Contacts of the helix formed by residues 75 - 100 (chain A) in PDB entry 4J7Y
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 HIS 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA 3.1 2.5 + - - +
71A GLY* 3.5 6.6 + - - -
74A PHE* 1.3 102.7 - + + +
76A GLU* 1.3 65.0 + - - +
77A GLY* 3.2 23.5 + - - -
78A ALA* 3.0 25.3 + - + +
79A ALA* 3.3 23.0 + - - +
121A LEU* 5.5 0.2 - - - +
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Residues in contact with GLU 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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3A ASP 4.2 5.2 - - - +
4A GLU* 3.1 26.3 - - - +
5A VAL 3.2 13.5 - - - -
6A ALA 3.3 1.0 + - - -
7A LEU* 3.0 47.5 + - + +
8A LEU* 3.5 23.6 + - + +
71A GLY* 3.2 16.8 + - - +
75A HIS* 1.3 75.4 - - - +
77A GLY* 1.3 57.9 + - - +
79A ALA* 3.3 4.2 + - - +
80A ALA* 2.9 27.9 + - - +
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.5 12.9 - - - +
75A HIS* 3.2 16.2 + - - -
76A GLU* 1.3 77.2 - - - +
78A ALA* 1.3 58.3 + - - +
80A ALA* 3.2 7.0 + - - +
81A LEU* 2.9 39.5 + - - +
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 4.5 5.8 - - + -
75A HIS* 3.0 27.5 + - + +
77A GLY* 1.3 74.1 - - - +
79A ALA* 1.3 56.4 + - - +
81A LEU* 3.3 13.4 + - - +
82A CYS* 2.9 38.4 + - - -
121A LEU* 4.0 20.0 - - + -
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.2 0.9 - - + -
67A LEU* 3.2 23.7 - - + +
70A ALA* 4.1 3.4 - - + -
71A GLY* 3.5 26.7 - - - +
75A HIS 3.3 14.8 + - - +
76A GLU 3.3 3.3 + - - +
77A GLY 3.2 0.4 - - - -
78A ALA* 1.3 78.0 - - - +
80A ALA* 1.3 58.6 + - - +
82A CYS* 3.4 3.3 + - - +
83A GLY 2.9 24.3 + - - -
118A LEU* 3.6 19.1 - - + +
121A LEU* 4.7 1.9 - - + +
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.1 25.4 - - + +
8A LEU* 4.5 1.8 - - + +
11A VAL* 3.7 27.8 - - + +
67A LEU* 4.0 6.0 - - - +
76A GLU 2.9 17.3 + - - +
77A GLY* 3.6 5.6 - - - +
79A ALA* 1.3 77.8 - - - +
81A LEU* 1.3 56.6 + - + +
83A GLY* 3.2 2.4 + - - -
84A LEU* 2.9 29.0 + - - +
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Residues in contact with LEU 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 GLY* 2.9 26.4 + - - +
78A ALA* 3.5 12.8 - - - +
79A ALA 3.3 0.2 - - - -
80A ALA* 1.3 72.9 - - + +
82A CYS* 1.3 68.8 + - - +
84A LEU* 3.0 12.5 + - + +
85A VAL* 2.9 29.3 + - + +
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Residues in contact with CYS 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 ALA* 2.9 26.9 + - - +
79A ALA 3.6 4.9 - - - +
81A LEU* 1.3 77.2 - - - +
83A GLY* 1.3 57.8 + - - +
85A VAL* 3.4 8.5 + - - +
86A TYR* 2.9 30.0 + - - +
114A ALA* 3.7 10.6 - - + +
117A LEU* 3.5 39.3 - - - -
118A LEU* 3.7 21.3 - - + -
121A LEU* 4.4 10.3 - - - -
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 4.1 9.9 - - - -
63A PHE* 3.4 28.0 - - - -
67A LEU* 4.6 0.2 - - - -
79A ALA 2.9 15.1 + - - -
80A ALA 3.2 5.1 + - - -
81A LEU 3.2 0.2 - - - -
82A CYS* 1.3 76.5 - - - +
84A LEU* 1.3 55.0 + - - +
86A TYR* 3.5 1.6 + - - +
87A LEU* 2.9 34.7 + - - +
118A LEU* 4.3 1.9 - - - +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 4.3 17.7 - - + -
14A LEU* 3.5 32.1 - - + -
80A ALA 2.9 14.4 + - - +
81A LEU* 3.0 15.7 + - + +
83A GLY* 1.3 74.2 - - - +
85A VAL* 1.3 63.1 + - + +
87A LEU* 3.3 2.9 + - + +
88A PHE* 2.9 32.0 + - - +
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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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81A LEU* 2.9 18.8 + - + +
82A CYS* 3.6 9.0 - - - +
84A LEU* 1.3 78.4 - - + +
86A TYR* 1.3 57.3 + - - +
88A PHE* 3.7 7.0 - - + +
89A ALA* 2.9 30.7 + - + +
92A ARG* 5.2 0.2 + - - -
110A ALA* 4.7 10.5 - - + +
114A ALA* 4.1 14.4 - - + -
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Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A CYS 4.9 1.6 + - - -
59A TYR* 3.4 28.2 + - - +
60A PHE* 4.6 3.6 + + - -
63A PHE* 3.4 43.1 - + + -
82A CYS 2.9 18.5 + - - +
83A GLY* 3.5 6.1 - - - +
85A VAL* 1.3 77.7 - - - +
87A LEU* 1.3 69.4 + - + +
89A ALA* 3.3 5.8 + - - +
90A ARG* 2.9 68.3 + - + +
111A SER* 3.2 28.7 - - - +
114A ALA* 3.9 10.7 - - + +
115A LEU* 4.3 21.5 - - + +
118A LEU* 5.5 1.3 - - + -
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.6 33.0 - - + +
14A LEU* 3.9 22.2 - - + +
15A GLY* 3.7 27.4 - - - +
18A LEU* 3.4 27.5 - - + +
19A GLN* 5.9 1.1 - - - +
60A PHE* 4.8 4.3 - - + -
63A PHE* 3.8 18.8 - - + -
83A GLY 2.9 20.9 + - - +
84A LEU* 3.8 4.0 - - + +
86A TYR* 1.3 86.9 - - + +
88A PHE* 1.3 58.3 + - - +
90A ARG* 3.3 2.5 + - + -
91A LEU* 2.9 25.8 + - - +
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Residues in contact with PHE 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 LEU 2.9 17.9 + - - +
85A VAL* 3.7 6.5 - - - +
87A LEU* 1.3 76.3 - - - +
89A ALA* 1.3 55.7 + - - +
91A LEU* 3.2 19.5 + - + +
92A ARG* 2.9 73.0 + - + +
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 2.9 18.8 + - + +
86A TYR 3.5 4.5 - - - +
88A PHE* 1.3 77.0 - - - +
90A ARG* 1.3 57.9 + - - +
92A ARG* 3.5 13.7 + - - +
93A TYR* 2.9 24.8 + - - +
107A PRO* 3.2 17.7 - - - +
110A ALA* 3.7 12.8 - - + -
111A SER* 3.4 31.2 - - - +
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Residues in contact with ARG 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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18A LEU* 4.7 7.2 - - + -
19A GLN* 6.0 0.2 - - - +
22A PHE* 3.7 6.1 - - + -
55A ASN* 3.7 7.3 + - - +
56A CYS* 3.4 49.1 - - + +
59A TYR* 3.0 38.5 - - - -
86A TYR* 2.9 52.1 + - + +
87A LEU* 3.3 7.6 + - + +
89A ALA* 1.3 73.0 - - - +
91A LEU* 1.3 60.9 + - - +
93A TYR* 3.2 20.6 - - - +
94A PHE* 2.9 28.4 + - - +
108A LEU* 4.3 8.7 - - - +
111A SER* 3.4 22.5 + - - -
203A 1JP 4.1 11.7 + - - -
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Residues in contact with LEU 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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18A LEU* 3.9 20.0 - - + -
21A TYR* 3.6 31.2 - - + -
22A PHE* 3.9 10.0 - - + -
87A LEU 2.9 14.0 + - - +
88A PHE* 3.5 24.0 - - + +
90A ARG* 1.3 75.4 - - - +
92A ARG* 1.3 58.3 + - + +
94A PHE* 3.2 2.6 + - + +
95A GLN* 3.0 56.1 + - + +
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Residues in contact with ARG 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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85A VAL 5.2 0.4 + - - -
88A PHE* 2.9 67.0 + - + +
89A ALA* 3.7 13.0 - - - +
91A LEU* 1.3 73.0 - - + +
93A TYR* 1.3 60.5 + - - +
95A GLN* 3.5 16.7 + - - +
96A GLY* 2.9 24.9 + - - -
106A ALA 4.7 0.8 + - - -
107A PRO* 3.4 33.3 - - + +
110A ALA* 3.4 30.1 - - - +
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Residues in contact with TYR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 3.6 28.0 - - + -
55A ASN* 3.4 13.8 + - + +
56A CYS* 3.7 19.7 - - - -
89A ALA 2.9 15.6 + - - +
90A ARG* 3.2 21.5 - - - +
92A ARG* 1.3 75.8 - - - +
94A PHE* 1.3 59.9 + - - +
96A GLY 3.4 0.2 + - - -
97A TYR* 2.9 46.2 + + - +
104A ARG* 3.5 33.1 - - + +
107A PRO* 3.2 13.3 - - + +
108A LEU* 3.6 22.7 - - + +
203A 1JP 2.7 40.4 + - - -
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Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 4.5 8.1 - + - -
22A PHE* 3.4 50.7 - + + -
25A GLN* 3.4 44.0 - - + -
49A VAL* 3.7 34.5 - - + -
52A ALA* 3.6 18.7 - - + +
53A GLN* 3.8 19.1 - - + -
56A CYS* 4.9 0.2 - - - -
90A ARG 2.9 8.3 + - - +
91A LEU 3.2 4.0 + - - +
93A TYR* 1.3 81.3 - - + +
95A GLN* 1.3 64.3 + - + +
97A TYR* 3.4 1.6 + - - +
98A ALA* 2.9 37.9 + - + +
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Residues in contact with GLN 95 (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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21A TYR* 4.7 10.8 + - - +
91A LEU* 3.0 42.6 + - + +
92A ARG* 3.7 20.7 - - - +
94A PHE* 1.3 84.4 - - + +
96A GLY* 1.3 62.4 + - - +
98A ALA* 3.6 5.6 + - - +
99A ARG* 3.5 27.1 + - - +
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG 2.9 17.2 + - - -
93A TYR 3.7 0.2 - - - -
95A GLN* 1.3 71.0 - - - +
97A TYR* 1.3 65.1 + - - +
99A ARG* 2.9 17.9 + - - +
100A SER 2.9 18.0 + - - +
103A LEU* 3.5 31.1 - - - +
104A ARG 3.7 2.5 - - - -
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Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 3.4 41.4 + - + +
51A ARG* 3.1 37.8 - - + +
52A ALA* 3.3 31.4 - - + -
55A ASN* 5.2 0.9 - - - -
93A TYR* 2.9 36.4 + + - +
94A PHE 3.8 0.2 - - - +
96A GLY* 1.3 71.3 - - - +
98A ALA* 1.3 62.8 + - - +
99A ARG 3.1 0.9 + - - -
100A SER 3.3 12.6 + - - -
101A ALA* 4.0 15.8 - - + +
104A ARG* 3.3 38.4 + - + +
203A 1JP 5.1 0.7 - - - -
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLU* 4.4 4.9 - - - +
48A ARG* 3.6 13.6 + - - -
49A VAL* 3.5 36.3 - - + +
94A PHE* 2.9 27.4 + - + +
95A GLN* 3.7 8.3 - - - +
96A GLY 3.2 0.2 - - - -
97A TYR* 1.3 75.5 - - - +
99A ARG* 1.3 61.7 + - + +
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Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 3.3 15.4 + - - -
95A GLN* 3.6 16.1 - - - +
96A GLY* 2.9 9.0 + - - +
98A ALA* 1.3 82.3 - - + +
100A SER* 1.3 61.7 + - - +
103A LEU* 3.5 33.8 - - + +
202A SO4 4.0 3.1 + - - -
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Residues in contact with SER 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 3.8 2.2 - - - +
96A GLY 2.9 14.7 + - - +
97A TYR* 3.3 10.6 + - - -
99A ARG* 1.3 80.7 - - - +
101A ALA* 1.3 64.4 - - - +
102A GLN* 4.0 2.8 + - - +
103A LEU* 3.0 38.6 + - - +
202A SO4 3.2 29.4 - - - -
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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