Contacts of the helix formed by residues 61 - 96 (chain A) in PDB entry 2LOR
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 GLN 61 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 4.4 20.7 - - + +
53A GLN* 3.4 45.6 + - + +
54A ARG* 4.2 25.7 + - - +
56A PHE* 5.4 1.7 + - - +
58A TYR 3.8 9.1 + - - -
59A PRO 2.7 27.6 + - - +
60A LEU* 1.3 76.3 - - - +
62A TRP* 1.3 54.6 + - - +
63A SER* 4.0 2.2 - - - +
64A LEU* 2.7 30.9 + - + +
65A LEU* 2.5 37.6 + - - +
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Residues in contact with TRP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLN* 5.3 8.1 - - - -
53A GLN* 3.1 33.0 + - - +
56A PHE* 6.0 6.7 - - + -
60A LEU 4.0 1.4 + - - -
61A GLN* 1.3 71.1 - - - +
63A SER* 1.3 59.5 + - - +
65A LEU* 4.2 13.9 - - + -
66A VAL* 2.8 47.2 + - + +
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 5.1 18.0 + - - -
49A GLN* 3.3 34.8 + - - +
50A MET* 5.3 2.5 - - - -
53A GLN* 4.1 19.0 - - - +
61A GLN* 2.9 3.9 - - - +
62A TRP* 1.3 81.7 - - - +
64A LEU* 1.3 52.0 + - - +
66A VAL* 3.2 11.2 - - - +
67A ALA* 2.7 39.0 + - - +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO 5.4 0.2 - - - +
60A LEU* 3.3 31.6 - - + -
61A GLN* 2.7 38.4 + - + +
63A SER* 1.3 73.9 - - - +
65A LEU* 1.3 52.2 + - - +
67A ALA* 3.6 6.5 - - + -
68A VAL* 2.6 56.6 + - + +
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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
----------------------------------------------------------
58A TYR* 5.7 10.3 - - + -
60A LEU* 4.4 30.5 - - + +
61A GLN 2.5 17.9 + - - +
62A TRP* 3.8 15.7 - - + +
64A LEU* 1.3 74.6 - - - +
66A VAL* 1.3 58.1 + - - +
68A VAL* 3.6 5.2 - - + +
69A VAL* 2.8 51.8 + - + +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 6.4 0.4 - - + -
62A TRP* 2.8 34.2 + - + +
63A SER* 3.2 20.4 - - - +
65A LEU* 1.3 78.2 - - - +
67A ALA* 1.3 57.4 + - + +
69A VAL* 4.5 4.3 - - + +
70A ALA* 2.6 48.3 + - + +
----------------------------------------------------------
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.9 29.8 - - + -
63A SER 2.7 21.7 + - - +
64A LEU* 3.8 9.4 - - + +
66A VAL* 1.3 79.8 - - + +
68A VAL* 1.3 58.0 + - + +
70A ALA* 4.6 2.0 - - - -
71A GLY* 2.7 29.9 + - - +
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 5.6 4.7 - - + -
64A LEU* 2.6 46.0 + - + +
65A LEU* 3.6 6.1 - - + +
67A ALA* 1.3 77.4 - - - +
69A VAL* 1.3 62.5 + - + +
71A GLY* 3.5 0.4 - - - -
72A SER* 2.7 38.4 + - - -
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 2.8 39.4 + - + +
66A VAL* 4.3 4.9 - - + +
68A VAL* 1.3 78.1 - - + +
70A ALA* 1.3 59.9 + - + +
72A SER* 3.2 5.1 + - - -
73A VAL* 3.0 41.6 + - + +
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 2.6 33.4 + - + +
67A ALA* 4.6 1.8 - - - -
69A VAL* 1.3 77.3 - - + +
71A GLY* 1.3 50.6 + - - +
73A VAL* 4.6 3.4 - - - +
74A VAL* 2.6 51.9 + - + +
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ALA 2.7 25.6 + - - -
68A VAL* 3.5 0.7 - - - -
69A VAL 3.2 0.2 - - - -
70A ALA* 1.3 78.5 - - - +
72A SER* 1.3 50.3 + - - +
74A VAL* 4.3 3.3 - - - +
75A SER* 2.4 44.4 + - - -
----------------------------------------------------------
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Residues in contact with SER 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 2.7 22.3 + - - -
69A VAL* 3.2 6.5 + - - -
71A GLY* 1.3 71.9 - - - +
73A VAL* 1.3 63.1 + - - +
75A SER* 3.1 7.0 + - - -
76A TYR* 2.9 48.1 + - - -
----------------------------------------------------------
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 3.0 25.6 + - + +
70A ALA* 4.2 4.7 - - - +
72A SER* 1.3 76.3 - - - +
74A VAL* 1.3 66.8 + - + +
76A TYR* 3.0 12.8 + - + +
77A GLY* 3.0 19.8 + - - -
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 2.6 40.3 + - + +
71A GLY* 4.3 2.9 - - - +
73A VAL* 1.3 76.1 - - + +
75A SER* 1.3 53.3 + - - +
77A GLY* 4.5 1.3 - - - +
78A VAL* 2.8 46.9 + - + +
----------------------------------------------------------
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLY 2.4 26.8 + - - -
72A SER* 3.2 9.0 - - - -
74A VAL* 1.3 77.8 - - - +
76A TYR* 1.3 57.4 + - - +
78A VAL* 3.2 8.7 - - - +
79A THR* 2.8 36.3 + - - -
----------------------------------------------------------
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Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 2.9 37.1 + - - -
73A VAL* 3.2 11.4 - - + +
75A SER* 1.3 75.5 - - - +
77A GLY* 1.3 54.8 - - - +
79A THR* 3.0 11.7 + - + +
80A ARG* 2.8 46.7 + - + +
----------------------------------------------------------
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL 3.0 9.8 + - - -
74A VAL* 3.9 1.8 - - - -
76A TYR* 1.3 79.3 - - - +
78A VAL* 1.3 62.7 + - - +
80A ARG* 3.0 19.6 + - - +
81A VAL* 3.0 16.6 + - - +
----------------------------------------------------------
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A MET* 6.2 3.8 - - + -
74A VAL* 2.8 28.1 + - + +
75A SER* 3.2 17.7 - - - +
77A GLY* 1.3 72.3 - - - -
79A THR* 1.3 58.7 + - - +
81A VAL* 3.1 10.3 - - + +
82A GLU* 2.6 61.0 + - + +
----------------------------------------------------------
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A SER* 2.8 23.0 + - - -
76A TYR* 3.2 13.9 - - + +
78A VAL* 1.3 80.8 - - - +
80A ARG* 1.3 54.1 + - + +
82A GLU* 4.2 4.9 - - - -
83A SER* 2.5 52.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 2.8 23.3 + - + +
77A GLY* 3.0 12.3 + - - +
79A THR* 1.3 80.3 - - + +
81A VAL* 1.3 57.2 + - - +
83A SER* 3.8 3.8 - - - -
84A GLU* 2.9 30.3 + - - +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLY 3.0 14.3 + - - +
78A VAL* 3.1 26.9 - - + +
80A ARG* 1.3 77.2 - - - +
82A GLU* 1.3 62.9 + - + +
84A GLU* 4.0 5.9 - - - +
85A LYS* 3.0 48.1 + - + +
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 5.8 5.7 - - - -
32A MET* 4.6 26.5 - - + +
78A VAL* 2.6 50.9 + - + +
79A THR* 4.1 4.5 - - - +
81A VAL* 1.3 76.5 - - + +
83A SER* 1.3 52.0 - - - +
85A LYS* 4.7 3.3 - - - +
86A CYS* 2.6 44.2 + - - +
----------------------------------------------------------
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 2.5 34.9 + - - +
80A ARG* 3.8 5.2 - - - -
82A GLU* 1.3 76.4 - - - +
84A GLU* 1.3 56.4 + - - +
86A CYS* 3.7 4.3 - - - +
87A ASN* 2.7 35.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG 2.9 19.5 + - - +
81A VAL* 4.0 6.2 - - - +
83A SER* 1.3 78.9 - - - +
85A LYS* 1.3 58.8 + - - +
87A ASN* 3.4 8.8 + - + +
88A ASN* 3.0 48.0 + - - +
----------------------------------------------------------
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Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 3.0 32.2 + - + +
82A GLU* 4.3 4.7 - - - +
84A GLU* 1.3 76.9 + - - +
86A CYS* 1.3 55.3 + - - +
87A ASN 3.0 2.0 - - - -
88A ASN* 3.1 12.0 + - + +
89A LEU* 2.7 55.0 + - + +
----------------------------------------------------------
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Residues in contact with CYS 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 6.1 1.3 - - - -
28A SER* 4.1 25.4 - - - -
82A GLU* 2.6 29.2 + - + +
83A SER* 4.0 4.3 - - - +
85A LYS* 1.3 74.3 - - - +
87A ASN* 1.3 56.7 + - - +
89A LEU* 3.5 9.2 + - - +
90A TRP* 2.8 39.0 + - - +
----------------------------------------------------------
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Residues in contact with ASN 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 5.5 4.9 - - - +
83A SER 2.7 21.7 + - - +
84A GLU* 3.4 10.2 + - - +
86A CYS* 1.3 76.7 - - - +
88A ASN* 1.3 66.4 + - - +
90A TRP* 2.9 11.2 + - - +
91A LEU* 2.9 37.1 + - - +
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Residues in contact with ASN 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 3.0 39.3 + - - +
85A LYS* 3.5 11.4 - - + +
87A ASN* 1.3 82.6 + - - +
89A LEU* 1.3 54.2 + - + +
91A LEU* 3.4 9.6 + - - +
92A PHE* 2.7 52.5 + - + -
----------------------------------------------------------
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 6.2 6.7 - - - -
85A LYS* 2.7 40.7 + - + +
86A CYS* 3.7 9.0 - - - +
88A ASN* 1.3 78.8 - - + +
90A TRP* 1.3 56.5 + - - +
92A PHE* 3.4 11.7 - - + +
93A LEU* 2.8 60.3 + - + +
100A LYS* 5.9 10.8 - - + -
----------------------------------------------------------
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Residues in contact with TRP 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 4.0 30.1 + - - -
14A ALA* 4.2 16.2 - - + +
15A ALA* 5.7 0.9 - - - -
21A GLY* 3.9 37.9 - - - -
24A ALA* 5.1 9.1 - - + +
25A ALA* 4.1 19.3 - - + -
86A CYS* 2.8 30.3 + - - +
87A ASN* 2.9 13.2 + - - +
89A LEU* 1.3 78.0 - - - +
91A LEU* 1.3 58.4 + - - +
93A LEU* 3.5 5.1 + - - +
94A GLU* 2.8 51.5 + - + +
----------------------------------------------------------
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 5.4 9.0 - - + -
7A SER* 4.7 15.3 - - - +
87A ASN* 2.9 23.6 + - - +
88A ASN* 3.7 10.5 - - - +
90A TRP* 1.3 78.6 - - - +
92A PHE* 1.3 60.6 + - + +
94A GLU* 3.0 10.1 + - + +
95A THR* 2.9 39.7 + - - +
----------------------------------------------------------
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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 ASN* 2.7 43.8 + - + +
89A LEU* 3.4 15.9 - - + +
91A LEU* 1.3 79.1 - - + +
93A LEU* 1.3 55.6 + - + +
95A THR* 3.1 7.5 + - + -
96A GLY 2.9 8.0 + - - -
97A GLN* 2.8 73.4 + - + +
----------------------------------------------------------
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.8 24.8 - - + +
23A TYR* 5.1 8.3 - - + -
24A ALA* 3.8 47.1 - - + +
27A GLN* 5.1 13.7 - - + +
89A LEU* 2.8 45.1 + - + +
90A TRP 3.9 1.6 - - - +
92A PHE* 1.3 72.8 - - + +
94A GLU* 1.3 61.2 - - - +
95A THR 3.0 2.0 - - - -
96A GLY* 3.2 13.8 + - - +
97A GLN 4.7 2.5 - - - +
----------------------------------------------------------
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP* 4.4 28.0 - - - +
11A ASP* 4.4 6.6 - - - +
14A ALA* 4.2 16.1 - - - +
20A LEU* 5.1 21.1 - - + +
21A GLY* 5.3 2.5 + - - -
90A TRP* 2.8 41.7 + - + +
91A LEU* 3.4 10.7 - - + +
93A LEU* 1.3 78.0 - - - +
95A THR* 1.3 60.0 + - - +
96A GLY 3.4 0.2 - - - -
----------------------------------------------------------
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 2.9 23.4 + - - +
92A PHE* 3.5 6.7 - - + +
93A LEU 3.0 0.4 - - - -
94A GLU* 1.3 80.1 + - - +
96A GLY* 1.3 56.7 + - - +
97A GLN* 4.0 16.8 - - + +
----------------------------------------------------------
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 6.0 1.8 - - - -
92A PHE 2.9 3.2 + - - -
93A LEU* 3.2 12.5 + - - -
94A GLU 3.4 0.2 - - - -
95A THR* 1.3 81.4 - - - +
97A GLN* 1.3 71.3 + - - +
----------------------------------------------------------
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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