
112B LEU* 1.3 66.3 + - - +
114B GLY 3.3 1.6 + - - -
115B LYS* 2.9 47.3 + - - +
367B PRO 4.5 0.2 - - - +
368B GLY* 3.5 1.9 - - - -
369B LEU* 2.9 42.7 + - + +
370B GLY 4.1 3.6 + - - -
371B ILE* 4.4 7.3 + - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 4.1 7.2 - - + -
31B VAL* 3.8 31.9 - - + +
33B ASP* 3.9 18.8 - - + +
37B VAL* 3.5 33.9 - - + +
38B TYR* 4.0 2.2 - - - +
39B GLY* 3.5 14.1 - - - +
75B PRO* 3.7 26.0 - - + -
108B ALA 2.8 18.6 + - - +
109B LEU* 3.9 4.9 - - + +
111B ASP* 1.3 77.4 - - - +
113B ALA* 1.3 58.8 + - - +
115B LYS* 3.0 3.9 + - - -
116B GLN* 2.9 39.3 + - + +
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Residues in contact with ALA 113 (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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75B PRO* 3.9 24.4 - - - +
76B LEU* 4.0 9.9 - - + +
78B PHE* 3.9 16.4 - - + -
109B LEU 2.8 21.7 + - - +
112B LEU* 1.3 74.1 - - - +
114B GLY* 1.3 57.9 + - - +
116B GLN* 3.7 11.7 - - - +
117B LEU* 3.0 34.9 + - + +
124B LEU* 3.8 6.5 - - + -
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Residues in contact with GLY 114 (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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110B TYR 3.1 12.2 + - - -
111B ASP 3.6 1.8 - - - -
112B LEU 3.1 0.8 - - - -
113B ALA* 1.3 77.4 - - - +
115B LYS* 1.3 54.7 + - - +
117B LEU 3.4 0.5 + - - -
118B GLY* 2.8 25.1 + - - -
119B VAL* 3.0 30.9 + - - +
121B ALA 5.2 0.2 - - - -
124B LEU* 3.5 13.6 - - - +
367B PRO* 3.8 0.3 - - - +
368B GLY* 3.5 10.5 - - - -
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Residues in contact with LYS 115 (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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37B VAL* 4.0 20.5 - - + +
38B TYR* 2.7 49.0 + - - +
40B LEU* 5.5 1.8 - - - +
111B ASP* 2.9 41.0 + - - +
112B LEU 3.7 2.9 - - - +
114B GLY* 1.3 72.8 - - - +
116B GLN* 1.3 68.0 + - - +
118B GLY* 3.3 9.5 + - - -
367B PRO* 4.0 27.7 - - + +
368B GLY* 4.2 0.2 - - - -
371B ILE 5.9 1.0 + - - -
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Residues in contact with GLN 116 (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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5B ALA* 3.1 31.5 + - - +
33B ASP* 2.5 38.0 + - - +
37B VAL* 5.0 5.2 - - + -
74B ASP* 4.5 3.8 - - - +
75B PRO* 3.2 30.3 - - - +
112B LEU* 2.9 24.4 + - + +
113B ALA* 3.7 7.3 - - - +
115B LYS* 1.3 78.5 - - - +
117B LEU* 1.3 64.1 + - + +
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Residues in contact with LEU 117 (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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76B LEU* 4.5 20.2 - - + -
113B ALA* 3.0 17.2 + - + +
116B GLN* 1.3 79.9 - - + +
118B GLY* 1.3 61.7 + - - +
119B VAL* 3.8 21.9 - - + +
124B LEU* 3.8 27.8 - - + -
76D LEU* 4.8 1.3 - - + -
117D LEU* 3.7 53.0 - - + +
119D VAL* 5.7 2.7 - - + -
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Residues in contact with GLY 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLY 2.8 10.1 + - - -
115B LYS 3.3 10.8 + - - -
117B LEU* 1.3 78.8 - - - +
119B VAL* 1.3 60.2 + - - +
120B PRO* 4.7 1.0 - - - +
367B PRO* 4.1 21.5 - - - +
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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