Contacts of the helix formed by residues 90 - 119 (chain M) in PDB entry 6O81
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 SER 90 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M ARG 3.7 2.5 + - - -
89M VAL* 1.3 76.7 - - - +
91M PRO* 1.3 75.5 - - - +
92M GLU* 3.3 16.5 + - - +
93M GLU* 3.3 13.5 + - - +
94M ALA* 2.8 28.7 + - - +
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Residues in contact with PRO 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D SER* 6.0 3.8 - - - +
134D ILE* 4.4 14.1 - - + -
135D GLU* 5.3 10.1 - - + -
138D ASN* 3.7 25.6 - - - +
89M VAL 4.6 1.6 - - - +
90M SER* 1.3 90.3 - - - +
92M GLU* 1.3 56.2 + - - +
94M ALA* 3.6 8.1 - - + +
95M ILE* 2.9 28.9 + - - +
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Residues in contact with GLU 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90M SER* 3.3 10.0 + - - +
91M PRO* 1.3 76.1 - - - +
93M GLU* 1.3 59.3 + - - +
95M ILE* 3.3 6.1 + - - +
96M LYS* 2.9 37.4 + - + +
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Residues in contact with GLU 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M VAL* 4.5 12.8 - - + +
89M VAL* 4.0 15.3 - - + -
90M SER* 3.3 20.7 + - - +
92M GLU* 1.3 77.2 - - - +
94M ALA* 1.3 58.7 + - - +
96M LYS* 3.7 13.3 - - - +
97M CYS* 2.9 30.1 + - - +
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Residues in contact with ALA 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M MET* 4.8 0.3 - - - +
69M CYS* 4.3 20.4 - - + +
89M VAL* 4.0 10.2 - - + +
90M SER 2.8 18.1 + - - +
91M PRO* 3.6 9.6 - - + +
92M GLU 3.2 0.4 - - - -
93M GLU* 1.3 74.3 - - - +
95M ILE* 1.3 59.5 + - - +
97M CYS* 3.4 1.9 + - - +
98M GLU* 2.9 28.8 + - - +
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Residues in contact with ILE 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91M PRO 2.9 17.5 + - - +
92M GLU* 3.8 7.0 - - - +
94M ALA* 1.3 72.6 - - - +
96M LYS* 1.3 61.5 + - - +
98M GLU* 3.3 7.3 + - - +
99M ASP* 3.0 30.1 + - - +
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Residues in contact with LYS 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M GLU* 2.9 24.8 + - + +
93M GLU* 3.7 11.2 - - - +
94M ALA 3.3 0.2 - - - -
95M ILE* 1.3 76.6 - - - +
97M CYS* 1.3 56.0 + - - +
99M ASP* 3.4 5.6 + - - +
100M LYS* 2.9 29.7 + - - +
146M TYR* 4.7 21.7 - - + -
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Residues in contact with CYS 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M VAL* 3.7 35.0 - - + +
19M VAL 5.4 1.8 - - - -
20M MET* 3.7 6.0 - - + +
69M CYS* 4.1 9.2 - - + -
93M GLU 2.9 18.5 + - - +
94M ALA 3.8 3.8 - - - +
96M LYS* 1.3 73.2 - - - +
98M GLU* 1.3 61.8 + - - +
100M LYS* 3.9 8.7 - - - +
101M PHE* 2.9 31.7 + - - +
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Residues in contact with GLU 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M MET* 3.8 14.5 - - + +
94M ALA 2.9 18.3 + - - +
95M ILE* 3.7 7.9 - - - +
97M CYS* 1.3 77.2 - - - +
99M ASP* 1.3 56.7 + - - +
101M PHE* 3.4 4.9 + - - +
102M THR* 2.9 29.7 + - - -
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Residues in contact with ASP 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95M ILE 3.0 18.0 + - - +
96M LYS* 3.9 5.2 - - - +
98M GLU* 1.3 77.1 - - - +
100M LYS* 1.3 58.2 + - - +
102M THR* 3.3 6.2 + - - -
103M LYS* 3.0 48.7 + - + +
146M TYR* 5.9 0.2 - - + -
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Residues in contact with LYS 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M TYR* 3.2 32.8 - - + -
18M VAL 5.0 7.0 + - - +
37M GLU* 3.4 16.4 + - - -
96M LYS 2.9 18.4 + - - +
97M CYS* 3.9 8.1 - - - +
99M ASP* 1.3 77.0 - - - +
101M PHE* 1.3 57.0 + - - +
103M LYS* 3.4 13.0 + - - +
104M SER* 2.9 28.2 + - - -
144M PRO* 3.4 26.7 - - - +
145M GLY* 4.9 4.2 - - - -
146M TYR* 3.7 31.0 - - + -
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Residues in contact with PHE 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M PHE* 3.8 27.4 - + - -
20M MET* 3.7 37.5 - - + -
36M LEU* 3.9 36.8 - - + -
37M GLU* 4.5 16.1 + - + +
67M ASN* 4.3 12.3 - - - -
97M CYS 2.9 18.7 + - - +
98M GLU* 3.9 4.7 - - - +
100M LYS* 1.3 73.8 - - - +
102M THR* 1.3 63.0 + - - +
104M SER* 4.5 2.9 - - - -
105M LYS* 2.9 48.2 + - + +
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Residues in contact with THR 102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M GLU 2.9 18.7 + - - -
99M ASP* 3.6 7.2 - - - -
100M LYS 3.3 0.2 - - - -
101M PHE* 1.3 81.0 - - - +
103M LYS* 1.3 58.4 + - - +
105M LYS* 3.4 6.4 + - - +
106M THR* 2.9 29.1 + - - -
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Residues in contact with LYS 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99M ASP* 3.0 45.3 + - - +
100M LYS* 3.6 5.8 - - - +
102M THR* 1.3 75.6 - - - +
104M SER* 1.3 58.3 + - - +
106M THR* 3.3 3.8 + - - -
107M VAL* 3.0 28.4 + - - +
145M GLY 4.5 4.5 - - - +
146M TYR* 3.5 42.4 - - - +
149M TYR* 3.6 57.2 - - + +
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Residues in contact with SER 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M PHE* 3.6 26.0 - - - +
8M TYR* 4.1 25.1 - - - -
37M GLU* 5.2 0.2 - - - -
100M LYS 2.9 18.8 + - - -
101M PHE* 4.0 4.0 - - - -
103M LYS* 1.3 76.2 - - - +
105M LYS* 1.3 57.8 + - - +
107M VAL* 3.4 7.2 + - - +
108M TYR* 2.9 28.4 + - - +
145M GLY* 4.8 7.5 + - - -
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Residues in contact with LYS 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M PHE* 3.7 22.4 - - + -
101M PHE* 2.9 38.9 + - + +
102M THR* 3.8 5.6 - - - +
104M SER* 1.3 73.2 - - - +
106M THR* 1.3 61.4 + - - +
108M TYR* 3.6 6.5 - - + +
109M SER* 2.9 31.0 + - - -
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Residues in contact with THR 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M THR 2.9 17.4 + - - -
103M LYS* 3.3 6.3 + - - -
105M LYS* 1.3 76.6 - - - +
107M VAL* 1.3 56.1 + - - +
109M SER* 3.4 6.2 + - - -
110M ILE* 2.9 28.9 + - - +
149M TYR* 4.3 16.2 - - - -
182M ARG* 5.9 1.0 - - - +
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Residues in contact with VAL 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M LYS 3.0 16.2 + - - +
104M SER* 3.8 7.4 - - - +
105M LYS 3.3 0.2 - - - -
106M THR* 1.3 75.7 - - - +
108M TYR* 1.3 57.2 + - - +
110M ILE* 3.3 6.1 + - - +
111M LEU* 3.0 35.9 + - + +
130M PHE* 5.6 1.1 - - - -
134M ALA* 5.6 3.6 - - + -
145M GLY 6.2 0.2 - - - +
148M ALA* 5.2 8.7 - - + -
149M TYR* 5.1 8.2 - - + +
152M PHE* 4.2 26.9 - - + -
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Residues in contact with TYR 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3M LEU 5.2 3.4 - - - -
4M SER* 4.7 15.7 - - - -
5M CYS* 4.4 17.3 - - + -
7M PHE* 3.4 37.2 - + + -
104M SER 2.9 18.1 + - - +
105M LYS* 3.6 10.3 - - + +
106M THR 3.3 0.2 - - - -
107M VAL* 1.3 77.2 - - - +
109M SER* 1.3 60.8 + - - +
111M LEU* 3.5 0.9 + - - +
112M ARG* 2.9 40.9 + - + +
126M LEU* 5.8 1.8 - - + -
130M PHE* 3.5 34.3 - + + -
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Residues in contact with SER 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M LYS* 2.9 20.9 + - - -
106M THR* 3.8 6.5 - - - -
107M VAL 3.3 0.2 - - - -
108M TYR* 1.3 78.1 - - - +
110M ILE* 1.3 59.6 + - - +
112M ARG* 3.7 5.4 - - - +
113M HIS* 2.9 30.0 + - - +
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Residues in contact with ILE 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M THR 2.9 17.7 + - - +
107M VAL* 3.7 7.0 - - - +
108M TYR 3.3 0.2 - - - -
109M SER* 1.3 76.5 - - - +
111M LEU* 1.3 63.0 + - + +
113M HIS* 3.3 6.8 + - - +
114M VAL* 2.9 27.4 + - - +
152M PHE* 5.7 4.5 - - + -
178M ASN* 4.1 17.0 - - + +
179M ILE* 5.4 4.3 - - + +
182M ARG* 4.9 18.2 - - + -
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Residues in contact with LEU 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107M VAL* 3.0 26.1 + - + +
108M TYR 4.1 2.5 - - - +
110M ILE* 1.3 78.1 - - + +
112M ARG* 1.3 60.6 + - - +
114M VAL* 3.6 9.0 - - + +
115M ALA* 2.9 29.3 + - - +
126M LEU* 5.8 0.6 - - - +
129M LEU* 4.0 6.5 - - + +
130M PHE* 3.7 55.4 - - + +
133M THR* 3.8 18.8 - - - -
134M ALA* 4.5 6.7 - - + -
152M PHE* 3.6 34.3 - - + -
175M LEU* 6.4 2.7 - - + -
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Residues in contact with ARG 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108M TYR* 2.9 35.4 + - + +
109M SER* 3.7 7.6 - - - +
111M LEU* 1.3 74.3 - - - +
113M HIS* 1.3 58.7 + - - +
115M ALA* 3.4 5.6 + - - +
116M GLU* 2.9 29.6 + - - +
126M LEU* 5.6 5.4 - - + -
130M PHE* 5.4 2.1 - - - -
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Residues in contact with HIS 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109M SER 2.9 18.1 + - - +
110M ILE* 3.7 6.7 - - - +
112M ARG* 1.3 75.5 - - - +
114M VAL* 1.3 59.3 + - - +
116M GLU* 3.4 7.5 + - - +
117M VAL* 2.9 29.1 + - - +
178M ASN* 4.9 8.7 - - + -
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Residues in contact with VAL 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110M ILE 2.9 17.2 + - - +
111M LEU* 3.6 11.7 - - + +
113M HIS* 1.3 77.5 - - - +
115M ALA* 1.3 57.4 + - - +
117M VAL* 3.4 6.6 + - - +
118M LEU* 2.9 27.9 + - - +
129M LEU* 5.4 3.1 - - + -
171M GLU 5.5 1.3 - - - +
174M VAL* 4.6 9.8 - - + +
175M LEU* 4.4 28.5 - - + +
178M ASN* 4.7 5.1 - - + +
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Residues in contact with ALA 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M LEU* 6.0 2.2 - - + -
111M LEU 2.9 17.6 + - - +
112M ARG 3.9 3.4 - - - +
114M VAL* 1.3 73.5 - - - +
116M GLU* 1.3 60.9 + - - +
118M LEU* 3.5 6.2 - - - +
119M GLU 2.8 22.7 + - - -
120M TYR* 3.0 18.7 + - + +
126M LEU* 3.7 31.2 - - + -
129M LEU* 4.1 20.4 - - + +
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Residues in contact with GLU 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M LEU* 6.3 2.2 - - + +
112M ARG 2.9 18.3 + - - +
113M HIS* 3.7 7.6 - - - +
115M ALA* 1.3 75.2 - - - +
117M VAL* 1.3 63.6 + - - +
119M GLU* 3.4 12.3 + - - +
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Residues in contact with VAL 117 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M HIS 2.9 16.7 + - - +
114M VAL* 3.7 7.4 - - - +
115M ALA 3.3 0.2 - - - -
116M GLU* 1.3 76.8 - - - +
118M LEU* 1.3 60.8 + - - +
119M GLU* 3.5 2.3 + - - +
174M VAL* 4.7 13.9 - - + -
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Residues in contact with LEU 118 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M VAL 2.9 17.3 + - - +
115M ALA* 3.4 7.6 + - - +
116M GLU 3.3 0.2 - - - -
117M VAL* 1.3 74.4 - - - +
119M GLU* 1.3 69.6 + - - +
120M TYR* 3.3 8.1 + - + +
129M LEU* 5.0 7.9 - - + -
171M GLU* 5.6 12.1 - - + -
174M VAL* 5.7 3.1 - - + +
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Residues in contact with GLU 119 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115M ALA 2.8 9.6 + - - -
116M GLU* 3.4 10.5 + - - +
117M VAL 3.3 5.2 - - - +
118M LEU* 1.3 79.0 - - - +
120M TYR* 1.3 57.9 + - - +
121M THR* 3.2 10.0 + - - -
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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