Contacts of the helix formed by residues 76 - 101 (chain A) in PDB entry 4M83
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 THR 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A SER* 1.3 84.7 - - - +
77A LEU* 1.3 59.4 + - - +
78A LEU* 3.7 2.6 + - - +
79A ASP* 2.7 39.2 + - - +
80A ASN* 2.8 35.2 + - - -
157A ARG* 4.2 5.7 + - - +
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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
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76A THR* 1.3 72.6 - - - +
78A LEU* 1.3 63.0 + - - +
80A ASN* 3.1 13.4 + - + +
81A VAL* 3.1 30.7 + - + +
148A MET* 3.6 56.1 - - + +
149A TRP* 3.7 41.5 - - + -
152A PRO* 4.0 13.7 - - + -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A THR* 3.3 2.9 + - - +
77A LEU* 1.3 78.9 - - - +
79A ASP* 1.3 57.7 + - - +
81A VAL* 4.1 2.0 - - + -
82A GLU* 3.0 43.8 + - + +
149A TRP* 3.5 29.2 - - + -
152A PRO* 3.7 28.9 - - + +
155A THR* 4.4 2.0 - - - +
157A ARG* 3.5 36.1 - - - +
158A GLY* 3.9 18.6 - - - +
161A TYR* 3.7 30.3 - - + -
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TRP 3.5 8.1 - - - +
74A GLY* 4.1 13.2 - - - -
75A SER 4.9 0.9 + - - -
76A THR* 2.7 41.0 + - - +
78A LEU* 1.3 77.0 - - - +
80A ASN* 1.3 58.8 + - - +
82A GLU* 4.5 1.6 - - - +
83A PRO* 3.1 25.5 - - - +
157A ARG* 2.6 32.1 + - - +
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Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TRP 3.2 10.6 - - - +
74A GLY 3.1 26.0 - - - +
75A SER* 5.0 2.2 - - - +
76A THR 2.8 24.5 + - - +
77A LEU* 3.1 12.3 + - + +
79A ASP* 1.3 79.3 - - - +
81A VAL* 1.3 61.3 + - + +
83A PRO* 3.6 5.2 - - - +
84A PHE* 3.2 27.4 - - - -
1400A ERY 3.5 46.6 - - + +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 3.1 30.8 + - + +
78A LEU* 3.9 5.8 - - + +
80A ASN* 1.3 77.1 - - + +
82A GLU* 1.3 69.8 + - - +
83A PRO 3.2 2.5 - - - -
84A PHE* 3.0 24.8 + - - +
85A LEU* 3.7 3.3 + - - +
114A TYR* 4.9 3.2 + - - +
148A MET* 6.3 0.2 - - + -
149A TRP* 3.8 21.8 - - + -
161A TYR* 3.5 34.0 + - + +
1400A ERY 3.7 30.1 - - + +
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Residues in contact with GLU 82 (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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78A LEU* 3.0 26.1 + - + +
79A ASP* 4.5 1.1 - - - +
81A VAL* 1.3 79.4 - - - +
83A PRO* 1.3 66.3 - - + +
85A LEU* 3.2 6.1 + - - +
86A ASN* 3.1 31.0 + - - +
157A ARG* 2.8 51.7 + - - +
161A TYR* 3.9 32.7 - - + +
164A ARG* 5.0 10.3 + - - +
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Residues in contact with PRO 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A THR* 4.7 1.0 + - - -
63A LEU* 3.6 20.8 - - + +
64A PRO* 5.7 3.4 - - + -
73A TRP* 5.2 7.6 - - + +
79A ASP* 3.1 27.4 - - - +
80A ASN 3.6 5.8 - - - +
81A VAL 3.4 3.8 - - - -
82A GLU* 1.3 94.6 - - + +
84A PHE* 1.3 57.3 - - + +
86A ASN* 4.0 6.6 - - + +
87A ASP* 2.9 31.5 + - - +
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Residues in contact with PHE 84 (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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14A ILE* 4.1 5.8 - - + -
63A LEU* 4.2 13.0 - - + -
73A TRP* 3.8 35.0 - + - -
80A ASN 3.2 27.8 - - - -
81A VAL* 3.0 10.6 + - - +
83A PRO* 1.3 78.0 - - + +
85A LEU* 1.3 60.6 + - - +
87A ASP* 4.1 2.6 - - - +
88A ALA* 3.1 26.3 + - - +
112A THR* 3.7 46.9 - - + +
114A TYR* 3.6 24.2 - - + +
1400A ERY 3.8 44.9 - - + -
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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
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81A VAL 3.7 2.6 + - - +
82A GLU 3.2 7.7 + - - +
84A PHE* 1.3 77.2 - - - +
86A ASN* 1.3 66.9 + - - +
88A ALA* 3.0 2.8 + - - +
89A ILE* 3.0 43.7 + - + +
114A TYR* 3.8 10.8 - - + -
161A TYR* 3.8 30.7 - - + +
164A ARG* 4.0 21.3 - - + +
165A PHE* 3.9 40.4 - - + +
168A TRP* 3.7 33.4 - - + -
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Residues in contact with ASN 86 (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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62A THR* 4.4 4.7 + - - +
82A GLU* 3.1 20.6 + - - +
83A PRO* 4.0 6.4 - - + +
85A LEU* 1.3 81.7 - - - +
87A ASP* 1.3 62.4 + - - +
89A ILE* 3.5 15.6 + - - +
90A GLN* 3.5 14.2 + - - +
164A ARG* 3.8 22.3 + - - +
143B GLU* 4.6 14.0 - - - +
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 4.6 2.1 - - - +
59A TYR* 4.6 9.9 + - - -
61A SER* 3.2 16.5 + - - -
62A THR* 3.1 29.4 + - - +
63A LEU* 3.3 21.9 - - + +
83A PRO 2.9 18.7 + - - +
84A PHE* 4.1 3.6 - - - +
86A ASN* 1.3 74.2 - - - +
88A ALA* 1.3 60.7 + - - +
90A GLN* 2.6 35.9 + - - -
91A ALA* 2.8 29.9 + - - +
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Residues in contact with ALA 88 (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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84A PHE 3.1 19.8 + - - +
85A LEU 3.0 5.9 + - - +
87A ASP* 1.3 76.9 - - - +
89A ILE* 1.3 58.7 + - - +
91A ALA* 4.3 0.2 - - - -
92A LEU* 2.9 34.8 + - - +
114A TYR* 3.6 30.5 - - + -
115A PRO* 3.7 15.8 - - + +
168A TRP* 3.7 14.6 - - + -
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Residues in contact with ILE 89 (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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85A LEU* 3.0 41.7 + - + +
86A ASN* 3.9 11.0 - - - +
87A ASP 3.2 0.6 - - - -
88A ALA* 1.3 77.0 - - - +
90A GLN* 1.3 56.3 + - - +
92A LEU* 4.4 1.2 - - - +
93A PRO* 3.2 21.7 - - - +
164A ARG* 5.5 3.1 - - + +
168A TRP* 3.5 45.2 + - + +
143B GLU* 3.8 50.3 - - + +
144B VAL* 6.2 0.7 - - + -
199B HIS* 5.9 2.7 - - + -
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Residues in contact with GLN 90 (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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60A HIS* 2.9 30.7 + - - +
62A THR* 3.6 25.5 - - + +
86A ASN 3.5 9.9 + - - +
87A ASP* 2.6 36.4 + - - +
89A ILE* 1.3 78.0 - - - +
91A ALA* 1.3 67.5 + - - +
93A PRO* 3.6 13.3 - - - +
94A GLN* 3.0 36.0 + - - +
143B GLU 5.3 1.1 - - - +
147B PRO* 3.7 35.2 - - + +
150B ARG* 4.6 4.2 + - - -
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Residues in contact with ALA 91 (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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59A TYR* 3.6 31.9 - - + -
87A ASP* 2.8 19.8 + - - +
88A ALA* 3.9 2.5 - - - +
90A GLN* 1.3 83.9 - - - +
92A LEU* 1.3 65.6 + - - +
94A GLN* 3.0 21.7 + - - +
95A LEU* 3.1 15.0 + - + +
115A PRO* 3.9 14.8 - - + -
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Residues in contact with LEU 92 (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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88A ALA 2.9 17.5 + - - +
89A ILE 4.4 0.9 - - - +
91A ALA* 1.3 75.1 - - - +
93A PRO* 1.3 65.5 - - + +
95A LEU* 3.1 2.5 + - - -
96A ALA* 2.8 27.4 + - + +
115A PRO* 4.0 14.8 - - + +
118A VAL* 3.8 18.4 - - + -
119A LEU* 3.6 35.0 - - + -
122A ARG* 3.9 11.2 - - - +
168A TRP* 3.7 26.2 - - + +
172A ASN* 3.7 26.0 - - - +
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Residues in contact with PRO 93 (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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89A ILE 3.2 20.4 - - - +
90A GLN* 3.6 10.3 - - - +
91A ALA 3.5 2.7 - - - -
92A LEU* 1.3 95.2 - - + +
94A GLN* 1.3 61.4 + - + +
96A ALA* 4.1 7.0 - - + +
97A ASP* 3.3 29.7 + - - +
147B PRO* 6.2 1.8 - - + -
148B MET* 6.5 1.6 - - + -
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Residues in contact with GLN 94 (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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58A LEU 4.7 1.1 - - - +
59A TYR* 3.5 13.1 - - + -
60A HIS 2.8 35.9 + - - +
90A GLN* 3.0 40.4 + - - +
91A ALA* 3.0 11.3 + - - +
93A PRO* 1.3 79.5 - - + +
95A LEU* 1.3 60.5 + - - +
97A ASP* 3.4 7.5 - - - +
98A ALA* 3.2 23.9 + - - +
150B ARG* 3.3 22.5 + - - +
151B GLU* 4.1 5.6 - - - +
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Residues in contact with LEU 95 (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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12A PHE* 3.9 22.9 - - + -
40A ALA* 3.7 24.7 - - + -
57A VAL* 4.7 13.5 - - + +
58A LEU 5.6 0.2 - - - -
59A TYR* 3.7 38.8 - - + -
91A ALA* 3.1 10.3 + - + +
92A LEU 3.1 4.7 + - - +
94A GLN* 1.3 75.2 - - - +
96A ALA* 1.3 65.8 + - - +
97A ASP 3.1 1.8 - - - -
98A ALA* 3.0 13.4 + - + +
99A TYR* 3.1 20.8 + - + +
113A SER* 5.4 1.1 - - - +
115A PRO* 3.9 25.1 - - + -
119A LEU* 3.7 16.9 - - + +
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Residues in contact with ALA 96 (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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92A LEU 2.8 17.0 + - - +
93A PRO* 4.4 7.0 - - + +
95A LEU* 1.3 75.6 - - - +
97A ASP* 1.3 63.8 + - - +
99A TYR* 3.6 1.0 + - - +
100A ALA* 3.3 22.3 + - - +
119A LEU* 3.7 16.2 - - + +
122A ARG* 3.2 31.4 - - - +
123A TRP* 5.1 3.4 + - - +
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PRO* 3.3 15.1 + - - +
94A GLN* 3.4 11.9 + - - +
95A LEU 3.1 0.4 - - - -
96A ALA* 1.3 80.3 - - - +
98A ALA* 1.3 62.5 + - - +
99A TYR 3.2 1.0 + - - -
100A ALA* 3.4 17.4 + - - +
101A ASP* 4.3 2.9 + - - +
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Residues in contact with ALA 98 (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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55A ARG* 5.6 3.6 + - - -
57A VAL* 3.7 30.4 - - + +
94A GLN 3.2 11.1 + - - +
95A LEU* 3.0 13.5 + - + +
97A ASP* 1.3 80.6 - - - +
99A TYR* 1.3 64.6 + - + +
100A ALA 3.9 0.3 + - - -
101A ASP* 4.4 5.7 + - - +
102A ASP* 5.0 5.7 - - - +
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Residues in contact with TYR 99 (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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8A HIS* 3.5 12.1 - - - -
10A ALA* 3.2 18.3 - - + +
11A MET 4.5 0.2 + - - -
12A PHE* 3.6 24.2 - + - -
38A THR* 2.6 36.5 + - + -
39A TYR 4.3 0.7 + - - -
40A ALA* 4.4 8.3 + - + -
55A ARG* 5.8 2.7 - - - -
57A VAL* 3.7 26.3 - - + +
95A LEU* 3.1 21.8 + - + +
96A ALA 4.1 0.4 - - - +
98A ALA* 1.3 81.0 - - + +
100A ALA* 1.3 64.2 + - - +
101A ASP 3.4 2.2 - - - -
102A ASP* 3.0 30.7 - - + -
103A ILE* 3.1 9.7 + - - +
104A PRO* 3.4 16.8 - - + -
123A TRP* 3.4 35.9 - + + -
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA 3.3 13.8 + - - +
97A ASP* 3.4 14.9 + - - +
99A TYR* 1.3 78.8 - - - +
101A ASP* 1.3 63.2 + - - +
102A ASP 3.1 4.5 + - - -
103A ILE* 4.1 14.1 - - - +
123A TRP* 6.2 0.4 - - - +
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP 4.3 4.0 + - - +
98A ALA 4.4 5.2 + - - +
99A TYR* 3.4 1.0 - - - +
100A ALA* 1.3 80.8 - - - +
102A ASP* 1.3 64.2 + - - +
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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