Contacts of the helix formed by residues 68 - 92 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LYS* 4.7 4.5 - - - +
67A GLU* 1.3 75.4 - - - +
69A ALA* 1.3 63.2 + - - +
70A GLY* 3.0 16.2 + - - -
71A ASP* 3.0 27.0 + - - +
72A VAL* 3.1 20.4 + - - +
146A ARG* 3.0 19.5 + - - +
250A LEU* 3.5 8.5 - - - -
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASP* 1.3 73.9 - - - +
70A GLY* 1.3 60.5 + - - +
72A VAL* 4.0 1.1 - - - +
73A GLN* 3.0 30.7 + - - +
250A LEU* 3.8 15.0 - - + +
251A VAL* 3.7 26.2 - - + +
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 3.0 8.0 + - - -
69A ALA* 1.3 73.7 - - - +
71A ASP* 1.3 66.3 + - - +
73A GLN* 3.9 4.2 - - - +
74A GLN* 2.9 26.9 + - - +
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Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 3.5 3.3 - - + -
68A ASP* 3.0 32.8 + - - +
70A GLY* 1.3 77.2 - - - +
72A VAL* 1.3 56.4 + - - +
74A GLN* 3.5 8.7 + - - +
75A PHE* 3.1 26.5 + - - +
143A GLN 5.6 1.9 - - - +
146A ARG* 2.8 47.2 + - + +
147A GLY* 3.9 21.6 - - - +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 3.9 17.7 - - + -
68A ASP 3.1 16.2 + - - +
69A ALA* 3.4 4.7 + - - +
70A GLY 3.3 0.2 - - - -
71A ASP* 1.3 76.7 - - + +
73A GLN* 1.3 60.3 + - - +
75A PHE* 3.1 7.6 + - - +
76A TYR* 2.9 54.8 + - + -
147A GLY* 5.1 1.6 - - - -
245A LEU* 3.7 37.5 - - + +
248A GLU* 4.1 1.3 - - - +
250A LEU* 4.0 13.7 - - + +
251A VAL* 3.7 15.7 - - + +
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Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA 3.0 18.0 + - - +
70A GLY* 3.9 4.3 - - - +
72A VAL* 1.3 76.6 - - - +
74A GLN* 1.3 65.8 + - - +
76A TYR* 4.0 13.5 - - - +
77A ASP* 2.8 60.2 + - - +
251A VAL* 3.8 27.4 - - + +
252A PRO* 4.8 6.4 + - - +
254A PRO* 5.5 2.8 - - - +
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Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LYS* 4.8 13.7 - - - +
70A GLY 2.9 18.8 + - - +
71A ASP* 3.8 7.4 - - - +
73A GLN* 1.3 77.1 - - - +
75A PHE* 1.3 62.3 + - - +
77A ASP* 3.3 8.3 + - + +
78A LEU* 2.9 39.8 + - + +
137A LEU* 4.5 9.6 - - + +
139A LEU* 3.9 32.0 - - - +
143A GLN* 4.5 10.6 - - - +
144A CYS* 5.9 0.2 - - - -
148A PHE* 5.7 2.9 - - + -
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Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ASP 3.1 13.9 + - - +
72A VAL* 3.1 11.5 + - - +
74A GLN* 1.3 77.5 - - - +
76A TYR* 1.4 82.9 + + - +
78A LEU* 3.2 3.6 + - - +
79A LEU* 3.1 48.0 + - + +
147A GLY* 3.6 19.5 - - - +
148A PHE* 3.8 34.9 - + + -
151A TRP* 3.8 25.1 - + - -
241A ARG* 3.9 17.7 - - + -
242A ILE* 3.9 15.3 - - + -
245A LEU* 3.3 29.8 - - + -
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Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A VAL* 2.9 36.9 + - + +
73A GLN* 3.9 11.0 - - - +
75A PHE* 1.4 96.8 - + - +
77A ASP* 1.3 65.0 + - - +
79A LEU* 3.1 11.1 + - + +
80A SER* 2.8 25.1 + - - -
242A ILE* 4.4 12.3 + - + +
245A LEU* 3.6 22.4 + - + +
246A LYS* 4.0 10.2 - - - +
251A VAL* 3.8 25.8 + - + -
252A PRO 3.8 8.1 - - - -
253A PRO* 3.6 34.8 - - + +
254A PRO* 3.6 26.5 - - + +
257A ILE* 4.9 3.8 - - + -
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLN* 2.8 53.2 + - - +
74A GLN* 3.8 7.7 - - + +
76A TYR* 1.3 72.3 - - - +
78A LEU* 1.3 61.2 + - + +
80A SER* 3.7 6.1 - - - -
81A GLY* 2.8 30.3 + - - -
254A PRO* 5.8 0.9 - - - +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLN* 2.9 38.4 + - + +
75A PHE 3.3 4.5 - - - +
77A ASP* 1.3 78.9 - - + +
79A LEU* 1.3 63.0 + - - +
81A GLY* 4.3 0.3 - - - -
82A SER* 3.1 25.5 + - - -
116A PHE* 4.2 4.5 - - + -
133A PHE* 3.8 47.7 - - + -
134A CYS* 5.5 0.5 - - - -
135A SER* 5.3 3.8 - - - +
137A LEU* 3.9 22.0 - - + -
139A LEU* 4.1 9.2 - - + -
148A PHE* 4.1 20.2 - - + -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE* 3.1 46.9 + - + +
76A TYR* 3.4 10.1 - - + +
78A LEU* 1.3 73.2 - - - +
80A SER* 1.3 64.9 + - - +
82A SER* 3.2 2.3 + - - -
83A LEU* 3.0 19.1 + - - +
112A PHE* 3.2 28.8 - - + -
113A LEU* 5.1 2.0 - - + -
116A PHE* 3.6 39.3 - - + -
148A PHE* 5.1 1.8 - - + -
151A TRP* 4.6 10.5 - - + -
242A ILE* 4.2 18.4 - - + -
257A ILE* 4.1 20.0 - - + -
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR 2.8 15.2 + - - -
77A ASP* 3.7 7.4 - - - -
79A LEU* 1.3 72.2 - - - +
81A GLY* 1.3 67.4 + - - +
83A LEU* 3.2 6.2 + - - +
84A GLU* 3.1 28.2 + - - +
254A PRO* 3.1 35.2 - - - +
257A ILE* 3.9 8.2 - - - +
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Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP 2.8 19.4 + - - -
78A LEU 4.3 0.2 - - - -
80A SER* 1.3 73.4 - - - +
82A SER* 1.3 61.4 + - - +
84A GLU* 3.2 9.2 + - - +
85A VAL* 3.0 28.6 + - - +
134A CYS* 4.3 5.6 - - - -
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU 3.1 19.3 + - - -
79A LEU 3.5 4.9 - - - -
80A SER 3.0 0.8 - - - -
81A GLY* 1.3 78.2 - - - +
83A LEU* 1.3 57.7 + - - +
85A VAL* 3.3 3.1 + - - +
86A ILE* 2.8 40.2 + - - +
112A PHE* 3.4 8.6 - - - -
116A PHE* 3.3 29.4 - - - +
119A ARG* 5.7 0.2 + - - -
134A CYS* 3.8 18.9 - - - -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU 3.0 10.8 + - - +
80A SER* 3.2 6.3 + - - +
82A SER* 1.3 76.7 + - - +
84A GLU* 1.3 62.1 + - + +
86A ILE* 4.2 6.1 - - + +
87A ARG* 3.0 48.4 + - - +
108A LEU* 4.7 17.3 - - + +
109A GLU* 5.4 0.9 - - + +
112A PHE* 3.5 36.1 - - + -
256A ILE* 3.7 34.1 - - + -
257A ILE* 4.0 13.0 - - + -
260A ILE* 3.9 15.5 - - + -
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A SER* 3.1 19.4 + - - +
81A GLY* 3.2 9.2 + - - +
83A LEU* 1.3 78.4 - - - +
85A VAL* 1.3 63.9 + - + +
87A ARG* 3.3 29.7 + - - +
88A LYS* 3.2 36.4 + - - +
256A ILE* 4.9 12.3 - - - +
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A SER* 3.1 34.6 - - - +
81A GLY 3.0 19.8 + - - +
82A SER 3.6 4.0 - - - +
84A GLU* 1.3 77.6 - - + +
86A ILE* 1.3 64.3 + - - +
88A LYS* 3.4 11.0 + - + +
89A TRP* 3.1 21.7 + - - +
119A ARG* 3.6 13.0 - - - +
134A CYS* 3.8 21.1 - - + -
135A SER* 5.6 2.2 - - - +
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A SER* 2.8 40.0 + - - +
83A LEU* 3.4 8.9 + - + +
85A VAL* 1.3 72.9 - - - +
87A ARG* 1.3 53.9 + - - +
89A TRP* 3.2 17.5 + - + -
90A ALA* 2.8 32.4 + - - +
108A LEU* 4.2 12.3 - - + +
112A PHE* 4.0 16.4 - - + -
115A LEU* 3.7 44.9 - - + -
116A PHE* 4.0 6.5 - - - +
119A ARG* 3.8 28.0 - - - +
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.0 41.9 + - - +
84A GLU* 3.3 34.3 + - - +
86A ILE* 1.3 75.4 - - - +
88A LYS* 1.3 63.1 + - + +
90A ALA* 3.3 2.4 + - - +
91A GLU* 3.0 22.9 + - - +
96A PHE* 5.5 0.5 - - - -
105A ASP* 3.9 20.2 + - - +
108A LEU* 3.9 31.8 - - + +
109A GLU* 5.1 7.7 + - - +
256A ILE* 4.0 22.6 - - - +
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Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLU* 3.2 26.6 + - - +
85A VAL* 3.4 9.6 + - + +
87A ARG* 1.3 77.3 - - + +
89A TRP* 1.3 63.5 + - - +
91A GLU* 3.5 14.6 + - - +
92A LYS* 3.6 28.9 + - - +
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Residues in contact with TRP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU 4.9 1.4 + - - -
40A ALA* 3.4 36.5 - - + +
41A HIS* 3.8 16.0 + - - +
44A SER* 3.7 21.3 - - - -
85A VAL 3.1 14.1 + - - +
86A ILE* 3.3 34.8 - - + +
88A LYS* 1.3 76.8 - - - +
90A ALA* 1.3 69.3 + - - +
92A LYS* 3.0 24.1 + - - +
93A ILE* 3.5 14.6 + - + +
115A LEU* 3.8 25.8 - - + -
119A ARG* 4.3 13.4 - - - +
173A ALA 4.8 2.2 + - - -
176A SER* 3.6 31.3 + - - -
177A ALA* 3.7 28.0 - - + -
180A LEU* 3.7 24.5 - - + -
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ILE 2.8 19.7 + - - +
87A ARG 3.7 3.1 - - - +
89A TRP* 1.3 74.1 - - + +
91A GLU* 1.3 63.0 + - - +
92A LYS 2.9 6.0 + - - -
93A ILE* 2.9 18.5 + - - +
96A PHE* 3.4 32.9 - - + +
108A LEU* 3.5 25.1 - - + -
180A LEU* 3.7 15.3 - - + -
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG 3.0 13.3 + - - +
88A LYS* 3.8 13.5 - - - +
89A TRP 3.4 0.4 - - - -
90A ALA* 1.3 73.8 - - - +
92A LYS* 1.3 61.8 + - + +
93A ILE 3.8 4.3 + - - +
96A PHE* 4.1 8.3 - - - -
97A ALA* 3.9 33.6 - - - +
104A GLN* 4.9 6.3 - - - +
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A SER* 4.7 5.4 - - - +
39A ARG* 5.6 2.5 - - + -
40A ALA* 3.7 30.0 + - + +
43A ASP* 3.8 33.7 + - + +
88A LYS* 3.6 24.5 + - - +
89A TRP* 3.0 11.5 + - - +
90A ALA 2.9 1.4 - - - -
91A GLU* 1.3 80.8 - - + +
93A ILE* 1.3 64.9 + - - +
94A PRO* 3.3 10.7 - - - +
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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) + - + + + + + -
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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