Contacts of the helix formed by residues 84 - 110 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A GLY* 2.8 22.8 + - - -
77A GLU* 2.5 38.9 + - - +
82B ARG 3.6 2.0 + - - -
83B LEU* 1.3 71.4 - - - +
85B LEU* 1.3 65.7 + - - +
86B ASP* 3.0 24.0 + - - +
87B LYS* 3.1 34.5 + - - +
88B MET* 3.1 9.5 + - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 6.2 0.4 - - + -
83B LEU* 3.1 22.2 + - + +
84B ASN* 1.3 72.6 - - - +
86B ASP* 1.3 63.0 + - - +
88B MET* 3.3 10.1 + - + +
89B MET* 3.0 38.2 + - + +
174B LEU 3.8 13.0 - - - +
175B LYS 3.5 24.7 - - - +
176B LYS* 3.9 1.3 - - - -
177B VAL* 3.8 26.2 - - + +
197B TRP* 4.0 22.7 - - + -
200B LEU* 4.2 14.6 - - + -
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Residues in contact with ASP 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASN* 3.0 13.3 + - - +
85B LEU* 1.3 79.4 - - - +
87B LYS* 1.3 57.3 + - - +
89B MET* 3.5 6.5 + - - +
90B GLU* 3.1 23.0 + - - +
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Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ALA 3.1 28.7 - - - +
73A SER* 4.0 12.7 - - - +
74A ARG 4.2 1.8 - - - -
75A GLY* 3.9 5.4 - - - +
77A GLU* 4.6 4.0 - - - +
84B ASN* 3.1 32.2 + - - +
86B ASP* 1.3 77.5 - - - +
88B MET* 1.3 66.8 + - - +
89B MET 3.2 0.4 - - - -
90B GLU* 3.0 27.6 + - - +
91B GLN* 3.0 23.6 + - - +
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Residues in contact with MET 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ARG* 3.0 32.1 + - - +
76A ILE* 4.2 6.1 - - + -
56B LEU* 4.2 14.9 - - + +
59B ASN* 3.6 52.7 + - + +
60B SER* 4.4 2.5 - - - -
63B TYR* 4.0 11.4 - - + -
83B LEU* 3.3 31.6 - - + -
84B ASN 3.1 10.1 + - - +
85B LEU* 3.7 14.4 - - + +
87B LYS* 1.3 76.5 - - - +
89B MET* 1.3 62.6 + - - +
91B GLN* 3.6 0.9 + - - +
92B LYS* 3.3 17.0 + - - +
200B LEU* 4.0 22.0 - - + -
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Residues in contact with MET 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 4.1 15.7 - - + -
85B LEU* 3.0 29.6 + - + +
86B ASP* 3.8 6.5 - - - +
87B LYS 3.2 0.2 - - - -
88B MET* 1.3 73.7 - - - +
90B GLU* 1.3 55.1 + - - +
92B LYS* 3.1 22.0 - - - +
93B SER* 2.7 39.0 + - - +
172B LEU 3.3 26.5 - - - +
173B SER* 4.2 3.4 - - - -
174B LEU 3.6 26.9 - - - +
197B TRP* 3.6 26.5 - - + -
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER 5.8 0.4 - - - +
86B ASP 3.1 14.1 + - - +
87B LYS* 3.0 40.2 + - + +
89B MET* 1.3 75.8 - - - +
91B GLN* 1.3 56.0 + - - +
93B SER* 2.9 9.9 + - - -
94B THR* 2.8 44.9 + - - +
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A SER* 3.6 25.6 - - - +
74A ARG* 4.1 18.5 - - + +
395A LYS 4.6 2.2 + - - -
396A THR 3.4 20.7 + - - +
398A ALA* 3.4 30.9 - - + +
55B ALA* 3.9 3.3 - - - +
59B ASN* 3.0 26.2 + - - +
87B LYS 3.0 7.7 + - - +
88B MET 3.7 9.0 - - - +
89B MET 3.3 0.2 - - - -
90B GLU* 1.3 75.8 - - - +
92B LYS* 1.3 68.3 + - - +
94B THR* 3.5 7.9 + - - -
95B ALA* 3.2 18.9 + - - +
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Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B PRO* 3.8 39.1 - - + +
55B ALA* 4.0 9.4 - - + +
56B LEU* 3.9 21.3 - - + -
59B ASN* 5.2 0.2 - - - +
88B MET 3.3 9.9 + - - +
89B MET* 3.1 31.0 + - - +
91B GLN* 1.3 88.4 + - - +
93B SER* 1.3 75.3 + - - +
95B ALA* 3.1 3.8 + - - +
96B VAL* 3.1 24.4 + - + +
172B LEU* 2.7 31.3 + - - +
173B SER* 2.9 19.4 + - - -
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B MET* 2.7 18.9 + - - +
90B GLU* 3.3 11.8 - - - -
92B LYS* 1.3 84.6 + - - +
94B THR* 1.3 57.0 + - - +
96B VAL* 3.4 7.9 + - - +
97B LYS* 2.9 30.6 + - - +
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A LYS* 6.2 2.0 - - - -
90B GLU* 2.8 30.6 + - - +
91B GLN* 3.6 11.8 - - - -
93B SER* 1.3 69.8 - - - +
95B ALA* 1.3 70.0 + - - +
97B LYS* 2.9 8.7 + - + +
98B ALA* 2.8 27.3 + - + +
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A LYS* 4.1 13.2 - - + +
396A THR* 3.9 36.3 - - + +
51B ILE* 4.8 5.4 - - + -
55B ALA* 5.1 0.4 - - + -
91B GLN* 3.2 10.6 + - - +
92B LYS* 3.1 11.2 + - - +
94B THR* 1.3 80.0 - - - +
96B VAL* 1.3 63.7 + - - +
98B ALA* 3.4 6.0 + - - +
99B LEU* 3.0 30.3 + - + +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 3.3 31.8 - - - +
47B ASN* 4.1 14.1 - - + +
51B ILE* 4.3 6.7 - - + -
52B PRO* 4.2 26.5 - - + -
92B LYS* 3.1 17.6 + - + +
93B SER* 3.6 8.3 - - - +
94B THR 3.1 0.8 - - - -
95B ALA* 1.3 77.3 - - - +
97B LYS* 1.3 64.6 + - - +
99B LEU* 3.3 1.4 + - - +
100B THR* 2.9 39.8 + - + +
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Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B SER 2.9 17.6 + - - +
94B THR* 3.5 6.7 - - + +
96B VAL* 1.3 77.1 - - - +
98B ALA* 1.3 62.9 + - - +
100B THR* 2.6 25.2 + - - +
101B GLY* 3.0 8.3 + - - -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A LYS* 3.7 28.9 - - - -
94B THR* 2.8 23.9 + - + +
95B ALA 3.6 4.3 - - - +
97B LYS* 1.3 74.2 - - - +
99B LEU* 1.3 58.0 + - - +
101B GLY* 3.1 3.9 + - - -
102B GLY* 2.9 24.1 + - - -
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A ALA 5.4 4.7 - - - +
390A ALA* 5.4 5.2 - - - +
391A ASN 5.3 0.9 - - - +
392A SER* 3.7 36.3 - - - +
395A LYS* 3.8 29.4 - - + -
396A THR* 4.2 2.0 - - - +
46B LEU* 3.4 21.7 - - + +
51B ILE* 3.9 28.0 - - + -
95B ALA 3.0 16.3 + - - +
98B ALA* 1.3 77.1 - - - +
100B THR* 1.3 61.2 + - - +
102B GLY* 3.3 10.6 + - - +
103B ILE* 3.4 19.2 + - - +
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Residues in contact with THR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B THR* 4.4 18.7 - - + +
41B LEU* 3.7 16.2 + - - +
46B LEU* 3.7 19.7 - - + -
47B ASN* 3.4 24.9 - - - +
96B VAL* 2.9 29.7 + - + +
97B LYS* 2.6 26.4 + - - +
99B LEU* 1.3 73.6 - - - +
101B GLY* 1.3 65.6 + - - +
103B ILE* 3.3 13.8 + - - +
104B ALA* 3.4 9.0 + - - +
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LYS 3.0 13.8 + - - -
98B ALA 3.6 3.6 - - - -
100B THR* 1.3 75.7 + - - +
102B GLY* 1.3 60.3 + - - +
104B ALA* 2.9 12.8 + - - +
105B HIS* 2.9 27.9 + - - +
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Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA 2.9 12.7 + - - -
99B LEU* 3.3 8.0 + - - -
100B THR 3.1 0.6 - - - -
101B GLY* 1.3 79.0 - - - +
103B ILE* 1.3 56.9 + - - +
105B HIS* 3.5 7.0 + - - +
106B LEU* 3.0 36.7 + - - +
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 3.7 61.7 - - + +
41B LEU* 3.8 23.1 - - + -
42B GLY* 3.8 13.2 - - - +
46B LEU* 3.7 25.6 - - + -
99B LEU 3.4 9.6 + - - +
100B THR 3.3 8.2 + - - +
101B GLY 3.1 0.8 - - - -
102B GLY* 1.3 75.2 - - - +
104B ALA* 1.3 59.7 + - - +
106B LEU* 3.8 7.4 - - + -
107B PHE* 3.0 33.8 + - + +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 4.1 14.3 - - + +
100B THR 3.4 5.1 + - - +
101B GLY* 2.9 19.2 + - - +
103B ILE* 1.3 78.3 - - - +
105B HIS* 1.3 57.9 + - - +
107B PHE* 3.5 3.0 + - - +
108B LYS* 3.0 31.8 + - - +
114B HIS* 6.2 1.6 - - + -
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Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLY 2.9 13.6 + - - +
102B GLY* 3.8 7.6 - - - +
104B ALA* 1.3 76.6 - - - +
106B LEU* 1.3 60.3 + - + +
108B LYS* 3.1 16.2 + - + +
109B GLN* 2.7 58.6 + - + +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A ILE 3.8 9.4 - - - +
473A ASN* 3.6 55.4 - - + +
474A PHE* 3.7 12.3 - - - +
19B TYR* 4.5 3.1 - - + -
23B ILE* 4.0 16.2 - - + -
102B GLY 3.0 29.8 + - - +
103B ILE* 4.0 9.0 - - + +
105B HIS* 1.3 78.7 - - + +
107B PHE* 1.3 66.8 + - - +
109B GLN* 3.2 16.1 + - - +
110B ASN* 2.8 34.1 + - - +
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Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B SER* 4.8 0.7 - - - -
19B TYR* 3.4 45.3 - - + -
22B ALA* 3.8 8.5 - - + -
23B ILE* 3.8 13.2 - - + -
34B CYS* 3.5 42.6 - - + -
41B LEU* 3.9 30.3 - - + -
103B ILE* 3.0 21.5 + - + +
104B ALA* 3.8 4.9 - - - +
106B LEU* 1.3 75.2 - - - +
108B LYS* 1.3 60.6 + - - +
110B ASN 3.4 0.2 + - - -
111B LYS 3.1 3.6 + - - -
112B VAL* 2.7 55.0 + - + +
114B HIS* 4.4 15.9 - - + -
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ALA* 3.0 16.6 + - - +
105B HIS* 3.2 20.6 - - + +
107B PHE* 1.3 76.5 - - - +
109B GLN* 1.3 54.7 + - - +
111B LYS* 2.8 29.6 + - - +
112B VAL 5.0 2.5 - - - -
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Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A PHE* 3.3 33.7 + - - +
27B GLN* 6.0 0.4 - - - +
105B HIS* 2.7 46.0 + - + +
106B LEU* 3.2 13.3 + - - +
108B LYS* 1.3 74.0 - - - +
110B ASN* 1.3 72.1 + - - +
111B LYS* 3.2 12.4 + - - +
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Residues in contact with ASN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A LYS* 4.9 5.9 + - - +
472A ILE 4.9 1.0 + - - -
23B ILE* 3.7 26.7 - - + +
26B ALA* 3.3 23.8 - - + +
27B GLN* 3.5 25.2 + - + +
106B LEU* 2.8 37.4 + - - +
109B GLN* 1.3 94.7 + - - +
111B LYS* 1.3 72.0 + - - +
112B VAL* 3.2 15.1 + - + -
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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
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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