Contacts of the helix formed by residues 84 - 110 (chain G) in PDB entry 1ZMC
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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G ARG 3.9 0.8 + - - -
83G LEU* 1.3 73.1 - - - +
85G LEU* 1.3 61.2 + - - +
86G ASP* 3.2 10.4 + - - +
87G LYS* 2.9 38.5 + - + +
88G MET* 3.1 17.8 + - - +
75H GLY* 2.9 18.6 + - - +
77H GLU* 2.6 39.5 + - - +
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Residues in contact with LEU 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G LEU* 6.3 0.2 - - + -
83G LEU* 3.5 25.3 + - + -
84G ASN* 1.3 73.1 + - - +
86G ASP* 1.3 64.8 + - - +
88G MET* 3.4 6.9 + - + -
89G MET* 2.9 36.0 + - + +
174G LEU 3.4 18.2 - - - +
175G LYS* 3.3 29.4 - - - +
176G LYS* 3.7 15.3 - - - +
177G VAL* 4.3 2.7 - - + +
197G TRP* 4.0 23.8 - - + -
200G LEU* 4.4 13.0 - - + -
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Residues in contact with ASP 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G ASN* 3.2 7.2 + - - +
85G LEU* 1.3 84.4 - - - +
87G LYS* 1.3 59.0 + - - +
89G MET* 3.2 7.2 + - - +
90G GLU* 2.9 27.6 + - - +
175G LYS* 4.6 8.7 - - - +
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Residues in contact with LYS 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G ASN* 2.9 30.1 + - - +
86G ASP* 1.3 76.0 - - - +
88G MET* 1.3 64.8 + - - +
90G GLU* 2.7 45.5 + - - +
91G GLN 3.0 18.9 + - - -
72H ALA 3.4 20.2 - - - +
73H SER* 3.7 33.4 - - - +
75H GLY* 3.9 3.6 - - - +
77H GLU* 5.3 2.5 - - - +
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Residues in contact with MET 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G LEU* 4.1 14.2 - - + +
59G ASN* 3.4 47.3 + - + +
60G SER* 4.1 3.4 - - - +
63G TYR* 4.3 7.0 - - + -
83G LEU* 4.0 23.1 - - + -
84G ASN 3.1 16.1 + - - +
85G LEU* 3.8 9.9 - - + +
86G ASP 3.3 0.2 - - - -
87G LYS* 1.3 77.1 - - - +
89G MET* 1.3 61.9 + - - +
90G GLU 3.4 0.5 + - - -
91G GLN* 3.4 4.9 + - - +
92G LYS* 3.4 15.6 + - - +
200G LEU* 4.1 21.8 - - + -
74H ARG* 3.0 35.6 + - - +
75H GLY 4.7 0.2 - - - +
76H ILE* 4.2 11.9 - - + -
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Residues in contact with MET 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G LEU* 4.1 17.0 - - + -
85G LEU* 2.9 32.5 + - + +
86G ASP* 3.6 7.0 - - - +
88G MET* 1.3 74.2 - - - +
90G GLU* 1.3 56.6 + - - +
91G GLN 3.4 0.2 - - - -
92G LYS* 3.3 22.7 + - - +
93G SER* 2.7 37.7 + - - +
172G LEU 3.3 27.4 - - - +
173G SER* 3.9 6.5 - - - +
174G LEU 3.8 14.1 - - - +
197G TRP* 3.7 35.0 - - + -
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Residues in contact with GLU 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G ASP 2.9 13.6 + - - +
87G LYS* 2.7 52.0 + - - +
89G MET* 1.3 75.1 - - - +
91G GLN* 1.3 60.7 + - - +
93G SER* 3.2 6.5 + - - -
94G THR* 2.8 46.8 + - - +
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Residues in contact with GLN 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G ALA* 3.9 6.6 - - - +
59G ASN* 2.7 28.9 + - - +
87G LYS 3.0 6.2 + - - +
88G MET 3.7 7.9 - - - +
89G MET 3.4 0.2 - - - -
90G GLU* 1.3 77.1 - - - +
92G LYS* 1.3 67.0 + - - +
94G THR* 3.9 6.9 - - - +
95G ALA* 3.1 23.0 + - - +
73H SER* 3.5 26.4 + - - +
74H ARG* 3.9 21.9 - - + +
396H THR 3.2 24.0 + - - +
398H ALA* 3.8 21.7 - - + +
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Residues in contact with LYS 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G PRO* 3.6 39.6 - - + +
55G ALA* 4.0 13.1 - - + +
56G LEU* 4.1 20.4 - - + -
88G MET 3.4 8.5 + - - +
89G MET* 3.3 20.4 + - - +
90G GLU 3.1 0.8 - - - -
91G GLN* 1.3 86.3 + - - +
93G SER* 1.3 80.1 + - - +
95G ALA* 3.2 4.2 + - - +
96G VAL* 3.1 24.1 + - + +
172G LEU* 2.9 29.8 + - + +
173G SER* 3.1 17.0 + - - -
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Residues in contact with SER 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G MET* 2.7 18.9 + - - +
90G GLU* 3.2 6.9 + - - -
92G LYS* 1.3 88.1 + - - +
94G THR* 1.3 60.6 - - - +
96G VAL* 3.4 5.6 + - - +
97G LYS* 2.9 30.8 + - - +
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Residues in contact with THR 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G GLU* 2.8 32.5 + - - +
91G GLN* 3.9 6.3 - - - +
93G SER* 1.3 75.7 - - - +
95G ALA* 1.3 64.8 + - - +
97G LYS* 4.0 7.0 - - - +
98G ALA* 3.2 23.9 + - + +
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Residues in contact with ALA 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ILE* 5.1 1.8 - - + -
55G ALA* 5.3 0.2 - - + -
91G GLN* 3.1 23.3 + - - +
92G LYS* 3.5 6.5 - - - +
93G SER 3.2 0.2 - - - -
94G THR* 1.3 76.7 - - - +
96G VAL* 1.3 65.7 + - + +
98G ALA* 3.3 6.1 + - - +
99G LEU* 3.1 29.2 + - + +
395H LYS* 3.8 26.9 - - + +
396H THR* 4.2 17.7 - - + +
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Residues in contact with VAL 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G LEU* 3.3 32.5 - - - +
47G ASN* 4.3 13.5 - - - +
51G ILE* 3.8 15.5 - - + -
52G PRO* 4.0 20.9 - - + -
92G LYS* 3.1 17.2 + - + +
93G SER* 3.8 7.4 - - - +
95G ALA* 1.3 73.1 - - - +
97G LYS* 1.3 66.4 + - - +
99G LEU* 3.3 1.7 + - - +
100G THR* 2.9 40.4 + - + +
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Residues in contact with LYS 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G SER 2.9 18.7 + - - +
94G THR* 4.0 7.2 - - - +
95G ALA 3.3 0.2 - - - -
96G VAL* 1.3 78.4 - - - +
98G ALA* 1.3 65.4 + - - +
100G THR* 3.0 10.9 + - - +
101G GLY* 3.0 20.4 + - - -
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Residues in contact with ALA 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G THR* 3.2 17.5 + - + +
95G ALA 3.7 4.5 - - - +
96G VAL 3.3 0.2 - - - -
97G LYS* 1.3 80.9 - - - +
99G LEU* 1.3 57.8 + - - +
101G GLY* 3.3 3.4 + - - -
102G GLY* 2.9 23.4 + - - -
395H LYS* 3.8 27.4 - - - +
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Residues in contact with LEU 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G LEU* 3.5 21.7 - - + +
51G ILE* 3.8 31.0 - - + -
95G ALA 3.1 14.5 + - - +
96G VAL 3.3 0.2 + - - -
98G ALA* 1.3 73.4 - - - +
100G THR* 1.3 65.4 + - - +
101G GLY 3.1 1.1 - - - -
102G GLY* 3.3 10.4 + - - +
103G ILE* 3.3 19.2 + - - +
389H ALA 5.4 4.0 - - - +
390H ALA* 5.2 5.8 - - - +
391H ASN 4.9 2.7 - - - +
392H SER* 4.3 27.6 - - - +
395H LYS* 3.9 33.4 - - + -
396H THR* 4.4 1.6 - - - +
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Residues in contact with THR 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G THR* 4.1 19.8 - - + +
41G LEU* 3.9 15.1 + - - +
46G LEU* 3.6 21.1 - - + -
47G ASN* 3.5 24.7 - - - +
96G VAL* 2.9 25.7 + - + +
97G LYS* 3.0 19.5 + - - +
99G LEU* 1.3 72.1 - - - +
101G GLY* 1.3 67.1 + - - +
103G ILE* 3.3 11.9 + - - +
104G ALA* 3.4 12.0 + - - +
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Residues in contact with GLY 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G LYS 3.0 14.8 + - - -
98G ALA* 3.6 4.5 - - - -
100G THR* 1.3 79.2 + - - +
102G GLY* 1.3 61.8 + - - +
104G ALA* 3.1 17.1 + - - +
105G HIS* 3.2 23.0 + - - -
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Residues in contact with GLY 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G ALA 2.9 14.4 + - - -
99G LEU* 3.3 6.9 + - - -
100G THR 3.3 0.6 - - - -
101G GLY* 1.3 75.7 - - - +
103G ILE* 1.3 54.6 + - - +
105G HIS* 3.3 7.8 + - - +
106G LEU* 2.9 39.8 + - - +
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Residues in contact with ILE 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G TYR* 3.8 51.6 - - + +
41G LEU* 3.8 23.3 - - + -
42G GLY* 3.7 19.7 - - - +
46G LEU* 3.5 28.3 - - + -
99G LEU 3.3 10.4 + - - +
100G THR 3.8 5.8 - - - +
101G GLY 3.2 0.6 - - - -
102G GLY* 1.3 72.8 - - - +
104G ALA* 1.3 67.5 + - - +
106G LEU* 3.2 8.9 + - + +
107G PHE* 2.9 31.9 + - + +
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Residues in contact with ALA 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G LEU* 3.8 18.5 - - + +
100G THR 3.4 8.2 + - - +
101G GLY* 3.1 12.6 + - - +
103G ILE* 1.3 78.3 - - - +
105G HIS* 1.3 66.5 - - + +
107G PHE* 3.3 5.6 + - - +
108G LYS* 3.1 28.8 + - - +
114G HIS* 6.0 1.8 - - - +
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Residues in contact with HIS 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G GLY* 3.2 20.9 + - - +
102G GLY* 3.6 10.3 - - - +
103G ILE 3.1 0.6 - - - -
104G ALA* 1.3 80.3 - - + +
106G LEU* 1.3 61.2 + - + +
108G LYS* 3.1 12.7 + - + +
109G GLN* 2.9 30.8 + - - +
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Residues in contact with LEU 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G TYR* 4.8 2.0 - - + -
23G ILE* 3.9 17.7 - - + -
102G GLY* 2.9 26.3 + - - +
103G ILE* 3.7 8.7 - - + +
105G HIS* 1.3 75.1 - - + +
107G PHE* 1.3 65.1 + - - +
109G GLN* 3.2 20.3 + - - +
110G ASN* 3.0 32.9 + - - +
472H ILE 3.9 8.5 - - - +
473H ASN* 3.7 36.8 - - - +
474H PHE* 3.7 29.4 - - - +
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Residues in contact with PHE 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G SER* 4.5 1.3 - - - -
19G TYR* 3.8 38.1 - - + -
22G ALA* 4.1 7.9 - - + -
23G ILE* 4.1 8.3 - - + -
34G CYS* 3.8 35.7 - - + -
41G LEU* 3.7 33.0 - - + -
103G ILE* 2.9 21.3 + - + +
104G ALA* 3.4 10.3 - - - +
105G HIS 3.2 0.2 - - - -
106G LEU* 1.3 76.7 - - - +
108G LYS* 1.3 62.8 + - + +
110G ASN 3.4 0.5 + - - -
111G LYS 3.1 3.6 + - - -
112G VAL* 2.8 56.4 + - + +
114G HIS* 4.1 17.7 - + + -
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Residues in contact with LYS 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G ALA* 3.1 15.4 + - - +
105G HIS* 3.1 15.5 + - + +
107G PHE* 1.3 79.4 - - + +
109G GLN* 1.3 62.9 + - - +
110G ASN 3.3 0.9 + - - -
111G LYS* 3.3 12.7 + - - +
112G VAL 4.9 2.9 - - - +
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Residues in contact with GLN 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G GLN* 6.1 0.2 - - - +
105G HIS* 2.9 17.4 + - - +
106G LEU* 3.5 17.8 - - - +
108G LYS* 1.3 75.7 - - - +
110G ASN* 1.3 71.8 + - - +
111G LYS* 3.7 6.9 + - - +
474H PHE* 3.1 32.8 + - - +
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Residues in contact with ASN 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G ILE* 3.9 20.0 - - + +
26G ALA* 3.1 32.7 - - + +
27G GLN* 3.3 31.0 + - - +
106G LEU* 3.0 34.7 + - - +
107G PHE 4.3 1.3 - - - +
108G LYS 3.2 0.2 - - - -
109G GLN* 1.3 95.5 + - - +
111G LYS* 1.3 76.8 + - - +
112G VAL* 3.3 7.4 - - + -
470H LYS* 4.6 7.6 + - - +
472H ILE 4.9 0.6 + - - -
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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