Contacts of the helix formed by residues 58 - 87 (chain A) in PDB entry 4KNF
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 TRP 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 3.9 9.2 - - + -
55A SER* 2.7 15.6 + - - +
57A LYS* 1.3 92.8 - - + +
59A LYS* 1.3 63.5 + - - +
60A THR 3.4 2.0 - - - -
61A SER* 3.1 36.7 + - - -
62A LEU* 3.3 7.8 + - + +
112A ILE* 5.6 5.8 - - + -
181A ALA* 3.7 28.5 - - + -
182A VAL* 4.5 11.9 - - + -
185A ALA* 4.0 21.8 - - + -
239A ILE* 4.5 15.7 - - + -
242A VAL* 3.9 19.5 - - + -
243A ALA* 3.4 32.1 - - + -
246A GLU* 3.6 24.9 + - + +
247A SER* 3.7 20.6 - - - -
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 2.9 45.0 + - + +
52A ASP* 4.1 9.1 + - - +
54A VAL* 2.5 39.8 + - + +
55A SER* 3.3 5.7 + - - +
56A ALA* 4.0 11.2 + - - +
57A LYS 3.9 0.2 - - - -
58A TRP* 1.3 76.2 - - - +
60A THR* 1.3 58.5 + - - +
62A LEU* 2.9 8.7 + - - +
63A THR* 2.9 29.5 + - - -
50E GLU* 4.3 0.2 - - - -
52E ASP* 3.8 24.2 - - - +
53E GLN* 3.1 35.7 - - - +
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Residues in contact with THR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA 5.2 0.8 + - - -
58A TRP 3.4 0.8 - - - -
59A LYS* 1.3 75.7 - - - +
61A SER* 1.3 52.3 + - - +
63A THR* 3.2 2.8 + - - -
64A VAL* 2.8 37.3 + - + +
111A LEU* 4.3 19.7 - - + -
46E PHE* 4.2 14.1 - - + -
50E GLU* 2.8 28.9 + - - +
53E GLN* 4.2 9.1 + - - +
240E TRP* 4.1 26.1 - - + -
244E VAL* 5.8 0.3 - - - +
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS 4.6 2.1 + - - -
58A TRP* 3.1 29.7 + - - -
60A THR* 1.3 78.3 - - - +
62A LEU* 1.3 52.5 + - - +
64A VAL* 3.3 3.5 + - - +
65A SER* 2.8 37.1 + - - -
108A GLU* 3.3 26.2 - - - +
111A LEU* 4.7 11.9 - - - +
239A ILE* 4.1 17.5 - - - -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.6 25.3 - - + +
50A GLU* 3.7 27.8 - - + +
51A ARG* 3.6 18.6 - - + -
54A VAL* 3.7 24.7 - - + -
58A TRP 3.6 12.6 - - - +
59A LYS 2.9 9.4 + - - +
61A SER* 1.3 81.2 - - - +
63A THR* 1.3 56.0 + - - +
65A SER* 3.3 8.0 + - - +
66A GLY* 2.8 31.5 + - - -
239A ILE* 4.5 14.4 - - + -
240A TRP* 4.2 24.0 - - + +
243A ALA* 4.5 8.1 - - + -
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.7 21.1 - - + -
51A ARG* 2.8 21.8 + - - +
59A LYS 2.9 4.7 + - - -
60A THR* 3.2 9.0 - - - -
62A LEU* 1.3 75.4 - - - +
64A VAL* 1.3 57.1 + - - +
66A GLY* 3.2 3.1 + - - -
67A LEU* 2.9 29.7 + - + +
46E PHE* 3.9 32.3 - - + -
49E VAL* 4.3 6.7 - - + -
50E GLU* 2.6 32.0 + - + +
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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
----------------------------------------------------------
60A THR* 2.8 31.7 + - + +
61A SER* 3.8 5.2 - - - +
63A THR* 1.3 70.7 - - - +
65A SER* 1.3 57.0 + - - +
67A LEU* 3.2 9.1 + - + +
68A ILE* 2.9 41.4 + - + +
104A LEU* 3.6 42.8 - - + +
107A VAL* 5.0 12.6 - - + -
108A GLU* 4.1 13.5 - - + +
111A LEU* 5.2 4.3 - - + -
46E PHE* 4.6 13.5 - - + -
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.5 28.2 - - - -
61A SER 2.8 16.9 + - - -
62A LEU* 3.3 9.8 - - - +
64A VAL* 1.3 73.7 - - - +
66A GLY* 1.3 58.5 + - - +
68A ILE* 3.6 9.5 + - - +
69A THR* 2.9 26.7 + - - +
108A GLU* 3.0 23.6 + - - -
232A LYS 6.0 0.4 - - - -
236A GLY* 4.2 15.8 + - - -
239A ILE* 4.9 2.9 - - - +
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 3.7 6.1 - - - +
47A PHE* 3.8 12.7 - - - +
48A PHE* 3.5 22.1 - - - -
62A LEU 2.8 16.7 + - - -
63A THR 3.6 2.9 - - - -
65A SER* 1.3 70.2 - - - +
67A LEU* 1.3 54.5 + - - +
69A THR* 2.9 7.9 + - - -
70A GLY* 2.6 35.2 + - - -
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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
----------------------------------------------------------
48A PHE* 3.5 5.3 - - + -
63A THR* 2.9 18.4 + - + +
64A VAL* 3.2 13.4 + - + +
66A GLY* 1.3 76.1 - - - +
68A ILE* 1.3 52.5 + - - +
70A GLY* 4.7 0.9 - - - -
71A ILE* 2.7 45.1 + - + +
104A LEU* 4.0 22.4 - - + -
42E ALA* 3.4 40.2 - - + +
45E VAL* 3.8 26.0 - - + -
46E PHE* 3.9 30.7 - - + +
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Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 2.9 32.9 + - + +
65A SER* 3.9 6.7 - - - +
67A LEU* 1.3 70.6 - - - +
69A THR* 1.3 57.6 + - - +
72A ALA* 3.0 30.9 + - - +
101A THR* 3.6 20.0 - - + +
104A LEU* 3.7 20.0 - - + -
105A LEU* 3.7 46.4 - - + +
108A GLU* 4.1 3.6 - - - +
232A LYS* 3.5 41.3 - - + +
301A RET 4.6 1.1 - - + -
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Residues in contact with THR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 3.0 33.3 - - + +
43A ALA* 3.9 6.3 - - + -
44A THR* 3.1 25.5 + - - -
47A PHE* 3.5 26.9 - - + -
65A SER 2.9 13.4 + - - +
66A GLY* 2.9 16.6 + - - -
68A ILE* 1.3 76.2 - - + +
70A GLY* 1.3 54.0 + - - +
72A ALA* 3.3 1.9 + - - +
73A PHE* 2.9 28.8 + - - +
232A LYS* 4.2 14.6 - - + +
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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
----------------------------------------------------------
44A THR* 3.0 18.0 + - - -
48A PHE* 5.6 0.4 - - - -
66A GLY 2.6 22.6 + - - -
67A LEU* 3.5 1.6 - - - -
69A THR* 1.3 67.9 - - - +
71A ILE* 1.3 64.0 + - - +
73A PHE* 3.4 14.4 + - - +
74A TRP* 3.2 24.6 - - - -
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Residues in contact with ILE 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 26.5 + - + +
68A ILE 4.2 2.9 - - - +
70A GLY* 1.3 72.1 - - - -
72A ALA* 1.3 61.5 + - - +
74A TRP* 3.5 7.9 + - - +
75A HIS* 2.9 52.9 + - + +
97A ASN* 3.7 7.2 - - - +
100A LEU* 4.0 26.7 - - + +
101A THR* 4.2 7.2 - - + -
104A LEU* 3.8 25.4 - - + -
38E ALA* 4.9 11.0 - - + +
41E LEU* 6.4 2.7 - - + -
42E ALA* 4.1 24.9 - - + -
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 3.7 22.7 - - + -
68A ILE 3.0 19.5 + - - +
69A THR 3.6 4.3 - - - +
70A GLY 3.2 0.2 - - - -
71A ILE* 1.3 77.6 - - - +
73A PHE* 1.4 50.8 + - - +
75A HIS* 3.2 2.4 + - - +
76A TYR* 2.7 45.3 + - + -
97A ASN* 3.4 23.5 + - - +
232A LYS* 3.9 11.9 - - + -
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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
----------------------------------------------------------
37A THR* 3.8 32.5 - - + -
40A MET* 3.9 14.8 - - + +
41A LEU* 3.9 42.8 - - + +
44A THR* 4.8 0.9 - - - +
69A THR 2.9 14.1 + - - +
70A GLY* 3.5 10.3 - - - +
72A ALA* 1.4 74.6 - - - +
74A TRP* 1.3 106.5 + + - +
76A TYR* 3.2 6.0 + - - +
77A LEU* 3.0 39.0 + - + +
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Residues in contact with TRP 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLY* 3.2 27.6 + - - -
71A ILE* 4.0 7.2 - - - +
72A ALA 3.4 0.4 - - - -
73A PHE* 1.3 93.8 - + - +
75A HIS* 1.3 68.4 + - + +
77A LEU* 3.2 43.7 - - + +
78A TYR* 3.2 26.5 + + + -
34E TRP* 6.2 1.8 - - + -
41E LEU* 4.1 27.6 - - + +
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Residues in contact with HIS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 2.9 30.8 + - + -
72A ALA 3.8 0.9 - - - +
74A TRP* 1.3 78.1 - - + +
76A TYR* 1.3 54.3 + - - +
78A TYR* 3.2 5.6 + - - +
79A MET* 2.7 42.7 + - + +
93A PHE* 4.0 19.6 - + + +
96A ILE* 3.5 14.3 - - + +
97A ASN* 3.3 33.0 + - + +
100A LEU* 3.4 24.9 - - + -
34E TRP* 2.8 42.8 + + - -
38E ALA* 4.8 5.6 - - + -
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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
----------------------------------------------------------
33A PHE* 3.5 25.6 - + - -
36A VAL* 3.3 31.6 - - + +
37A THR* 3.5 25.1 + - - +
40A MET* 4.4 5.6 - - + -
72A ALA* 2.7 38.3 + - + +
73A PHE* 3.2 5.6 + - - +
75A HIS* 1.3 70.8 - - - +
77A LEU* 1.3 54.3 + - - +
79A MET* 3.6 13.8 - - + +
80A ARG* 2.8 35.9 + - - +
94A ARG* 3.1 12.2 + - - -
97A ASN* 4.4 4.3 - - - -
225A ASN* 3.3 28.0 + - - -
228A ASP* 2.6 43.8 + - + +
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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
----------------------------------------------------------
37A THR* 4.3 15.4 + - + -
73A PHE* 3.0 33.2 + - + +
74A TRP* 3.2 42.4 + - + +
76A TYR* 1.3 75.8 - - - +
78A TYR* 1.3 61.3 + - + +
80A ARG* 3.4 5.6 + - - +
81A GLY* 2.9 24.3 + - - -
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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 TRP* 3.2 34.0 + + + -
75A HIS* 3.2 6.3 + - - +
77A LEU* 1.3 81.5 - - + +
79A MET* 1.3 66.9 + - - +
81A GLY* 3.0 12.6 + - - -
82A VAL* 3.0 17.8 + - - +
93A PHE* 3.7 37.5 - + + -
34E TRP* 3.5 34.6 - + - -
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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
----------------------------------------------------------
33A PHE* 3.9 10.6 - - + -
75A HIS* 2.7 21.1 + - + +
76A TYR* 3.6 52.9 - - + +
78A TYR* 1.3 73.6 - - - +
80A ARG* 1.3 61.6 + - - +
82A VAL 3.7 0.3 + - - -
83A TRP* 3.3 19.4 + - - +
90A PRO* 3.5 29.4 - - + +
93A PHE* 3.6 20.6 - - + -
94A ARG* 3.5 51.4 - - - +
97A ASN* 4.2 13.2 - - - +
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Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.3 29.5 - - - +
30A GLY* 2.4 40.4 + - - +
33A PHE* 3.4 34.2 - - + -
34A TRP* 3.7 35.2 - - - +
37A THR* 4.8 3.8 - - - +
76A TYR 2.8 21.4 + - - +
77A LEU* 3.8 6.3 - - + +
79A MET* 1.3 70.0 - - - +
81A GLY* 1.3 66.3 + - - +
83A TRP* 3.3 2.1 + - - +
84A ILE* 3.0 50.9 + - + +
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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 LEU 2.9 14.7 + - - -
78A TYR* 3.0 5.9 + - - -
80A ARG* 1.3 76.8 - - - +
82A VAL* 1.3 62.4 + - - -
84A ILE* 3.1 6.8 + - - +
85A ASP* 2.9 32.7 + - - +
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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 TYR 3.0 15.4 + - - +
79A MET 3.8 7.2 - - - +
81A GLY* 1.3 70.2 - - - +
83A TRP* 1.3 58.2 + - - +
85A ASP* 3.2 4.7 + - - -
86A THR* 2.8 47.0 + - + +
88A ASP* 3.6 20.0 - - + +
90A PRO* 3.8 15.0 - - + -
93A PHE* 3.9 14.1 - - + -
21E GLY* 3.5 29.6 - - - +
22E ASP* 3.6 19.7 - - + +
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Residues in contact with TRP 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASP* 2.9 36.1 + - - -
29A VAL* 3.2 36.5 - - + +
30A GLY* 3.9 9.0 - - - -
33A PHE* 3.9 10.8 - + + -
79A MET 3.3 11.2 + - - +
80A ARG 3.7 6.3 - - - +
82A VAL* 1.3 77.9 - - - +
84A ILE* 1.3 70.4 + - + +
87A GLY* 2.8 56.7 + - - +
88A ASP 3.6 15.9 + - - +
89A THR* 4.2 4.5 - - - -
90A PRO* 4.8 2.5 - - + -
217A ALA* 4.3 8.5 - - + -
218A SER* 4.4 18.2 - - - -
221A ASN* 3.7 24.7 - - - -
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASP* 3.7 23.8 - - - +
30A GLY* 4.1 4.0 - - - -
80A ARG* 3.0 57.7 + - + +
81A GLY* 3.6 4.9 - - - +
83A TRP* 1.3 85.9 - - + +
85A ASP* 1.3 74.5 + - - +
87A GLY 5.2 0.2 + - - -
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Residues in contact with ASP 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 20.1 + - - +
82A VAL* 3.9 3.1 - - - +
84A ILE* 1.3 96.1 - - - +
86A THR* 1.3 67.8 + - + +
87A GLY 3.9 0.2 - - - -
21E GLY 6.3 0.4 - - - +
----------------------------------------------------------
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 2.8 21.7 + - + +
85A ASP* 1.3 86.9 - - + +
87A GLY* 1.3 59.2 + - - +
88A ASP* 2.9 41.8 + - - +
21E GLY* 4.6 21.5 - - - +
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Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL 3.6 0.2 + - - -
83A TRP* 2.8 49.1 + - - -
86A THR* 1.3 78.2 + - - +
88A ASP* 1.3 61.1 + - - +
89A THR 3.7 0.5 + - - -
217A ALA* 5.3 2.4 - - - +
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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