Contacts of the helix formed by residues 56 - 85 (chain A) in PDB entry 3MRC
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 GLY 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN 3.7 2.4 + - - -
55A GLU* 1.3 73.9 - - - +
57A PRO* 1.3 77.8 - - - +
58A GLU* 3.1 21.7 + - - -
59A TYR* 2.9 18.7 + - - +
60A TRP* 3.3 7.8 - - - -
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Residues in contact with PRO 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY* 1.3 83.6 - - - +
58A GLU* 1.3 68.0 + - - +
59A TYR 3.3 0.2 + - - -
60A TRP* 3.4 9.7 + - + +
61A ASP* 3.1 33.8 + - - +
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 4.8 4.2 - - - +
56A GLY* 3.3 28.0 + - - +
57A PRO* 1.3 84.9 - - - +
59A TYR* 1.3 70.2 + - + +
61A ASP* 3.9 6.4 - - - +
62A GLY* 3.1 20.3 + - - -
170A ARG* 5.7 1.2 + - - -
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 4.3 2.6 + - - -
33A PHE* 3.8 9.0 - - - -
34A VAL* 4.4 4.5 - - + +
52A ILE* 3.6 21.7 - - + +
55A GLU* 3.6 22.9 - - + +
56A GLY 2.9 13.7 + - - +
58A GLU* 1.3 83.8 - - + +
60A TRP* 1.3 95.8 + + - +
62A GLY* 3.2 1.9 + - - -
63A GLU* 2.8 63.4 + - + +
167A TRP* 3.7 29.4 - + + -
171A TYR* 2.7 29.6 + - - -
1P ASN* 4.3 3.8 + - + -
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Residues in contact with TRP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.9 12.8 - - + -
44A ARG* 3.7 12.8 - - - +
45A MET* 3.4 30.0 - - + +
46A GLU 3.8 6.1 - - - -
47A PRO* 3.5 49.8 - - + -
52A ILE* 3.5 37.7 + - + -
53A GLU* 4.6 4.4 - - - +
55A GLU 3.3 19.4 + - - -
56A GLY 3.3 24.4 + - - -
57A PRO* 3.4 8.2 + - + +
59A TYR* 1.3 87.8 - + - +
61A ASP* 1.3 55.6 + - - +
63A GLU* 4.2 1.2 - - + +
64A THR* 2.6 37.8 + - - -
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 2.3 42.8 + - - +
57A PRO* 3.1 22.9 + - - +
58A GLU* 3.9 7.5 - - - +
60A TRP* 1.3 76.6 - - - +
62A GLY* 1.3 61.6 + - - +
64A THR* 3.4 2.4 + - - -
65A ARG* 3.1 35.5 + - - +
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Residues in contact with GLY 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU 3.1 16.2 + - - -
59A TYR* 3.7 2.0 - - - -
61A ASP* 1.3 76.0 - - - +
63A GLU* 1.3 63.3 + - - +
65A ARG* 3.4 22.7 + - - +
66A LYS* 3.2 35.0 + - - +
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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
----------------------------------------------------------
7A TYR* 4.0 3.6 + - - -
45A MET* 4.2 24.5 - - + +
59A TYR* 2.8 50.7 + - + +
60A TRP* 4.2 2.7 - - - +
62A GLY* 1.3 76.1 - - - +
64A THR* 1.3 57.0 + - - +
66A LYS* 2.7 29.7 + - - +
67A VAL* 2.9 31.5 + - - +
1P ASN* 3.5 17.3 + - - +
2P LEU* 2.8 38.6 + - - +
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 4.8 1.6 - - + -
43A GLN 3.4 26.7 - - - +
44A ARG* 3.7 28.8 - - - +
45A MET* 3.0 20.4 + - - +
60A TRP 2.6 23.8 + - - -
61A ASP 3.8 3.4 - - - -
62A GLY 3.3 0.2 - - - -
63A GLU* 1.3 74.1 - - - +
65A ARG* 1.3 65.5 + - - +
67A VAL* 3.5 6.8 - - - +
68A LYS* 3.0 39.5 + - + +
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 3.1 23.4 + - - +
62A GLY* 3.7 20.7 + - - +
63A GLU 3.4 0.2 - - - -
64A THR* 1.3 76.7 - - - +
66A LYS* 1.3 67.5 + - + +
68A LYS* 3.9 6.0 - - - +
69A ALA* 3.1 23.8 + - + +
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLY* 3.2 20.4 + - - +
63A GLU* 2.7 32.6 + - - -
65A ARG* 1.3 81.5 - - + +
67A VAL* 1.3 57.2 + - - +
69A ALA* 3.2 6.9 + - - +
70A HIS* 2.9 28.4 + - - +
1P ASN* 2.8 26.3 + - - +
2P LEU* 2.8 30.6 + - + +
3P VAL 4.7 4.7 - - - +
4P PRO* 4.2 28.5 - - + -
5P MET 5.5 2.9 + - - -
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 4.5 5.2 - - + -
22A PHE* 3.5 16.2 - - + -
24A ALA* 3.8 29.4 - - + -
36A PHE* 3.5 35.0 - - + -
45A MET* 3.8 16.6 - - + -
63A GLU 2.9 17.1 + - - +
64A THR* 3.5 13.7 - - - +
66A LYS* 1.3 75.1 - - - +
68A LYS* 1.3 64.6 + - - +
70A HIS* 3.4 4.4 + - - +
71A SER 3.0 22.0 + - - -
2P LEU* 3.7 12.8 - - + -
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 4.1 17.9 - - + -
43A GLN* 3.2 52.8 + - - +
44A ARG* 5.5 2.4 - - - +
64A THR* 3.0 27.5 + - + +
65A ARG* 3.9 5.8 - - - +
67A VAL* 1.3 79.5 - - - +
69A ALA* 1.3 60.7 + - - +
71A SER* 2.6 26.2 + - - +
72A GLN* 3.2 11.4 + - - +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 3.1 18.5 + - + +
66A LYS* 3.2 7.8 + - - +
68A LYS* 1.3 73.9 - - - +
70A HIS* 1.3 59.8 + - - +
72A GLN* 3.3 9.9 + - - +
73A THR* 3.0 30.4 + - - -
5P MET 4.7 6.5 - - - +
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Residues in contact with HIS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.4 49.3 - + + -
22A PHE* 4.3 4.5 - + + -
66A LYS 2.9 17.0 + - - +
67A VAL* 3.4 10.5 - - - +
69A ALA* 1.3 73.0 - - - +
71A SER* 1.3 65.7 + - - +
73A THR* 3.1 7.9 + - - -
74A HIS* 3.0 39.2 + + - +
97A ARG* 3.0 32.1 + - - -
99A TYR* 4.5 3.2 + - - -
2P LEU* 5.1 2.8 - - - +
3P VAL 5.0 2.4 + - - -
5P MET* 3.6 34.5 + - + +
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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
----------------------------------------------------------
11A SER* 4.9 0.5 + - - -
20A PRO* 5.8 0.3 - - - +
22A PHE* 3.4 46.1 - - - +
36A PHE* 5.4 3.0 - - - -
38A SER* 6.0 0.9 - - - -
67A VAL 3.0 8.9 + - - -
68A LYS* 2.6 25.3 + - - +
70A HIS* 1.3 75.9 - - - +
72A GLN* 1.3 65.6 + - - +
74A HIS* 3.4 4.0 + - - +
75A ARG* 3.0 26.9 + - - +
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Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 3.6 25.4 + - - +
68A LYS 3.2 12.8 + - - +
69A ALA* 3.6 9.9 - - - +
70A HIS 3.2 0.2 - - - -
71A SER* 1.3 80.7 + - - +
73A THR* 1.3 67.7 + - - +
75A ARG* 3.0 44.0 + - - +
76A VAL* 2.9 28.3 + - - +
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA 3.0 11.8 + - - -
70A HIS* 3.1 10.3 + - - -
72A GLN* 1.3 76.1 - - - +
74A HIS* 1.3 56.8 + - - +
76A VAL* 3.2 5.9 + - - +
77A ASP* 2.9 35.1 + - - +
97A ARG* 3.8 19.3 - - - +
5P MET* 2.5 28.5 + - + +
6P CYS* 4.0 7.8 + - - -
7P ALA 3.6 24.5 - - - +
8P THR* 4.1 14.9 - - + +
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Residues in contact with HIS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.6 21.8 + - + +
11A SER* 3.0 37.0 - - - +
22A PHE* 4.1 11.2 - + - -
70A HIS* 3.0 20.4 + - - +
71A SER* 3.6 8.1 - - - +
72A GLN 3.3 0.2 - - - -
73A THR* 1.3 72.7 - - - +
75A ARG* 1.3 60.2 + - - +
77A ASP* 3.2 8.7 + - - +
78A LEU* 2.9 35.1 + - - +
95A VAL* 3.7 17.4 - - + +
96A GLN 4.9 0.2 - - - -
97A ARG* 2.9 55.1 + - + +
116A TYR* 4.6 6.1 - + - -
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 4.5 11.7 - - + +
20A PRO* 3.6 38.0 - - + +
71A SER 3.0 14.1 + - - +
72A GLN* 3.0 41.5 + - - +
74A HIS* 1.3 72.0 - - - +
76A VAL* 1.3 95.9 + - - +
78A LEU* 3.4 11.8 + - - +
79A GLY* 3.4 8.3 + - - -
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLN 2.9 19.9 + - - +
73A THR* 3.5 7.6 - - - +
75A ARG* 1.3 102.6 - - - +
77A ASP* 1.3 64.5 + - - +
79A GLY* 3.1 4.3 + - - -
80A THR* 2.9 32.6 + - - +
8P THR* 3.7 29.8 - - + +
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR* 2.9 19.6 + - - +
74A HIS* 3.2 13.2 + - - +
76A VAL* 1.3 77.7 - - - +
78A LEU* 1.3 56.8 + - - +
80A THR* 3.1 2.1 + - - -
81A LEU* 2.8 37.4 + - + +
95A VAL* 4.6 2.0 - - + -
97A ARG* 3.7 12.6 + - - -
116A TYR* 2.9 38.9 + - - +
7P ALA 4.9 0.3 - - - +
8P THR* 3.3 11.2 - - - -
9P VAL* 2.8 37.0 + - + +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 3.9 15.7 - - - -
13A SER* 4.0 19.3 - - - +
20A PRO* 3.6 36.6 - - + -
74A HIS 2.9 18.6 + - - +
75A ARG 3.8 4.3 - - - +
76A VAL 3.3 0.2 - - - -
77A ASP* 1.3 76.2 - - - +
79A GLY* 1.3 61.2 + - - +
81A LEU* 4.1 2.3 - - - +
82A ARG* 3.1 27.2 + - - +
93A HIS* 3.5 40.3 - - + +
95A VAL* 3.8 24.9 - - + +
118A TYR* 4.2 4.6 + - + -
----------------------------------------------------------
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Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG 3.4 6.7 + - - -
76A VAL 3.1 7.1 + - - -
78A LEU* 1.3 76.5 - - - +
80A THR* 1.3 63.8 + - - +
82A ARG* 3.5 27.2 + - - +
83A GLY* 3.4 14.7 + - - -
----------------------------------------------------------
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Residues in contact with THR 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 2.9 25.1 + - - +
77A ASP* 3.6 6.2 - - - -
79A GLY* 1.3 76.0 - - - +
81A LEU* 1.3 58.2 + - - +
83A GLY* 3.1 5.2 + - - -
84A TYR* 2.9 63.1 + - + +
9P VAL* 3.6 22.5 + - + +
----------------------------------------------------------
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP 2.8 21.6 + - - +
78A LEU 4.1 0.9 - - - +
80A THR* 1.3 68.7 - - - +
82A ARG* 1.3 67.6 + - - +
84A TYR* 3.9 11.2 - - + +
85A TYR* 2.9 37.9 + - + +
95A VAL* 3.5 22.2 - - + -
116A TYR* 3.5 31.0 - - + +
118A TYR* 3.5 28.9 - - + -
123A TYR* 3.7 39.7 - - + +
9P VAL* 3.9 8.5 - - + -
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.1 17.5 + - - +
79A GLY* 3.6 26.5 + - - +
81A LEU* 1.3 75.9 - - - +
83A GLY* 1.3 56.6 + - - +
85A TYR 3.7 0.2 - - - -
86A ASN* 3.0 7.4 + - - -
87A GLN* 2.8 63.2 + - + +
88A SER 3.6 22.4 - - - +
89A GLU* 3.1 45.7 + - - +
93A HIS* 5.1 7.0 - - + -
118A TYR* 3.9 3.6 + - - +
----------------------------------------------------------
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLY 3.4 5.5 + - - -
80A THR* 3.1 7.8 + - - -
82A ARG* 1.3 76.6 - - - +
84A TYR* 1.3 65.6 + - - +
86A ASN* 3.0 22.7 + - - +
----------------------------------------------------------
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A THR* 2.9 40.9 + - + +
81A LEU* 3.2 19.5 + - + +
83A GLY* 1.3 73.8 - - - +
85A TYR* 1.3 68.0 + - + +
86A ASN* 3.3 6.5 + - - +
123A TYR* 3.4 27.1 - - - -
139A ALA* 4.1 23.5 - - + +
142A THR* 3.4 26.3 - - + +
143A THR* 3.9 2.0 - - - -
146A LYS* 5.5 1.9 + - - +
9P VAL* 3.0 24.6 + - - -
----------------------------------------------------------
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Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 2.9 40.1 + - + +
84A TYR* 1.3 78.6 - - + +
86A ASN* 1.3 70.8 + - - +
87A GLN* 3.2 32.4 + - - +
118A TYR* 3.6 30.4 - + - +
121A LYS* 6.0 4.3 - - - -
122A ASP 5.6 0.3 + - - -
123A TYR* 3.3 15.6 - + - -
137A ASP* 2.5 37.3 + - - -
139A ALA* 3.7 17.3 - - + -
----------------------------------------------------------
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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