Contacts of the helix formed by residues 60 - 86 (chain A) in PDB entry 6LGV
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 ARG 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG* 2.8 33.0 + - + +
59A SER* 1.3 91.2 - - - +
61A PRO* 1.3 65.5 - - - +
62A ALA 3.3 2.2 - - - -
63A PRO* 3.3 22.3 - - + +
64A VAL* 3.2 17.3 - - - +
118A ASP* 3.1 34.1 + - - -
120A ALA* 5.6 1.4 - - - +
121A LEU* 3.9 27.5 - - + +
247A THR* 3.6 16.8 + - - +
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Residues in contact with PRO 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 3.0 20.4 - - + +
58A LEU* 3.5 16.2 - - + +
59A SER 3.3 9.2 - - - +
60A ARG* 1.3 90.6 - - - +
62A ALA* 1.4 54.5 + - + +
64A VAL* 3.3 2.1 + - + +
65A ALA* 2.7 40.5 + - + +
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG 3.3 0.2 - - - -
61A PRO* 1.4 81.9 - - + +
63A PRO* 1.4 65.0 - - + +
65A ALA* 3.9 3.9 - - - +
66A ALA* 2.8 29.3 + - - +
243A PHE* 3.5 19.1 - - + -
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Residues in contact with PRO 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 3.3 30.1 - - + +
62A ALA* 1.4 90.8 - - + +
64A VAL* 1.3 59.1 + - - +
66A ALA* 4.3 0.4 - - + -
67A ALA* 3.0 30.8 + - - +
121A LEU* 3.8 33.7 - - + -
125A ILE* 3.8 2.6 - - - +
243A PHE* 3.3 30.2 - - + -
247A THR* 3.9 9.4 - - + -
251A LEU* 3.8 6.5 - - + +
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG* 4.5 2.0 - - + +
57A VAL* 4.3 22.4 - - + -
60A ARG* 3.2 17.7 - - + +
61A PRO* 3.3 8.9 + - + +
62A ALA 3.2 0.8 - - - -
63A PRO* 1.3 75.9 - - - +
65A ALA* 1.3 63.4 + - - +
67A ALA* 3.9 1.4 - - - +
68A THR* 2.7 34.5 + - - +
121A LEU* 3.8 20.4 - - + -
124A THR* 3.9 19.1 - - + -
125A ILE* 4.0 12.3 - - + +
128A VAL* 4.2 28.3 - - + -
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PRO* 2.7 23.1 + - + +
62A ALA* 4.0 3.4 - - - +
64A VAL* 1.3 72.9 - - - +
66A ALA* 1.3 64.1 + - - +
68A THR* 3.8 4.2 - - - -
69A PHE* 2.9 28.6 + - + +
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA 2.8 23.5 + - - +
63A PRO 4.0 0.7 - - - +
65A ALA* 1.3 72.3 - - - +
67A ALA* 1.3 54.6 + - - +
69A PHE* 4.0 4.7 - - - +
70A LEU* 2.8 43.3 + - + +
241A PHE* 3.7 36.6 - - + -
243A PHE* 3.9 13.2 - - + -
251A LEU* 4.2 6.3 - - + -
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PRO 3.0 19.8 + - - +
64A VAL 3.9 1.6 - - - +
66A ALA* 1.3 75.1 - - - +
68A THR* 1.3 59.2 + - - +
70A LEU* 4.7 0.2 - - - -
71A HIS* 2.9 33.5 + - - +
125A ILE* 3.8 35.7 - - + -
251A LEU* 3.9 14.5 - - + +
254A GLU* 4.8 3.1 - - + -
255A VAL* 3.8 15.7 - - + +
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 2.7 22.6 + - - +
65A ALA* 3.8 5.6 - - - -
67A ALA* 1.3 78.9 - - - +
69A PHE* 1.3 57.1 + - - +
71A HIS* 3.8 3.1 - - - +
72A TYR* 3.1 48.9 + - + +
125A ILE* 5.2 5.0 + - - +
128A VAL* 3.6 22.1 - - + +
129A SER* 5.1 5.0 + - - +
132A VAL* 4.3 22.2 - - + -
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA 2.9 17.8 + - - +
66A ALA* 4.2 5.8 - - - -
68A THR* 1.3 75.3 - - - +
70A LEU* 1.3 90.4 + - + +
72A TYR* 5.4 0.9 - - - -
73A LEU* 2.9 58.3 + - + +
241A PHE* 5.0 14.1 - + - -
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 2.8 34.2 + - + +
69A PHE* 1.3 93.1 - - + +
71A HIS* 1.3 58.6 + - - +
73A LEU* 5.8 0.9 - - + -
74A ILE* 2.9 58.2 + - + +
233A SER 3.9 17.7 - - - +
234A GLY* 4.4 7.9 - - - -
237A GLY* 4.0 19.1 - - - -
241A PHE* 4.7 6.5 - - + -
251A LEU* 4.5 7.6 - - + -
255A VAL* 3.9 18.1 - - + +
406A A6L 4.5 16.2 - - + -
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Residues in contact with HIS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ALA 2.9 18.7 + - - +
68A THR* 3.8 5.2 - - - +
70A LEU* 1.3 76.9 - - - +
72A TYR* 1.3 82.7 + + - +
75A MET* 3.0 36.4 + - + +
76A PRO* 3.4 0.9 - - - +
100A GLY 5.0 1.8 - - - -
102A VAL 2.9 24.5 - - - -
103A ALA* 3.7 14.8 - - - -
104A SER* 3.7 7.9 + - - +
129A SER* 3.9 1.8 + - - +
254A GLU 3.7 13.2 - - - +
255A VAL* 3.2 39.2 - - + +
258A GLN* 2.5 27.4 + - - -
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Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 3.1 31.1 + - + +
69A PHE* 4.7 0.9 - - - +
71A HIS* 1.3 105.1 - + + +
73A LEU* 1.3 60.2 + - - +
76A PRO* 3.4 18.9 - - + +
101A SER 3.5 21.8 - - - -
102A VAL 4.1 0.2 - - - -
103A ALA* 3.2 11.8 - - - -
129A SER* 2.7 34.7 + - - -
132A VAL* 3.5 30.5 - - + -
133A GLY* 3.1 16.3 - - - -
136A ALA* 4.5 4.5 - - + -
140A LEU* 3.6 32.7 - - + +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 2.9 51.2 + - + +
70A LEU* 4.2 1.1 - - + +
72A TYR* 1.3 82.5 - - - +
74A ILE* 1.3 78.8 + - + +
75A MET 3.6 0.2 - - - -
76A PRO* 4.0 0.4 - - - +
77A LEU* 3.4 31.0 + - + +
144A TYR* 4.8 4.9 + - - +
406A A6L 4.7 13.5 - - + -
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Residues in contact with ILE 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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70A LEU* 2.9 35.2 + - + +
73A LEU* 1.3 86.1 - - + +
75A MET* 1.3 66.9 + - + +
77A LEU* 3.4 3.2 + - - +
78A THR* 2.8 48.3 + - - +
229A ILE* 4.3 8.1 - - + +
230A GLY* 5.5 0.2 - - - -
233A SER* 3.6 37.5 - - - +
255A VAL* 5.4 1.1 - - + -
406A A6L 3.6 50.3 - - + -
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Residues in contact with MET 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A HIS* 3.0 20.9 + - + +
74A ILE* 1.3 82.8 - - - +
76A PRO* 1.3 63.5 - - - +
78A THR* 5.2 1.3 - - - -
79A ALA 3.1 7.6 + - - -
100A GLY* 3.3 20.7 - - - +
226A HIS* 2.8 68.6 + - + +
230A GLY* 3.6 24.9 - - - -
255A VAL* 3.3 24.2 - - + +
256A GLY* 3.9 21.8 - - - +
258A GLN* 4.0 16.6 - - + +
282A PHE* 4.3 2.7 - - + -
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Residues in contact with PRO 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A HIS 3.4 11.7 - - - +
72A TYR* 3.4 23.8 - - + +
73A LEU 3.9 0.7 - - - +
74A ILE 3.6 0.9 - - - -
75A MET* 1.3 88.2 - - - +
77A LEU* 1.3 66.1 + - - +
79A ALA* 3.3 3.6 + - + +
80A TRP* 3.1 23.4 + - - +
97A VAL* 5.0 2.8 - - - +
100A GLY* 3.3 22.0 - - - +
101A SER* 3.7 13.9 - - - +
140A LEU* 3.9 20.2 - - + -
144A TYR* 3.6 26.3 - - + +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.4 29.3 + - + +
74A ILE 3.4 2.6 + - - +
75A MET 3.4 0.2 - - - -
76A PRO* 1.3 81.4 - - - +
78A THR* 1.3 58.0 + - - +
80A TRP* 3.2 30.7 + - + +
81A ILE* 2.9 45.1 + - + +
144A TYR* 3.9 22.5 + - + +
406A A6L 3.7 30.1 - - + -
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Residues in contact with THR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 2.8 39.5 + - - +
75A MET* 4.5 0.7 - - - -
77A LEU* 1.3 72.5 - - - +
79A ALA* 1.3 59.4 + - - +
81A ILE* 3.4 2.1 + - + +
82A LEU* 2.9 44.8 + - + +
226A HIS* 3.6 24.7 - - + -
229A ILE* 3.9 27.2 - - + +
406A A6L 3.4 25.3 - - + +
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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
----------------------------------------------------------
75A MET 3.1 18.9 + - - +
76A PRO 3.6 4.9 - - - +
78A THR* 1.3 76.7 - - - +
80A TRP* 1.3 55.2 + - - +
82A LEU* 3.3 5.3 + - - +
83A ALA* 2.8 32.4 + - - +
96A MET* 3.2 39.6 - - + +
97A VAL* 3.9 5.8 - - - -
100A GLY* 4.0 2.2 - - - -
226A HIS* 3.5 17.4 + - + +
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Residues in contact with TRP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PRO 3.1 8.7 + - - +
77A LEU* 3.4 27.6 - - + +
79A ALA* 1.3 77.3 - - - +
81A ILE* 1.3 68.2 + - + +
83A ALA* 3.4 4.2 + - + +
84A MET* 3.1 67.0 + - + +
97A VAL* 4.3 8.6 - - + +
144A TYR* 3.4 63.6 + + + +
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 2.9 34.4 + - + +
78A THR* 3.8 4.5 - - - +
80A TRP* 1.3 89.9 - - + +
82A LEU* 1.3 60.3 + - + +
84A MET* 3.3 14.2 + - + +
85A LEU* 2.8 56.6 + - + +
406A A6L 3.6 33.2 - - + -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 2.9 32.9 + - + +
79A ALA 3.8 2.5 - - - +
81A ILE* 1.3 74.1 - - + +
83A ALA* 1.3 63.6 + - - +
85A LEU* 3.2 15.8 + - + +
86A PHE* 3.0 50.8 + - + +
88A MET* 4.9 1.3 - - - -
96A MET* 3.9 12.6 - - + -
222A ALA* 3.5 26.7 - - + +
225A LEU* 4.1 19.1 - - + -
226A HIS* 3.7 26.9 - - + +
229A ILE* 4.9 5.2 - - + -
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ALA 2.8 19.3 + - - +
80A TRP* 3.8 7.0 - - + +
82A LEU* 1.3 77.8 - - - +
84A MET* 1.3 60.5 + - + +
87A ARG 3.2 2.4 + - - -
88A MET* 2.9 47.4 + - - +
93A SER* 3.5 37.5 + - - +
96A MET* 4.2 6.7 - - + +
97A VAL* 5.6 0.9 - - + -
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Residues in contact with MET 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TRP* 3.1 70.6 + - + +
81A ILE* 3.7 16.8 - - + +
83A ALA* 1.3 75.5 - - + +
85A LEU* 1.3 68.8 + - + +
87A ARG* 2.9 20.6 + - - +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 2.8 46.6 + - + +
82A LEU* 3.2 19.7 + - + +
84A MET* 1.3 78.0 - - + +
86A PHE* 1.3 66.1 + - + +
87A ARG* 3.4 15.2 + - - +
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Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.0 44.6 + - + +
85A LEU* 1.3 81.2 - - + +
87A ARG* 1.3 71.7 + - - +
88A MET* 3.3 20.0 + - + +
218A VAL* 3.7 44.0 - - + +
221A ILE* 3.7 34.8 - - + -
222A ALA* 4.0 23.3 - - + -
225A LEU* 4.2 7.0 - - + -
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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