Contacts of the helix formed by residues 84 - 110 (chain A) in PDB entry 1ZMD
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 ASN 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ARG* 3.8 13.0 + - - +
83A LEU* 1.3 72.7 - - - +
85A LEU* 1.3 61.8 + - - +
86A ASP* 3.2 12.5 + - - +
87A LYS* 3.0 33.7 + - + +
88A MET* 3.0 17.8 + - - +
75B GLY* 2.9 18.5 + - - +
77B GLU* 2.8 39.8 + - + +
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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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83A LEU* 3.5 21.7 + - + -
84A ASN* 1.3 73.3 - - - +
86A ASP* 1.3 65.2 + - - +
88A MET* 3.8 25.1 - - + +
89A MET* 3.0 34.4 + - + +
174A LEU 3.7 10.5 - - - +
175A LYS 3.3 28.7 - - - +
176A LYS* 3.5 35.4 - - + +
177A VAL* 4.2 4.0 - - + +
197A TRP* 4.1 20.9 - - + -
200A LEU* 4.3 3.4 - - + -
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Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASN* 3.1 9.5 + - - +
85A LEU* 1.3 79.0 - - - +
87A LYS* 1.3 62.3 + - - +
89A MET* 3.3 7.4 + - - +
90A GLU* 3.1 22.5 + - - +
175A LYS* 4.0 20.4 + - - +
176A LYS* 3.6 22.2 + - - -
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Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASN* 3.0 33.4 + - + +
86A ASP* 1.3 76.0 - - - +
88A MET* 1.3 64.1 + - - +
90A GLU* 2.9 41.2 + - - +
91A GLN* 3.1 19.6 + - - +
72B ALA 3.2 11.7 - - - +
73B SER* 3.3 19.6 - - - +
75B GLY* 3.2 23.3 - - - +
77B GLU* 5.4 1.6 - - - +
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Residues in contact with MET 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 4.3 17.3 - - + +
59A ASN* 3.6 41.0 + - + +
60A SER* 4.2 3.4 - - - +
63A TYR* 5.4 1.8 - - - -
83A LEU* 4.1 11.4 - - + -
84A ASN 3.0 14.6 + - - +
85A LEU* 3.8 16.8 - - + +
87A LYS* 1.3 77.4 - - - +
89A MET* 1.3 62.7 + - + +
91A GLN* 3.4 5.6 + - - +
92A LYS* 3.3 18.0 + - - +
200A LEU* 3.2 41.1 - - + -
74B ARG 3.1 24.9 - - - +
75B GLY* 3.8 1.1 - - - -
76B ILE* 5.7 0.9 - - - -
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Residues in contact with MET 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.9 15.0 - - + -
85A LEU* 3.0 33.3 + - + +
86A ASP* 3.7 6.7 - - - +
87A LYS 3.2 0.2 - - - -
88A MET* 1.3 76.7 - - + +
90A GLU* 1.3 58.0 + - - +
92A LYS* 3.3 24.8 - - - +
93A SER* 3.0 31.5 + - - +
172A LEU 3.4 28.0 - - - +
173A SER* 4.3 4.5 - - - +
174A LEU 3.8 13.5 - - - +
197A TRP* 3.6 33.9 - - + -
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP 3.1 13.2 + - - +
87A LYS* 2.9 46.9 + - - +
89A MET* 1.3 75.0 - - - +
91A GLN* 1.3 61.3 + - - +
93A SER* 3.2 7.0 + - - -
94A THR* 2.8 41.4 + - - +
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Residues in contact with GLN 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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55A ALA* 3.7 8.3 - - - +
59A ASN* 2.8 36.0 + - - +
87A LYS 3.1 6.4 + - - +
88A MET 3.6 9.0 - - - +
89A MET 3.4 0.2 - - - -
90A GLU* 1.3 76.7 + - - +
92A LYS* 1.3 67.5 + - - +
94A THR* 3.3 7.7 + - - -
95A ALA* 3.2 22.1 + - - +
73B SER* 3.6 26.2 + - - +
74B ARG* 4.2 12.0 - - + +
395B LYS 4.7 0.6 + - - -
396B THR 3.1 24.2 + - - +
398B ALA* 3.8 21.2 - - + +
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PRO* 3.6 40.0 - - + +
55A ALA* 3.8 12.6 - - + +
56A LEU* 3.9 19.1 - - + -
88A MET 3.3 9.6 + - - +
89A MET* 3.3 28.9 - - - +
90A GLU 3.2 0.6 - - - -
91A GLN* 1.3 86.6 + - - +
93A SER* 1.3 73.3 + - - +
95A ALA* 3.4 5.4 + - - +
96A VAL* 3.2 27.0 + - + +
172A LEU* 2.9 30.7 + - - +
173A SER* 3.1 18.8 + - - -
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A MET* 3.0 18.4 + - - +
90A GLU* 3.6 8.3 - - - -
92A LYS* 1.3 85.5 + - - +
94A THR* 1.3 64.8 + - - +
95A ALA 3.1 2.0 - - - -
96A VAL* 3.3 8.0 + - - +
97A LYS* 2.9 25.5 + - - +
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Residues in contact with THR 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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90A GLU* 2.8 32.8 + - - +
91A GLN* 3.7 8.2 - - - -
93A SER* 1.3 73.3 - - - +
95A ALA* 1.3 58.0 + - - +
97A LYS* 3.9 5.9 - - - +
98A ALA* 3.0 29.8 + - + +
395B LYS* 6.4 1.1 - - - -
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Residues in contact with ALA 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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51A ILE* 4.5 9.9 - - + -
55A ALA* 5.2 0.7 - - + -
91A GLN* 3.2 11.8 + - - +
92A LYS* 3.6 9.9 - - - +
93A SER 3.1 0.6 - - - -
94A THR* 1.3 78.6 - - - +
96A VAL* 1.3 60.6 + - - +
98A ALA* 3.3 5.3 + - - +
99A LEU* 2.9 34.5 + - + +
395B LYS* 4.2 12.1 - - + +
396B THR* 4.1 31.6 - - + +
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Residues in contact with VAL 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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46A LEU* 3.4 26.9 - - - +
47A ASN* 4.1 17.5 - - - +
51A ILE* 3.9 11.2 - - + -
52A PRO* 3.9 26.2 - - + -
92A LYS* 3.2 17.6 + - + +
93A SER* 3.3 9.2 + - - +
95A ALA* 1.3 76.3 - - - +
97A LYS* 1.3 57.5 + - - +
99A LEU* 4.3 1.9 - - - +
100A THR* 2.8 42.5 + - + +
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Residues in contact with LYS 97 (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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93A SER 2.9 17.0 + - - +
94A THR* 3.9 6.1 - - - +
96A VAL* 1.3 74.4 - - - +
98A ALA* 1.3 66.8 + - - +
100A THR* 3.0 17.4 + - - +
101A GLY* 3.0 11.1 + - - -
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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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94A THR* 3.0 21.5 + - + +
95A ALA* 3.7 3.8 - - - +
97A LYS* 1.3 79.6 - - - +
99A LEU* 1.3 57.5 + - - +
101A GLY* 3.3 1.8 + - - -
102A GLY* 2.9 24.9 + - - -
395B LYS* 3.8 28.7 - - - +
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Residues in contact with LEU 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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46A LEU* 3.9 15.6 - - + +
51A ILE* 3.9 39.9 - - + -
95A ALA* 2.9 17.1 + - + +
96A VAL* 4.3 3.1 - - - +
98A ALA* 1.3 76.7 - - - +
100A THR* 1.3 61.9 + - - +
102A GLY* 3.1 11.6 + - - +
103A ILE* 3.2 17.5 + - - +
389B ALA 5.6 1.6 - - - +
390B ALA* 5.3 7.6 - - - +
391B ASN 5.1 1.3 - - - +
392B SER* 4.1 29.8 - - - +
395B LYS* 4.1 25.1 - - + -
396B THR* 4.2 2.2 - - - +
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Residues in contact with THR 100 (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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40A THR* 4.4 15.8 - - + +
41A LEU* 3.4 25.3 + - - +
46A LEU* 3.9 17.7 - - + -
47A ASN* 3.4 28.0 - - - +
96A VAL* 2.8 28.7 + - + +
97A LYS* 3.0 17.2 + - - +
99A LEU* 1.3 71.8 - - - +
101A GLY* 1.3 63.5 + - - +
103A ILE* 3.3 13.5 + - - +
104A ALA* 3.5 9.9 + - - +
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Residues in contact with GLY 101 (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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97A LYS 3.0 15.0 + - - -
98A ALA 3.7 4.0 - - - -
100A THR* 1.3 75.5 + - - +
102A GLY* 1.3 64.2 + - - +
104A ALA* 3.3 10.2 + - - +
105A HIS* 3.2 20.1 + - - +
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Residues in contact with GLY 102 (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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98A ALA 2.9 13.4 + - - -
99A LEU* 3.1 7.5 + - - -
101A GLY* 1.3 77.0 - - - +
103A ILE* 1.3 63.5 + - - +
105A HIS* 3.2 9.3 + - - +
106A LEU* 3.0 31.4 + - - +
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Residues in contact with ILE 103 (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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19A TYR* 3.8 55.6 - - + +
41A LEU* 3.8 20.2 - - + -
42A GLY* 3.7 21.8 - - - +
46A LEU* 3.4 28.3 - - + -
99A LEU 3.2 12.2 + - - +
100A THR* 3.3 6.5 + - - +
101A GLY 3.3 0.4 - - - -
102A GLY* 1.3 77.2 - - - +
104A ALA* 1.3 57.2 + - - +
106A LEU* 3.1 10.5 + - + +
107A PHE* 2.9 35.4 + - + -
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Residues in contact with ALA 104 (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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41A LEU* 3.7 20.3 - - + +
100A THR 3.5 5.3 + - - +
101A GLY* 3.3 14.7 + - - +
102A GLY 3.2 0.6 - - - -
103A ILE* 1.3 77.7 - - - +
105A HIS* 1.3 60.8 + - - +
107A PHE* 3.3 6.0 + - - +
108A LYS* 3.2 27.8 + - + +
114A HIS* 6.0 1.6 - - - +
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Residues in contact with HIS 105 (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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101A GLY 3.2 10.2 + - - +
102A GLY* 3.6 11.4 - - - +
104A ALA* 1.3 77.2 - - - +
106A LEU* 1.3 67.2 + - + +
108A LYS* 3.2 12.5 + - - +
109A GLN* 2.9 52.4 + - + +
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Residues in contact with LEU 106 (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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19A TYR* 4.6 2.0 - - + -
23A ILE* 3.8 19.4 - - + +
102A GLY 3.0 20.3 + - - +
103A ILE* 3.5 14.1 - - + +
105A HIS* 1.3 79.4 - - + +
107A PHE* 1.3 67.3 + - - +
109A GLN* 4.2 15.7 - - - +
110A ASN* 2.8 33.4 + - - +
472B ILE 3.9 8.3 - - - +
473B ASN* 3.6 56.1 - - + +
474B PHE* 3.7 14.1 - - - +
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Residues in contact with PHE 107 (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 SER* 4.8 0.4 - - - -
19A TYR* 3.6 47.3 - - + -
22A ALA* 4.1 5.6 - - + -
23A ILE* 4.0 14.1 - - + -
34A CYS* 3.8 33.4 - - + -
41A LEU* 3.9 30.3 - - + -
103A ILE* 2.9 17.9 + - + +
104A ALA* 3.6 10.1 - - - +
105A HIS 3.2 0.2 - - - -
106A LEU* 1.3 76.8 - - - +
108A LYS* 1.3 64.0 + - + +
110A ASN 3.4 0.3 + - - -
111A LYS 3.1 3.3 + - - -
112A VAL* 2.7 54.7 + - + +
114A HIS* 4.2 17.3 - + + -
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Residues in contact with LYS 108 (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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104A ALA* 3.2 15.1 + - + +
105A HIS* 3.2 14.3 + - + +
107A PHE* 1.3 80.4 - - + +
109A GLN* 1.3 61.8 + - - +
110A ASN 3.3 0.9 + - - -
111A LYS* 3.3 13.1 + - - +
112A VAL 5.0 1.8 - - - +
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Residues in contact with GLN 109 (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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27A GLN* 5.8 1.4 - - - +
105A HIS* 2.9 41.3 + - + +
106A LEU* 3.7 10.4 - - - +
107A PHE 3.4 0.2 - - - -
108A LYS* 1.3 76.3 - - - +
110A ASN* 1.3 73.3 + - - +
111A LYS* 3.8 3.5 + - - +
470B LYS* 6.4 0.4 - - - +
474B PHE* 3.0 34.2 + - - +
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 4.0 19.0 - - + +
26A ALA* 3.1 31.8 - - + +
27A GLN* 3.1 34.4 + - - +
106A LEU* 2.8 35.1 + - - +
107A PHE 4.2 1.3 - - - +
108A LYS 3.2 0.2 - - - -
109A GLN* 1.3 97.2 + - - +
111A LYS* 1.3 68.4 + - - +
112A VAL* 3.3 7.0 - - + -
470B LYS* 4.8 6.2 + - - +
472B ILE 4.8 0.8 + - - -
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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