Contacts of the helix formed by residues 84 - 110 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ARG* 5.8 0.4 - - - +
83C LEU* 1.3 74.0 - - - +
85C LEU* 1.3 63.1 + - - +
86C ASP* 3.5 11.6 + - - +
87C LYS* 2.9 38.7 + - - +
88C MET* 3.0 9.2 + - - +
75D GLY* 2.9 21.2 + - - +
77D GLU* 2.6 42.4 + - + +
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU* 6.2 0.2 - - + -
83C LEU* 3.6 17.7 + - + +
84C ASN* 1.3 72.4 - - - +
86C ASP* 1.3 59.0 + - - +
88C MET* 3.1 10.7 + - + +
89C MET* 2.9 48.5 + - + +
174C LEU 3.7 10.1 - - - +
175C LYS 3.3 30.3 - - - +
176C LYS* 3.5 23.8 - - + -
177C VAL* 3.8 7.0 - - + +
197C TRP* 3.9 25.4 - - + -
200C LEU* 4.4 12.3 - - + -
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Residues in contact with ASP 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ASN* 3.2 9.3 + - - +
85C LEU* 1.3 78.4 - - - +
87C LYS* 1.3 57.6 + - - +
89C MET* 3.5 7.6 + - - +
90C GLU* 3.0 25.9 + - - +
175C LYS* 4.9 15.8 - - - +
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Residues in contact with LYS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ASN* 2.9 24.4 + - - +
86C ASP* 1.3 75.0 - - - +
88C MET* 1.3 66.5 + - - +
89C MET 3.2 0.4 - - - -
90C GLU* 3.3 22.0 + - - +
91C GLN* 3.1 21.8 + - - +
72D ALA* 2.7 31.0 - - - +
73D SER* 4.0 9.8 - - - +
75D GLY* 3.5 10.5 - - - +
77D GLU* 3.3 26.0 - - - -
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Residues in contact with MET 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 4.5 13.8 - - + +
59C ASN* 3.5 46.4 + - + +
60C SER* 4.3 3.6 - - - -
63C TYR* 4.1 10.8 - - + -
83C LEU* 3.5 25.4 - - + -
84C ASN 3.0 11.0 + - - +
85C LEU* 3.6 13.0 - - + +
87C LYS* 1.3 76.2 - - - +
89C MET* 1.3 62.5 + - - +
91C GLN* 3.3 5.4 + - - +
92C LYS* 3.2 18.7 + - - +
200C LEU* 4.1 27.1 - - + -
74D ARG 3.1 28.9 + - - +
75D GLY 4.8 0.4 - - - +
76D ILE* 4.3 6.3 - - + -
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Residues in contact with MET 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 4.2 15.0 - - + -
85C LEU* 2.9 31.7 + - + +
86C ASP* 3.7 7.4 - - - +
88C MET* 1.3 77.0 - - - +
90C GLU* 1.3 60.1 + - - +
92C LYS* 3.1 21.4 - - - +
93C SER* 2.9 31.6 + - - +
172C LEU 3.3 26.7 - - - +
173C SER* 4.2 4.0 - - - -
174C LEU 3.5 18.4 - - - +
197C TRP* 3.5 37.0 - - + -
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Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASP 3.0 15.6 + - - +
87C LYS* 3.4 26.7 + - - +
88C MET 3.2 0.2 - - - -
89C MET* 1.3 75.6 - - - +
91C GLN* 1.3 66.9 + - - +
93C SER* 3.2 6.5 + - - +
94C THR* 2.9 35.1 + - - +
73D SER 5.7 0.7 - - - +
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Residues in contact with GLN 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ALA* 3.9 10.9 - - - +
59C ASN* 2.6 35.8 + - - +
87C LYS 3.1 8.2 + - - +
88C MET 3.5 8.7 - - - +
90C GLU* 1.3 78.6 - - - +
92C LYS* 1.3 66.7 + - - +
94C THR* 3.3 8.7 + - - +
95C ALA* 3.2 19.5 + - - +
73D SER* 3.6 26.2 + - - +
74D ARG* 4.4 14.1 - - + +
395D LYS 5.0 0.8 + - - -
396D THR 3.3 22.1 + - - +
398D ALA* 4.2 18.5 - - + +
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Residues in contact with LYS 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C PRO* 3.8 40.2 - - + +
55C ALA* 4.0 14.4 - - + +
56C LEU* 4.0 19.5 - - + -
88C MET 3.2 10.4 + - - +
89C MET* 3.1 29.5 - - - +
91C GLN* 1.3 80.1 + - - +
93C SER* 1.3 75.1 + - - +
95C ALA* 3.2 14.6 + - - +
96C VAL* 3.2 13.6 + - + +
172C LEU* 2.8 31.1 + - - +
173C SER* 3.1 19.4 + - - -
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Residues in contact with SER 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C MET* 2.9 15.0 + - - +
90C GLU* 3.2 8.9 + - - -
92C LYS* 1.3 83.7 + - - +
94C THR* 1.3 57.2 + - - +
96C VAL* 2.9 10.3 + - - +
97C LYS* 2.7 36.7 + - - +
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Residues in contact with THR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLU* 2.9 27.6 + - - +
91C GLN* 3.3 9.3 + - - +
93C SER* 1.3 75.7 - - - +
95C ALA* 1.3 61.5 + - - +
97C LYS* 3.9 6.2 - - - +
98C ALA* 3.1 27.3 + - + +
395D LYS* 6.5 0.7 - - - -
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Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ILE* 4.2 10.8 - - + -
91C GLN* 3.2 9.9 + - - +
92C LYS* 3.2 11.5 + - - +
93C SER 3.1 0.4 - - - -
94C THR* 1.3 78.1 - - - +
96C VAL* 1.3 65.9 + - - +
98C ALA* 3.9 3.7 - - - +
99C LEU* 3.1 31.7 + - + +
395D LYS* 4.4 9.6 - - - +
396D THR* 3.9 35.2 - - + +
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LEU* 3.5 26.6 - - - +
47C ASN* 4.1 25.1 - - - +
51C ILE* 4.0 15.3 - - + -
52C PRO* 4.0 19.5 - - + -
92C LYS* 3.2 13.6 + - + +
93C SER* 2.9 12.1 + - - +
95C ALA* 1.3 75.2 - - - +
97C LYS* 1.3 66.5 + - - +
99C LEU* 3.3 2.3 + - - +
100C THR* 2.9 27.2 + - + +
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Residues in contact with LYS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C SER 2.7 19.5 + - - +
94C THR* 3.9 7.2 - - - +
96C VAL* 1.3 74.2 - - - +
98C ALA* 1.3 62.9 + - - +
100C THR* 2.8 20.6 + - - +
101C GLY* 3.0 10.7 + - - -
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Residues in contact with ALA 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C THR* 3.1 19.4 + - + +
95C ALA 3.9 2.9 - - - +
97C LYS* 1.3 80.9 - - - +
99C LEU* 1.3 61.2 + - - +
101C GLY* 3.6 1.9 + - - -
102C GLY* 3.2 17.2 + - - -
395D LYS* 3.8 29.2 - - - +
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LEU* 3.4 22.7 - - + +
51C ILE* 3.4 48.9 - - + -
95C ALA 3.1 16.8 + - - +
96C VAL* 4.1 2.9 - - - +
97C LYS 3.3 0.2 - - - -
98C ALA* 1.3 76.4 - - - +
100C THR* 1.3 64.9 + - - +
102C GLY* 3.3 9.0 + - - +
103C ILE* 3.4 10.7 + - - +
390D ALA 5.7 3.8 - - - +
391D ASN 5.3 0.7 - - - +
392D SER* 4.4 17.5 - - - +
395D LYS* 3.5 31.0 - - + -
396D THR* 3.8 8.5 - - - +
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Residues in contact with THR 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C THR* 4.2 16.7 - - + +
41C LEU* 3.2 30.0 + - - +
46C LEU* 3.7 16.2 - - + -
47C ASN* 3.3 22.9 - - - +
96C VAL* 2.9 19.9 + - + +
97C LYS* 2.8 21.3 + - - +
99C LEU* 1.3 74.3 - - - +
101C GLY* 1.3 65.8 + - - +
103C ILE* 3.2 13.4 + - - +
104C ALA* 3.3 10.2 + - - +
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Residues in contact with GLY 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LYS 3.0 15.6 + - - -
98C ALA* 4.0 2.5 - - - -
100C THR* 1.3 77.7 + - - +
102C GLY* 1.3 57.5 + - - +
104C ALA* 3.0 11.3 + - - +
105C HIS* 2.8 28.7 + - - +
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Residues in contact with GLY 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ALA 3.2 13.6 + - - -
99C LEU* 3.3 6.9 + - - -
100C THR 3.1 0.8 - - - -
101C GLY* 1.3 78.2 - - - +
103C ILE* 1.3 55.9 + - - +
105C HIS* 3.2 9.0 + - - +
106C LEU* 2.8 39.4 + - - +
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Residues in contact with ILE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 3.8 56.8 - - + +
41C LEU* 3.7 23.3 - - + -
42C GLY* 3.5 20.4 - - - +
46C LEU* 3.4 26.2 - - + -
99C LEU 3.4 10.9 + - - +
100C THR 3.2 7.4 + - - +
102C GLY* 1.3 73.4 - - - +
104C ALA* 1.3 66.8 + - - +
106C LEU* 3.7 8.5 - - + +
107C PHE* 2.9 30.1 + - + +
473D ASN* 5.9 0.2 - - - +
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 3.8 16.5 - - + +
100C THR 3.3 7.3 + - - +
101C GLY* 3.0 15.8 + - - +
103C ILE* 1.3 80.4 - - - +
105C HIS* 1.3 61.6 + - - +
107C PHE* 3.3 4.2 + - - +
108C LYS* 3.2 24.0 + - - +
114C HIS* 6.3 1.3 - - + -
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Residues in contact with HIS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C GLY 2.8 12.0 + - - +
102C GLY* 3.6 11.0 - - - +
104C ALA* 1.3 76.7 - - - +
106C LEU* 1.3 67.9 + - + +
108C LYS* 3.2 17.4 + - + +
109C GLN* 2.9 49.6 + - + +
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 4.7 2.2 - - + -
23C ILE* 3.8 18.4 - - + -
102C GLY* 2.8 28.0 + - - +
103C ILE* 3.2 9.1 + - + +
105C HIS* 1.3 81.1 - - + +
107C PHE* 1.3 66.5 + - - +
109C GLN* 3.4 12.5 + - - +
110C ASN* 2.8 33.6 + - - +
472D ILE 3.9 7.4 - - - +
473D ASN* 3.6 57.4 - - - +
474D PHE* 3.8 12.8 - - + +
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Residues in contact with PHE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 3.5 50.0 - + + -
22C ALA* 4.0 9.9 - - + -
23C ILE* 3.7 16.8 - - + -
34C CYS* 3.6 31.4 - - + -
41C LEU* 3.9 29.6 - - + -
103C ILE* 2.9 19.4 + - + +
104C ALA* 3.6 5.8 - - - +
106C LEU* 1.3 72.0 - - - +
108C LYS* 1.3 66.9 + - - +
110C ASN 3.3 0.9 + - - -
111C LYS 2.9 4.2 + - - -
112C VAL* 2.7 54.1 + - + +
114C HIS* 4.3 15.5 - - + -
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Residues in contact with LYS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ALA 3.2 11.9 + - - +
105C HIS* 3.4 18.6 - - + +
107C PHE* 1.3 78.0 - - - +
109C GLN* 1.3 59.3 + - - +
111C LYS* 2.9 25.3 + - - +
112C VAL 5.0 2.0 - - - -
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Residues in contact with GLN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLN* 5.6 2.2 - - - +
105C HIS* 2.9 39.5 + - + +
106C LEU* 3.6 12.6 - - - +
108C LYS* 1.3 78.7 - - - +
110C ASN* 1.3 74.9 + - - +
111C LYS* 3.2 10.4 + - - +
474D PHE* 3.2 34.3 + - - +
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Residues in contact with ASN 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ILE* 3.6 26.7 - - + +
26C ALA* 3.3 29.2 - - + +
27C GLN* 3.1 30.1 + - - +
106C LEU* 2.8 31.5 + - - +
107C PHE 4.2 1.3 - - - +
109C GLN* 1.3 93.8 + - - +
111C LYS* 1.3 71.9 + - - +
112C VAL* 3.3 7.2 - - + -
470D LYS* 4.9 6.6 + - - +
472D ILE 4.8 2.4 + - - -
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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