Contacts of the helix formed by residues 62 - 91 (chain A) in PDB entry 4IKV
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 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLY 3.9 0.4 + - - -
61A LEU* 1.3 78.0 - - - +
63A GLU* 1.3 73.6 + - - +
64A HIS* 3.1 20.7 + - - +
65A LEU* 2.8 35.3 + - + +
66A ALA* 3.1 19.9 + - - +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 3.6 36.8 - - + -
61A LEU 3.8 0.8 + - - -
62A ASP* 1.3 76.3 + - - +
64A HIS* 1.3 62.3 + - + +
66A ALA* 3.3 1.6 + - - +
67A LEU* 2.9 39.2 + - + +
318A ASN* 2.9 30.2 + - - +
322A LYS* 3.6 22.4 + - - +
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Residues in contact with HIS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP* 3.1 17.8 + - - +
63A GLU* 1.3 82.3 - - + +
65A LEU* 1.3 57.6 + - - +
67A LEU* 3.3 7.2 + - + -
68A ALA* 2.9 28.2 + - - +
455A VAL* 3.3 35.9 + - + +
456A ARG* 3.6 30.6 - - + +
458A TYR 2.6 28.4 + - - -
459A THR* 3.6 14.5 - - + +
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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
----------------------------------------------------------
61A LEU* 4.2 28.7 - - + -
62A ASP* 2.8 28.0 + - + +
63A GLU 3.4 0.2 - - - -
64A HIS* 1.3 68.2 - - - +
66A ALA* 1.3 66.4 + - - +
68A ALA* 3.3 3.6 + - - +
69A ILE* 2.9 42.0 + - + +
256A VAL* 4.0 27.6 - - + -
257A GLU* 4.2 17.9 - - + +
260A ILE* 4.1 14.8 - - + -
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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
----------------------------------------------------------
47A VAL* 4.2 3.4 - - + +
50A MET* 3.3 45.9 - - + +
51A TYR* 3.9 21.8 - - + +
61A LEU* 4.8 2.4 - - + +
62A ASP 3.1 14.8 + - - +
63A GLU 3.7 7.0 - - - +
65A LEU* 1.3 77.2 - - - +
67A LEU* 1.3 57.9 + - - +
69A ILE* 3.3 1.1 + - - -
70A MET* 3.0 26.7 + - - +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 4.0 17.7 - - + -
51A TYR* 5.4 0.7 - - + -
63A GLU* 2.9 27.7 + - + +
64A HIS* 3.6 8.3 - - + +
66A ALA* 1.3 77.2 - - - +
68A ALA* 1.3 52.6 + - - +
70A MET* 3.5 5.1 + - - +
71A SER* 2.7 37.7 + - - -
314A THR* 3.3 40.6 - - - +
315A ILE* 4.0 17.9 - - + +
318A ASN* 4.0 27.4 - - + +
455A VAL* 3.7 18.2 - - + -
458A TYR* 4.4 9.4 - - + -
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A HIS 2.9 17.4 + - - +
65A LEU* 3.7 6.5 - - + +
67A LEU* 1.3 75.0 - - - +
69A ILE* 1.3 64.1 + - - +
71A SER* 3.2 6.1 + - - -
72A ILE* 3.1 22.0 + - - +
260A ILE* 3.9 24.7 - - + -
452A ALA* 3.7 22.9 - - - +
455A VAL* 3.9 10.5 - - + +
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 5.8 0.4 - - + -
50A MET* 3.8 24.9 - - + -
61A LEU* 4.3 10.8 - - + -
65A LEU* 2.9 44.1 + - + +
66A ALA 3.7 4.0 - - - +
68A ALA* 1.3 73.2 - - - +
70A MET* 1.3 66.2 + - - +
71A SER 3.3 0.2 + - - -
72A ILE* 3.3 20.9 + - + +
73A TYR* 3.4 13.1 + - + +
121A LEU* 4.5 7.2 - - + -
125A MET* 3.5 33.0 - - + +
256A VAL* 4.4 19.1 - - + -
260A ILE* 4.4 3.1 - - + -
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Residues in contact with MET 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 3.5 63.8 + - - +
46A LEU* 4.0 17.0 - - - -
47A VAL* 3.5 34.3 - - + -
50A MET* 3.5 20.9 - - + -
66A ALA 3.0 9.5 + - - +
67A LEU* 3.6 9.6 - - - +
69A ILE* 1.3 75.9 - - - +
71A SER* 1.3 64.3 + - - +
73A TYR* 3.3 20.6 + - - +
74A GLY 4.5 0.3 + - - -
313A SER* 3.5 22.4 - - - +
314A THR* 3.8 12.3 - - + -
448A GLN* 5.2 0.3 - - - +
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU 2.7 22.9 + - - -
68A ALA 3.3 9.9 - - - -
69A ILE 3.1 0.4 - - - -
70A MET* 1.3 78.4 - - - +
72A ILE* 1.3 61.6 + - - +
73A TYR 3.3 0.7 + - - -
314A THR* 3.7 19.0 + - - +
448A GLN* 3.5 32.1 - - - +
451A ASN* 4.1 9.6 - - - +
452A ALA* 3.5 25.4 + - - -
455A VAL* 3.9 11.4 - - - +
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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
----------------------------------------------------------
68A ALA 3.1 6.7 + - - +
69A ILE* 3.4 16.6 - - + +
71A SER* 1.3 74.6 - - - +
73A TYR* 1.3 67.1 - - - +
74A GLY 3.3 0.7 - - - -
75A ALA* 3.0 10.1 + - - +
76A LEU* 3.0 32.9 + - + +
125A MET* 5.1 4.5 - - + -
256A VAL* 6.0 1.1 - - + -
259A PHE* 3.8 34.3 - - + -
260A ILE* 4.1 21.1 - - + +
263A VAL* 3.8 30.3 - - + -
448A GLN 4.5 2.7 - - - +
452A ALA* 3.5 25.4 - - + -
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Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 4.2 8.7 - + - -
42A MET* 3.5 19.3 - - + +
43A ARG* 3.7 14.8 - - + +
46A LEU* 3.7 31.2 - - + -
69A ILE* 3.4 10.7 + - + +
70A MET* 3.3 17.7 + - - +
71A SER 3.2 1.2 - - - -
72A ILE* 1.3 77.2 - - - +
74A GLY* 1.3 62.4 + - - +
76A LEU* 3.1 10.1 + - - +
77A VAL* 3.1 29.4 + - + +
124A SER* 4.8 0.7 + - - -
125A MET* 3.7 35.8 + - + +
128A ILE* 3.3 38.8 - - + +
129A VAL* 3.9 21.8 - - + -
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Residues in contact with GLY 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 4.5 7.9 - - - -
43A ARG* 4.4 3.6 - - - +
71A SER 4.0 0.6 + - - -
72A ILE 3.3 0.8 - - - -
73A TYR* 1.3 75.6 - - - +
75A ALA* 1.3 64.5 + - - +
77A VAL* 3.4 11.4 + - - +
78A TYR* 3.1 21.1 + - - +
445A ALA* 5.0 0.2 - - - +
448A GLN* 3.1 31.3 + - - -
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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
----------------------------------------------------------
72A ILE 3.0 11.4 + - - +
74A GLY* 1.3 77.4 - - - +
76A LEU* 1.3 61.7 + - - +
78A TYR* 3.3 5.5 + - - +
79A MET* 3.2 31.7 + - + +
263A VAL* 4.4 10.1 - - + -
445A ALA* 3.5 33.4 - - + +
448A GLN* 3.8 6.9 + - + -
449A ALA* 4.1 20.0 - - + +
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.0 41.4 + - + +
73A TYR* 3.1 6.7 + - - +
75A ALA* 1.3 73.9 - - - +
77A VAL* 1.3 66.0 + - - +
79A MET* 3.3 23.3 + - + +
80A SER* 2.9 24.4 + - - -
125A MET* 4.4 17.3 - - + -
129A VAL* 3.7 24.8 - - + +
259A PHE* 3.8 29.4 - - + -
263A VAL* 4.4 9.0 - - + -
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 4.5 11.9 - - + +
73A TYR* 3.1 34.1 + - + +
74A GLY* 3.6 11.7 - - - +
75A ALA 3.3 0.2 - - - -
76A LEU* 1.3 76.6 - - - +
78A TYR* 1.3 58.5 + - - +
80A SER* 3.3 7.6 + - - -
81A GLY* 2.9 26.5 + - - -
128A ILE 5.5 0.2 - - - -
129A VAL* 4.4 13.7 - - + -
132A THR* 3.8 33.2 - - + -
133A GLY* 4.5 1.2 - - - -
136A LYS* 4.3 22.4 - - + +
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Residues in contact with TYR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLY 3.1 10.9 + - - +
75A ALA 3.3 7.4 - - - +
77A VAL* 1.3 78.0 - - - +
79A MET* 1.3 75.2 + - + +
81A GLY* 3.1 11.0 + - - -
82A ILE* 3.2 42.1 + - + +
270A ILE* 6.2 0.4 - - + -
438A SER* 2.8 34.0 + - - -
441A PHE* 3.7 26.0 - + + -
442A LEU* 3.4 32.6 - - + +
445A ALA* 3.4 27.4 - - + -
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Residues in contact with MET 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 3.2 21.0 + - + +
76A LEU* 3.3 22.4 + - + +
78A TYR* 1.3 87.9 - - + +
80A SER* 1.3 64.1 + - - +
82A ILE* 3.2 21.9 + - - +
83A ILE* 3.4 12.7 + - - +
263A VAL* 4.7 21.3 - - + +
266A LEU* 4.6 30.5 - - + -
267A GLY* 5.8 0.4 - - - +
270A ILE* 5.1 10.1 - - + -
445A ALA* 6.5 0.4 - - + -
449A ALA* 5.9 1.3 - - + -
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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 LEU 2.9 17.1 + - - -
77A VAL 3.5 4.9 - - - -
79A MET* 1.3 75.8 - - - +
81A GLY* 1.3 50.9 + - - +
83A ILE* 3.1 10.5 + - - +
84A GLY* 2.8 31.5 + - - -
129A VAL* 2.7 39.8 + - - -
130A LEU* 3.7 11.9 + - - +
133A GLY* 3.3 9.5 - - - -
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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
----------------------------------------------------------
77A VAL 2.9 15.2 + - - -
78A TYR* 3.1 4.6 + - - -
80A SER* 1.3 73.3 - - - +
82A ILE* 1.3 61.7 + - - +
85A GLY* 2.9 25.3 + - - -
133A GLY* 3.6 17.5 - - - -
137A PRO* 3.5 18.6 - - - +
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Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 3.2 45.6 + - + +
79A MET* 3.4 10.8 - - - +
80A SER 3.2 0.4 - - - -
81A GLY* 1.3 80.0 - - - +
83A ILE* 1.3 67.4 + - + +
85A GLY* 3.6 1.0 + - - -
86A TRP* 3.3 19.8 + - + +
438A SER* 3.4 28.5 - - - +
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A MET 3.6 14.1 - - - +
80A SER* 3.1 9.8 + - - +
82A ILE* 1.3 83.6 - - + +
84A GLY* 1.3 55.4 + - - +
86A TRP* 3.3 12.1 + - + +
87A LEU* 2.9 45.6 + - + +
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Residues in contact with GLY 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER 2.8 14.8 + - - -
83A ILE* 1.3 71.5 - - - +
85A GLY* 1.3 58.2 + - - +
87A LEU* 3.5 2.9 + - - +
88A ALA 3.0 23.2 + - - -
133A GLY 3.2 23.3 - - - -
134A LEU* 4.1 16.8 - - - +
138A ASN* 3.1 17.2 + - - -
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Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLY 2.9 16.7 + - - -
82A ILE 4.0 1.1 - - - -
83A ILE 3.4 0.2 - - - -
84A GLY* 1.3 74.5 - - - +
86A TRP* 1.3 56.8 + - - +
88A ALA* 3.5 2.3 + - - +
89A ASP* 3.0 29.7 + - - +
137A PRO* 4.1 7.7 - - - +
138A ASN* 3.8 14.2 - - - +
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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 ILE 3.3 12.0 + - - +
83A ILE* 3.3 13.4 + - + +
85A GLY* 1.3 73.3 - - - +
87A LEU* 1.3 85.6 + - + +
89A ASP* 3.3 3.9 + - - -
90A ARG* 2.9 64.8 + - + +
91A VAL* 4.0 9.9 - - + -
222A LEU* 4.1 17.3 - - + -
230A ALA* 4.0 26.5 - - + -
234A MET* 6.5 0.7 - - - -
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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 ILE* 2.9 39.4 + - + +
84A GLY* 3.7 5.4 - - - +
85A GLY 3.4 0.2 - - - -
86A TRP* 1.3 92.6 - - + +
88A ALA* 1.3 61.4 + - - +
91A VAL* 2.9 26.5 + - + +
92A PHE* 2.8 41.3 + - + -
134A LEU* 3.7 28.5 - - + -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY 3.0 6.6 + - - +
85A GLY 3.8 1.1 - - - +
87A LEU* 1.3 76.8 - - - +
89A ASP* 1.3 64.9 + - - +
90A ARG 3.3 0.3 + - - -
91A VAL 3.9 0.2 + - - -
92A PHE* 3.8 3.4 + - - +
93A GLY* 2.7 50.8 + - - +
94A THR* 4.1 7.2 - - + -
97A ALA* 3.9 3.6 - - + +
138A ASN* 3.3 40.4 - - - +
218A VAL* 4.4 0.2 - - - +
219A PRO* 3.9 3.0 - - - +
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Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLY 3.0 18.8 + - - +
86A TRP* 3.8 5.6 - - + +
88A ALA* 1.3 78.7 - - - +
90A ARG* 1.3 64.4 + - + +
94A THR* 6.1 0.7 - - - -
218A VAL* 3.6 0.9 - - - +
219A PRO* 3.4 27.1 - - - +
220A ASN* 3.0 54.3 + - - +
----------------------------------------------------------
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TRP* 2.9 55.0 + - + +
89A ASP* 1.3 87.4 - - + +
91A VAL* 1.3 64.0 + - + +
218A VAL* 3.5 12.7 - - - +
220A ASN* 2.9 48.4 + - - +
221A PRO 3.6 9.1 + - - -
222A LEU* 3.3 45.7 + - + +
226A GLU* 3.3 26.9 + - - +
----------------------------------------------------------
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TRP* 4.0 25.8 - - + -
87A LEU* 2.9 23.0 + - + +
90A ARG* 1.3 84.9 - - - +
92A PHE* 1.3 86.5 + - + +
93A GLY 3.8 0.4 - - - -
218A VAL* 3.5 17.1 - - - +
222A LEU* 4.2 11.4 - - + -
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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