Contacts of the helix formed by residues 68 - 92 (chain B) in PDB entry 3V3Q
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 ASP 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLY* 3.5 9.9 - - - +
67B GLU* 1.3 75.2 - - - +
69B ALA* 1.3 74.9 + - - +
70B GLY* 2.9 23.8 + - - -
71B ASP* 2.9 31.7 + - - +
72B VAL* 3.2 11.3 + - - +
146B ARG* 3.8 15.1 + - - +
250B LEU* 4.5 2.5 - - - -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU 4.2 0.6 + - - -
68B ASP* 1.3 78.1 + - - +
70B GLY* 1.3 54.0 + - - +
72B VAL* 2.9 4.9 + - - +
73B GLN* 2.7 37.4 + - + +
250B LEU* 4.5 9.8 - - + +
251B VAL* 4.1 20.5 - - + +
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Residues in contact with GLY 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASP* 2.9 16.2 + - - -
69B ALA* 1.3 78.1 - - - +
71B ASP* 1.3 62.4 + - - -
73B GLN* 3.4 5.5 + - - +
74B GLN* 2.9 26.1 + - - +
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Residues in contact with ASP 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU 5.2 0.2 - - - -
68B ASP* 2.9 35.2 + - - +
70B GLY* 1.3 71.8 - - - +
72B VAL* 1.3 58.7 - - + +
74B GLN* 3.2 10.6 + - - +
75B PHE* 2.8 28.9 + - - +
143B GLN 5.1 6.5 - - - +
146B ARG* 2.9 48.8 + - + +
147B GLY* 3.7 25.3 - - - +
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU* 4.2 18.2 - - + -
68B ASP 3.2 11.4 + - - +
69B ALA 2.9 9.7 + - - +
71B ASP* 1.3 71.6 - - + +
73B GLN* 1.3 61.5 + - - +
75B PHE* 3.3 7.7 + - - +
76B TYR* 2.9 51.5 + - + -
147B GLY* 5.0 3.6 - - - +
245B LEU* 3.8 33.4 - - + -
248B GLU* 4.7 3.1 - - - +
250B LEU* 4.8 3.4 - - + -
251B VAL* 3.5 27.6 - - + +
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Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ALA* 2.7 22.1 + - + +
70B GLY* 4.0 4.5 - - - +
72B VAL* 1.3 73.1 - - - +
74B GLN* 1.3 56.1 + - - +
76B TYR* 3.6 9.5 + - - +
77B ASP* 3.0 64.9 + - - +
251B VAL* 3.5 26.4 - - + +
252B PRO 5.3 0.3 - - - +
254B PRO* 5.7 2.8 - - - +
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LYS* 4.1 23.4 - - - +
70B GLY 2.9 19.3 + - - +
71B ASP* 3.4 8.0 - - - +
73B GLN* 1.3 73.7 - - - +
75B PHE* 1.3 59.3 + - - +
77B ASP* 2.9 7.3 + - + -
78B LEU* 2.7 52.9 + - + +
137B LEU* 5.0 0.4 - - - +
139B LEU* 3.6 28.5 - - - +
143B GLN* 3.9 18.7 - - - +
144B CYS* 5.3 1.2 - - - -
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Residues in contact with PHE 75 (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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71B ASP 2.8 16.1 + - - +
72B VAL* 3.4 9.9 - - - +
74B GLN* 1.3 74.6 - - - +
76B TYR* 1.3 90.8 - + - +
78B LEU* 3.3 3.8 + - - +
79B LEU* 3.1 40.4 + - + +
147B GLY* 3.8 20.6 - - - +
148B PHE* 3.7 53.7 - + - -
151B TRP* 4.0 17.3 - + - -
241B ARG* 4.1 14.8 - - + -
242B ILE* 4.2 11.4 - - + -
245B LEU* 3.6 23.6 - - + -
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 2.9 35.9 + - + +
73B GLN* 4.0 9.9 - - - +
75B PHE* 1.3 99.0 - + - +
77B ASP* 1.3 57.6 + - - +
79B LEU* 3.2 12.3 + - + +
80B SER* 2.8 32.4 + - - -
242B ILE* 4.2 12.7 - - + +
245B LEU* 3.6 26.2 - - + +
246B LYS* 4.3 3.8 - - - +
251B VAL* 3.3 27.3 + - + -
252B PRO 4.0 5.2 - - - -
253B PRO* 3.5 40.9 - - + +
254B PRO* 3.7 23.2 - - + +
257B ILE* 4.5 9.9 - - + -
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Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN* 3.0 51.9 + - - +
74B GLN* 2.9 8.1 + - - +
76B TYR* 1.3 73.2 - - - +
78B LEU* 1.3 72.3 + - + +
80B SER* 4.0 6.7 + - - +
81B GLY* 2.9 22.5 + - - -
254B PRO* 6.1 0.5 - - - +
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Residues in contact with LEU 78 (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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55B LYS* 6.1 0.7 - - - +
74B GLN* 2.7 53.6 + - + +
75B PHE 3.6 3.8 - - - +
77B ASP* 1.3 76.1 - - + +
79B LEU* 1.3 63.5 + - - +
81B GLY* 3.5 6.9 + - - -
82B SER* 3.7 7.8 + - - -
116B PHE* 3.9 12.5 - - + -
133B PHE* 3.9 39.7 - - + +
134B CYS* 5.9 0.3 - - - -
137B LEU* 4.2 20.6 - - + -
139B LEU* 4.3 5.4 - - + -
144B CYS* 4.9 1.1 - - - -
148B PHE* 3.8 28.9 - - + -
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Residues in contact with LEU 79 (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 PHE* 3.1 45.9 + - + +
76B TYR* 3.3 11.9 - - + +
77B ASP 3.1 0.2 - - - -
78B LEU* 1.3 74.3 - - - +
80B SER* 1.3 65.9 + - - +
82B SER* 3.2 11.3 + - - -
83B LEU 3.8 0.7 + - - -
112B PHE* 3.3 33.0 - - + -
113B LEU* 4.6 11.9 - - + -
116B PHE* 3.6 40.4 - - + -
148B PHE* 5.2 0.9 - - + -
151B TRP* 4.8 7.6 - - + -
242B ILE* 4.4 9.6 - - + -
257B ILE* 4.1 26.9 - - + -
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR 2.8 15.9 + - - -
77B ASP* 4.0 8.2 + - - -
79B LEU* 1.3 72.9 - - - +
81B GLY* 1.3 64.8 + - - +
82B SER 2.9 1.4 + - - -
83B LEU* 3.0 35.5 - - - +
84B GLU* 4.1 2.1 + - - +
254B PRO* 3.2 34.0 - - - +
257B ILE* 3.8 4.8 - - - +
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Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASP 2.9 18.0 + - - -
78B LEU* 3.9 3.8 - - - -
79B LEU 3.2 0.8 - - - -
80B SER* 1.3 77.0 - - - +
82B SER* 1.3 58.0 + - - +
83B LEU 3.5 0.5 + - - -
84B GLU* 4.3 4.2 + - - +
85B VAL* 3.9 18.5 + - - +
134B CYS* 4.1 7.7 - - - -
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU 3.7 3.8 + - - -
79B LEU 3.2 10.4 + - - -
80B SER 3.1 0.8 - - - -
81B GLY* 1.3 76.1 - - - +
83B LEU* 1.3 54.1 + - - +
84B GLU 3.5 0.4 - - - -
85B VAL* 3.2 2.3 + - - +
86B ILE* 2.6 43.0 + - - +
112B PHE* 4.1 7.0 - - - -
116B PHE* 3.7 26.6 - - - -
123B ARG* 5.6 0.3 + - - -
134B CYS* 3.4 16.8 + - - -
302B NA 2.8 22.9 - - - -
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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
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79B LEU 3.8 1.4 + - - -
80B SER* 3.0 33.9 - - - +
82B SER* 1.3 73.4 - - - +
84B GLU* 1.3 57.5 + - + +
86B ILE* 3.8 1.7 - - - +
87B ARG* 2.8 59.5 + - - +
112B PHE* 4.0 22.4 - - + -
254B PRO* 6.4 0.2 - - + -
256B ILE* 4.0 31.0 - - + -
257B ILE* 4.0 13.0 - - + -
260B ILE* 3.9 27.8 - - + -
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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
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80B SER 4.1 2.3 + - - +
81B GLY 4.3 4.7 + - - +
83B LEU* 1.3 79.5 - - + +
85B VAL* 1.3 64.6 + - + +
87B ARG* 3.5 31.0 + - - +
88B LYS* 3.1 48.9 + - - +
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Residues in contact with VAL 85 (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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44B SER* 3.1 35.0 - - - +
81B GLY 3.9 13.0 + - - +
82B SER 3.2 9.7 + - - +
83B LEU 3.1 1.0 - - - -
84B GLU* 1.3 77.7 - - + +
86B ILE* 1.3 61.3 + - - +
88B LYS* 3.3 9.5 + - + +
89B TRP* 2.9 25.8 + - - +
119B ARG* 3.5 13.7 - - - +
134B CYS* 4.1 18.6 - - + +
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Residues in contact with ILE 86 (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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82B SER* 2.6 30.7 + - - +
83B LEU* 4.0 3.1 - - - +
85B VAL* 1.3 72.1 - - - +
87B ARG* 1.3 57.1 + - - +
89B TRP* 3.4 13.6 + - + +
90B ALA* 3.0 27.0 + - - +
108B LEU* 3.8 13.9 - - + -
112B PHE* 3.8 30.7 - - + -
115B LEU* 3.4 48.7 - - + -
116B PHE* 3.9 9.9 - - - +
119B ARG* 3.9 20.2 - - - +
302B NA 4.1 2.9 - - - -
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Residues in contact with ARG 87 (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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83B LEU* 2.8 49.9 + - - +
84B GLU* 3.5 30.3 + - - +
85B VAL 3.2 0.2 - - - -
86B ILE* 1.3 79.1 - - - +
88B LYS* 1.3 60.3 + - + +
90B ALA* 3.6 2.8 + - - +
91B GLU* 3.4 24.4 + - + +
96B PHE* 5.7 0.2 - - - -
105B ASP* 5.6 6.7 + - - -
108B LEU* 4.1 31.7 - - + +
256B ILE* 4.7 18.4 - - - +
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Residues in contact with LYS 88 (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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84B GLU* 3.1 49.3 + - - +
85B VAL* 4.0 7.4 - - + +
87B ARG* 1.3 73.3 - - - +
89B TRP* 1.3 67.2 + - - +
91B GLU* 3.3 16.7 + - - +
92B LYS* 3.6 24.9 + - - +
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Residues in contact with TRP 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.8 2.4 + - + +
40B ALA* 3.3 34.7 - - + +
41B HIS* 3.6 20.8 + - - +
44B SER* 3.8 19.0 - - - -
85B VAL 2.9 17.3 + - - +
86B ILE* 3.6 20.0 - - + +
88B LYS* 1.3 77.8 - - - +
90B ALA* 1.3 74.6 + - + +
92B LYS* 3.0 22.4 + - - +
93B ILE* 3.6 28.4 + - + +
115B LEU* 3.9 24.5 - - + -
119B ARG* 4.3 12.5 - - - +
173B ALA 4.6 2.8 + - - -
176B SER* 3.3 50.0 + - - -
177B ALA* 3.5 13.9 - - + -
180B LEU* 4.0 9.0 - - + -
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE 3.0 18.1 + - - +
87B ARG 3.7 6.1 - - - +
88B LYS 3.3 0.2 - - - -
89B TRP* 1.3 76.9 - - + +
91B GLU* 1.3 57.7 + - - +
93B ILE* 3.0 37.6 + - - +
96B PHE* 3.4 34.2 - - + +
108B LEU* 3.8 11.7 - - + -
180B LEU* 3.8 15.0 - - + -
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 3.4 13.9 + - + +
88B LYS* 3.3 13.1 + - - +
89B TRP 3.2 0.4 - - - -
90B ALA* 1.3 79.4 - - - +
92B LYS* 1.3 61.3 + - + +
93B ILE 3.3 4.7 + - - +
96B PHE* 3.8 11.7 - - - -
97B ALA* 3.1 32.8 - - - +
104B GLN* 3.0 25.7 - - - +
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Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER* 4.6 1.4 - - - +
39B ARG* 3.5 36.6 + - - +
40B ALA* 3.6 26.6 + - + +
43B ASP* 4.0 25.4 + - + +
88B LYS* 3.6 21.9 + - - +
89B TRP* 3.0 11.8 + - - +
91B GLU* 1.3 78.7 - - + +
93B ILE* 1.3 64.0 + - - +
94B PRO* 3.2 10.9 - - - +
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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