Contacts of the helix formed by residues 64 - 97 (chain A) in PDB entry 5OY0
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 64 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A THR* 2.9 14.3 + - - +
63A SER* 1.3 76.6 + - - +
65A LEU* 1.3 68.6 + - - +
66A GLU* 3.3 23.3 + - - +
67A ASP* 4.0 15.6 + - + +
68A VAL* 3.1 25.3 + - - +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER 3.5 5.2 + - - +
64A ASP* 1.3 76.2 + - - +
66A GLU* 1.3 53.9 + - - +
68A VAL* 3.4 7.9 + - + +
69A SER* 2.7 36.6 + - - -
187A LEU* 3.7 34.1 - - + -
191A GLN* 5.2 0.9 - - - +
345A THR 5.3 0.2 - - - +
346A THR* 3.5 41.1 - - + +
348A TRP* 3.7 29.8 - - + +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP* 4.0 3.8 - - - +
64A ASP* 3.2 16.0 + - - +
65A LEU* 1.3 80.0 - - - +
67A ASP* 1.3 57.5 + - - +
69A SER* 3.2 6.1 + - - -
70A ARG* 3.0 66.3 + - - +
185A PRO 4.5 0.2 - - - +
186A LYS* 3.2 22.3 + - - +
187A LEU* 2.8 47.7 + - + +
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Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A THR* 3.8 14.7 + - + +
64A ASP* 3.3 25.3 + - + +
66A GLU* 1.3 75.4 - - - +
68A VAL* 1.3 61.3 + - - +
70A ARG* 3.3 11.9 + - - +
71A LYS* 2.9 44.1 + - - +
180A TYR* 3.3 24.6 + - - -
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 3.7 25.6 - - + +
59A ASP* 3.8 20.4 - - - +
62A THR* 3.6 26.5 - - + +
64A ASP 3.1 16.1 + - - +
65A LEU* 3.6 11.7 - - + +
66A GLU 3.3 0.2 - - - -
67A ASP* 1.3 76.8 - - - +
69A SER* 1.3 63.1 + - - +
71A LYS* 3.3 8.2 + - - +
72A ILE* 2.9 43.1 + - + +
348A TRP* 4.2 9.9 - - + -
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Residues in contact with SER 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU 2.7 19.1 + - - -
66A GLU* 3.2 9.8 + - - -
68A VAL* 1.3 75.4 - - - +
70A ARG* 1.3 57.7 + - - +
72A ILE* 3.3 3.1 + - - +
73A PHE* 2.9 29.6 + - - +
187A LEU* 3.6 14.3 - - - +
190A PHE* 3.7 24.9 - - - -
348A TRP* 3.0 37.5 + - - +
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP* 2.4 37.0 + - - +
20A PRO* 4.4 16.3 - - - +
66A GLU* 3.0 47.2 + - - +
67A ASP* 3.6 12.5 - - - +
68A VAL 3.2 0.2 - - - -
69A SER* 1.3 73.8 - - - +
71A LYS* 1.3 66.2 + - - +
73A PHE* 3.2 3.4 + - - +
74A SER* 3.0 28.4 + - - -
179A HIS 4.9 3.2 - - - +
180A TYR* 3.9 17.3 - - + -
184A ALA* 3.3 38.4 + - + +
185A PRO* 3.1 25.8 + - + +
186A LYS* 4.0 3.6 - - - +
190A PHE* 4.4 7.2 - - + -
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A HIS* 6.1 2.0 - - - -
34A PHE* 5.1 4.9 - - - +
58A PHE* 3.6 41.5 - - + -
61A GLN* 3.0 28.0 + - - +
62A THR* 4.6 7.6 - - + +
67A ASP* 2.9 39.0 + - - +
68A VAL* 3.6 2.7 - - - +
70A ARG* 1.3 74.5 - - - +
72A ILE* 1.3 58.1 + - - +
74A SER* 3.5 1.8 + - - -
75A ALA* 2.9 30.5 + - - +
180A TYR* 3.4 35.6 - - + -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 3.7 20.9 - - + -
68A VAL* 2.9 38.2 + - + +
69A SER* 3.6 4.0 - - - +
70A ARG 3.2 0.2 - - - -
71A LYS* 1.3 76.6 - - - +
73A PHE* 1.3 56.1 + - - +
75A ALA* 3.2 2.6 + - - +
76A HIS* 2.9 66.7 + - + +
348A TRP* 3.5 50.5 - - + -
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Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER 2.9 17.0 + - - +
70A ARG* 3.7 4.0 - - - +
72A ILE* 1.3 78.7 - - - +
74A SER* 1.3 62.4 + - - +
76A HIS* 3.2 16.4 + - + +
77A PHE* 3.1 60.2 + + - -
179A HIS* 4.0 27.4 - + + +
185A PRO* 4.0 18.4 - - + -
189A TRP* 3.6 29.4 - + - -
190A PHE* 3.6 18.2 - + + -
348A TRP* 6.1 0.2 - - - -
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG 3.0 13.1 + - - -
71A LYS* 4.1 2.5 - - - -
73A PHE* 1.3 77.1 - - - +
75A ALA* 1.3 57.2 + - - +
77A PHE* 3.2 4.7 + - - +
78A GLY* 3.0 24.6 + - - -
176A GLY* 2.8 37.4 + - - -
179A HIS* 3.7 4.3 - - - +
180A TYR* 3.0 30.1 + - - +
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 4.4 15.5 - - + -
71A LYS 2.9 19.0 + - - +
72A ILE* 3.6 8.1 - - - +
74A SER* 1.3 77.1 - - - +
76A HIS* 1.3 62.1 + - + +
78A GLY* 3.2 2.3 + - - +
79A HIS* 2.9 29.3 + - - +
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Residues in contact with HIS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 2.9 50.3 + - + +
73A PHE* 3.2 18.1 + - + +
75A ALA* 1.3 80.2 - - + +
77A PHE* 1.3 56.8 + - + +
79A HIS* 3.2 7.8 + - + +
80A LEU* 2.9 37.0 + - + +
348A TRP* 4.8 8.1 - + - -
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 3.1 63.6 + + - -
74A SER* 3.2 2.4 + - - +
76A HIS* 1.3 75.8 - - - +
78A GLY* 1.3 62.3 + - - +
80A LEU* 3.3 7.4 + - + +
81A ALA* 3.0 19.1 + - - +
172A MET* 3.4 53.7 - - + +
175A ALA* 3.8 20.2 - - + -
176A GLY* 3.5 26.7 - - - -
179A HIS* 3.9 15.3 - + + -
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER 3.0 13.9 + - - -
75A ALA* 3.2 4.0 + - - -
77A PHE* 1.3 75.9 - - - +
79A HIS* 1.3 56.7 + - - +
81A ALA* 3.2 9.3 + - - +
82A VAL* 3.0 33.9 + - - +
173A LEU* 4.5 14.8 - - - +
176A GLY* 5.2 1.0 - - - -
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Residues in contact with HIS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA 2.9 17.6 + - - +
76A HIS* 3.6 8.0 + - + +
78A GLY* 1.3 76.2 - - - +
80A LEU* 1.3 67.4 + - + +
82A VAL* 3.2 13.0 + - + +
83A VAL* 3.0 51.4 + - + +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A HIS* 2.9 24.9 + - + +
77A PHE* 3.6 9.0 - - + +
79A HIS* 1.3 85.2 + - + +
81A ALA* 1.3 58.6 + - - +
83A VAL* 3.2 10.4 + - + +
84A PHE* 2.9 40.8 + - + -
172A MET* 3.5 31.4 - - + -
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE 3.0 14.8 + - - +
78A GLY 3.2 8.5 + - - +
80A LEU* 1.3 77.1 - - - +
82A VAL* 1.3 57.6 + - + +
84A PHE 3.3 0.5 + - - -
85A VAL* 2.9 34.7 + - + +
169A ALA* 3.3 33.1 - - + +
172A MET* 3.7 9.1 - - + +
173A LEU* 3.9 19.5 - - + +
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLY 3.0 19.3 + - - +
79A HIS* 3.2 13.9 + - + +
81A ALA* 1.3 77.0 - - + +
83A VAL* 1.3 63.7 + - + +
85A VAL* 3.2 10.0 + - + +
86A TRP* 3.0 23.7 + - + +
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 3.0 45.6 + - + +
80A LEU* 3.2 15.5 + - + +
82A VAL* 1.3 77.0 - - + +
84A PHE* 1.3 58.7 + - + +
86A TRP* 3.3 20.0 + - + +
87A LEU* 2.9 32.4 + - + +
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Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 2.9 30.8 + - + +
81A ALA 3.6 4.9 - - - +
82A VAL 3.2 0.2 - - - -
83A VAL* 1.3 75.9 - - + +
85A VAL* 1.3 66.0 + - - +
87A LEU* 3.3 12.9 + - + +
88A SER* 2.9 28.2 + - - -
165A GLY* 3.6 14.4 - - - +
168A MET* 3.6 39.0 - - + -
169A ALA* 3.6 13.2 - - + -
172A MET* 3.5 35.9 - - + -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA 2.9 20.0 + - - +
82A VAL* 3.5 10.8 - - + +
84A PHE* 1.3 74.1 - - - +
86A TRP* 1.3 58.3 + - - +
88A SER* 2.9 20.0 + - - +
89A GLY* 2.9 14.7 + - - -
166A LEU* 4.6 13.1 - - + +
169A ALA* 3.7 15.0 - - + -
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Residues in contact with TRP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 3.0 14.7 + - + +
83A VAL* 3.6 23.1 - - + +
84A PHE 3.2 0.2 - - - -
85A VAL* 1.3 79.4 - - - +
87A LEU* 1.3 86.1 + - + +
89A GLY* 3.1 3.2 + - - -
90A MET* 3.0 63.1 + - + +
143A LEU* 6.5 0.4 - - + -
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 2.9 21.5 + - + +
84A PHE* 4.0 15.3 - - + +
86A TRP* 1.3 98.2 - - + +
88A SER* 1.3 63.1 + - - +
90A MET* 3.1 12.4 + - + +
91A TYR* 3.0 52.6 + - + -
143A LEU* 5.7 5.2 - - + -
146A LEU* 6.5 0.9 - - + -
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Residues in contact with SER 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE 2.9 14.3 + - - -
85A VAL 2.9 18.7 + - - -
87A LEU* 1.3 76.1 - - - +
89A GLY* 1.3 55.9 + - - +
91A TYR* 4.4 3.1 - - - +
92A PHE* 2.8 26.4 + - - +
161A THR 5.1 0.4 - - - -
162A ALA* 3.2 41.4 - - - +
165A GLY* 3.7 14.5 - - - -
166A LEU* 3.2 22.4 + - - +
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Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL 2.9 16.1 + - - -
86A TRP* 3.1 4.9 + - - -
88A SER* 1.3 75.2 + - - +
90A MET* 1.3 72.3 + - - +
92A PHE* 3.3 6.3 + - - +
93A HIS* 3.0 33.4 + - - +
----------------------------------------------------------
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Residues in contact with MET 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TRP* 3.0 64.2 + - + +
87A LEU* 3.4 17.0 - - + +
89A GLY* 1.3 83.0 - - - +
91A TYR* 1.3 58.7 + - + +
93A HIS* 3.3 9.9 + - + +
94A GLY 3.0 23.2 + - - -
143A LEU* 4.0 30.4 - - + +
147A TRP* 3.7 9.2 - - - -
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 3.0 56.1 + - + +
88A SER* 3.8 4.5 - - - +
90A MET* 1.3 77.2 - - + +
92A PHE* 1.3 57.1 + - - +
94A GLY* 3.3 1.9 + - - -
95A ALA* 2.9 27.7 + - - +
143A LEU* 5.9 1.6 - - + -
146A LEU* 4.2 12.7 - - + +
147A TRP* 3.2 42.8 + + - -
150A SER* 5.7 0.9 + - - -
152A PHE* 3.9 16.7 - + - -
158A LEU* 3.7 28.1 - - + +
161A THR* 3.5 33.0 - - + -
162A ALA* 4.1 10.3 - - + +
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER 2.8 17.2 + - - +
89A GLY* 3.7 7.2 - - - +
91A TYR* 1.3 77.7 - - - +
93A HIS* 1.3 62.3 + + + +
95A ALA* 3.0 5.2 + - - +
96A LYS* 2.9 49.4 + - + +
97A PHE* 3.8 27.1 - + - -
159A TYR* 3.8 36.1 - + - -
162A ALA* 3.6 13.8 - - + +
163A ILE* 5.4 4.7 - - + -
166A LEU* 6.3 2.9 - - + -
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Residues in contact with HIS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLY* 3.0 22.7 + - - +
90A MET* 3.8 9.4 - - + +
92A PHE* 1.3 81.7 - + - +
94A GLY* 1.3 58.1 + - - +
97A PHE* 2.9 61.2 + + + +
98A SER* 3.2 9.1 + - - -
114A ALA* 3.5 25.2 + - + +
115A GLN* 4.5 14.8 - - + +
116A VAL 5.6 1.8 - - - -
----------------------------------------------------------
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Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A MET 3.0 11.9 + - - -
91A TYR 3.3 1.8 + - - -
93A HIS* 1.3 77.7 - - - +
95A ALA* 1.3 59.3 + - - +
98A SER* 2.6 28.6 + - - +
100A TYR* 4.2 1.6 - - - +
114A ALA* 4.7 2.3 - - - +
147A TRP* 3.5 30.5 - - - -
155A SER* 5.4 0.9 - - - -
158A LEU* 3.4 14.6 - - - +
----------------------------------------------------------
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR 2.9 14.1 + - - +
92A PHE* 3.0 9.4 + - - +
94A GLY* 1.3 78.6 - - - +
96A LYS* 1.3 65.0 + - + +
98A SER 5.0 2.9 + - - +
155A SER* 2.4 47.4 + - - +
158A LEU* 3.7 7.1 - - + +
159A TYR* 3.6 23.1 - - + +
----------------------------------------------------------
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 2.9 48.2 + - + +
95A ALA* 1.3 83.4 - - + +
97A PHE* 1.3 84.9 + - + +
98A SER 3.7 2.0 - - - -
155A SER* 5.5 0.4 - - - +
159A TYR* 5.1 7.2 - - + -
----------------------------------------------------------
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Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.8 25.6 - + - -
93A HIS* 2.9 55.8 + + + +
96A LYS* 1.3 100.6 - - + +
98A SER* 1.3 57.8 + - - +
114A ALA* 3.4 17.8 - - - +
115A GLN 3.6 0.3 + - - -
116A VAL* 3.5 36.1 - - + +
134A PHE* 3.7 8.4 - - - -
----------------------------------------------------------
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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