Contacts of the helix formed by residues 85 - 114 (chain M) in PDB entry 7CRQ
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 GLN 85 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B THR* 4.2 12.7 - - + +
81B VAL 3.3 18.2 + - - +
82B THR* 3.8 22.6 - - - +
83B ALA* 3.8 15.8 + - - +
84M PHE* 1.3 73.4 - - - +
86M SER* 1.3 60.9 + - - +
87M SER* 3.9 13.4 + - - +
88M ALA* 2.9 26.1 + - + +
89M VAL* 3.0 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M PHE 3.9 1.8 + - - -
85M GLN* 1.3 72.7 - - - +
87M SER* 1.3 57.3 + - - +
89M VAL* 4.0 6.8 + - - +
90M NLE 3.5 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA* 3.9 15.9 - - - +
100B PHE* 4.4 12.9 - - - -
85M GLN* 3.1 15.3 + - - +
86M SER* 1.3 76.6 - - - +
88M ALA* 1.3 61.8 + - - +
89M VAL 3.4 0.4 - - - -
90M NLE 3.9 10.2 - - - +
91M ALA* 3.8 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 3.8 13.9 - - + +
82B THR 3.3 35.4 - - - +
83B ALA* 3.8 6.5 - - - +
86B VAL* 4.2 11.8 - - + +
84M PHE* 5.1 5.2 - - + -
85M GLN* 2.9 13.4 + - + +
87M SER* 1.3 78.8 + - - +
89M VAL* 1.3 63.7 + - - +
90M NLE 3.3 0.4 - - - -
91M ALA* 3.8 8.8 + - - +
92M LEU* 4.0 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M PHE* 4.4 10.4 - - + -
68M GLN* 4.3 35.7 - - + +
71M VAL* 5.2 11.7 - - + -
72M ARG* 5.1 7.6 - - - +
84M PHE* 3.9 29.8 - - + -
85M GLN 3.0 16.2 + - - +
86M SER* 4.0 6.9 + - - +
87M SER 3.4 0.2 - - - -
88M ALA* 1.3 79.8 - - - +
90M NLE 1.3 66.2 + - + +
91M ALA 3.3 0.6 + - - -
92M LEU* 3.8 14.6 + - - +
93M GLN* 3.8 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with NLE 90 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PHE* 4.0 12.6 - - + -
60M LEU* 5.0 11.4 - - + +
64M LYS* 4.1 31.4 - - + +
86M SER* 3.5 19.1 + - - +
87M SER* 3.9 9.6 + - - +
88M ALA 3.3 0.6 - - - -
89M VAL* 1.3 81.6 + - + +
91M ALA* 1.3 61.9 + - - +
92M LEU 3.4 0.4 - - - -
93M GLN* 3.9 23.5 + - - +
94M GLU* 3.5 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA* 5.4 5.4 - - + +
86B VAL* 4.5 17.7 - - + -
87B VAL* 5.7 2.0 - - + -
90B LEU* 4.9 2.4 - - - +
97B LEU* 4.2 13.2 - - + +
100B PHE* 4.2 28.0 - - + -
87M SER 3.8 14.4 + - - +
88M ALA* 4.2 7.4 - - - +
89M VAL 3.3 0.6 - - - -
90M NLE 1.3 78.4 + - - +
92M LEU* 1.3 62.6 + - - +
93M GLN 3.4 0.2 - - - -
94M GLU* 3.7 4.2 + - - +
95M ALA* 3.6 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 5.6 2.4 - - + -
62B LEU* 4.1 19.3 - - + -
65B VAL* 4.2 20.0 - - + -
66B ILE* 4.9 12.6 - - + -
86B VAL* 4.1 26.5 - - + -
90B LEU* 6.2 0.9 - - + -
67M PHE* 4.3 11.0 - - + -
71M VAL* 4.3 28.5 - - + -
84M PHE* 5.1 7.4 - - + -
88M ALA 4.0 14.3 + - - +
89M VAL* 3.8 10.6 + - - +
91M ALA* 1.3 77.3 - - - +
93M GLN* 1.3 60.3 + - - +
95M ALA* 3.3 7.3 + - + +
96M SER* 3.0 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M LEU* 4.1 23.0 - - + +
62M ILE* 3.4 33.8 + - + +
63M ARG 4.9 1.0 + - - -
64M LYS* 4.7 9.3 - - - +
67M PHE* 3.9 42.3 - - + +
89M VAL* 3.8 7.3 + - - +
90M NLE 3.9 26.6 + - + +
91M ALA 3.4 0.2 - - - -
92M LEU* 1.3 78.4 - - - +
94M GLU* 1.3 60.8 + - + +
96M SER* 4.1 2.2 - - - +
97M GLU* 3.5 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.8 9.1 - - + +
100B PHE* 4.1 19.1 - - + -
101G THR* 4.8 5.7 - - - +
102G ILE 4.8 0.2 - - - +
103G ALA* 3.5 28.7 - - - -
104G GLN* 3.5 24.3 + - - +
60M LEU* 4.0 26.7 - - + +
90M NLE 3.5 19.3 + - - +
91M ALA 4.0 6.1 - - - +
92M LEU 3.2 0.4 - - - -
93M GLN* 1.3 80.4 - - + +
95M ALA* 1.3 58.5 + - - +
97M GLU* 4.3 2.6 - - - +
98M ALA* 3.6 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 4.5 13.1 - - + -
90B LEU* 4.4 27.8 - - + -
95B ARG* 6.5 0.2 - - - -
97B LEU* 5.4 6.9 - - + +
101G THR* 5.7 2.0 - - - -
91M ALA 3.6 10.5 + - - +
92M LEU* 3.3 10.4 + - + +
94M GLU* 1.3 78.0 - - - +
96M SER* 1.3 65.3 + - - +
97M GLU 3.3 0.2 - - - -
98M ALA* 3.4 4.6 + - - +
99M TYR* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 96 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 4.1 22.1 - - - +
61B PHE* 4.2 14.3 - - - -
62B LEU* 4.1 19.6 - - - +
62M ILE* 6.1 2.5 - - - -
67M PHE* 4.1 14.3 - - - -
92M LEU 3.0 17.8 + - - -
93M GLN 4.3 3.8 - - - -
95M ALA* 1.3 77.6 - - - +
97M GLU* 1.3 58.7 + - - +
99M TYR* 3.2 4.9 + - - +
100M LEU* 3.0 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.3 22.4 - - + +
40B ARG* 4.9 5.2 + - - -
59M GLU 4.7 1.7 - - - +
60M LEU* 3.3 34.9 - - + +
61M LEU* 3.4 27.2 + - - +
62M ILE* 3.6 27.4 - - + +
93M GLN* 3.5 22.1 + - + +
94M GLU* 4.6 2.5 - - - +
95M ALA 3.3 0.2 - - - -
96M SER* 1.3 76.0 - - - +
98M ALA* 1.3 61.3 + - - +
100M LEU* 4.5 2.2 - - - +
101M VAL* 3.0 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G THR* 4.0 25.6 - - + +
94M GLU 3.6 17.6 + - - +
95M ALA* 3.4 6.0 + - - +
96M SER 3.4 0.4 - - - -
97M GLU* 1.3 78.2 - - - +
99M TYR* 1.3 61.6 + - - +
101M VAL* 4.7 4.1 - - - +
102M GLY* 3.7 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL* 4.1 29.5 + - + +
58B LEU* 6.1 2.2 - - + -
61B PHE* 4.3 40.2 - + + +
95B ARG* 4.1 33.4 - - - +
95M ALA 3.0 15.6 + - - +
96M SER* 3.5 6.3 - - - +
97M GLU 3.1 0.2 - - - -
98M ALA* 1.3 77.6 - - - +
100M LEU* 1.3 78.3 + - + +
102M GLY* 3.4 3.1 + - - -
103M LEU* 3.1 29.9 + - + +
128M ARG* 4.3 4.2 + - - -
131M ARG* 4.6 12.4 + - - -
133M GLU* 3.1 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 6.5 0.2 - - + -
37B LEU* 4.1 26.7 - - + -
54B THR* 4.4 27.1 - - + -
57B VAL* 4.7 11.7 - - + -
58B LEU* 4.3 29.8 - - + -
62M ILE* 5.8 4.5 - - + -
96M SER 3.0 18.1 + - - +
97M GLU* 3.3 3.1 + - + +
99M TYR* 1.3 95.5 - - + +
101M VAL* 1.3 63.4 + - - +
103M LEU* 3.1 10.5 + - + +
104M PHE* 3.0 40.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.7 33.4 - - + +
40B ARG* 4.3 20.4 - - + +
41B GLY* 4.1 13.9 - - - +
107G VAL* 4.3 19.3 - - + -
61M LEU* 5.6 0.2 - - + -
97M GLU* 3.0 22.2 + - + +
98M ALA* 4.7 4.3 - - - +
100M LEU* 1.3 76.2 - - - +
102M GLY* 1.3 58.8 + - - +
104M PHE* 3.7 8.8 + - - +
105M GLU* 3.1 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M ALA 3.7 9.2 + - - -
99M TYR 3.4 6.8 + - - -
100M LEU 3.2 0.6 - - - -
101M VAL* 1.3 77.6 - - - +
103M LEU* 1.3 60.7 + - - +
105M GLU* 3.9 17.1 + - - +
106M ASP* 3.9 7.8 + - - +
131M ARG* 3.2 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL* 4.0 26.5 - - + -
99M TYR* 3.1 27.4 + - + +
100M LEU* 3.1 11.6 + - + +
102M GLY* 1.3 75.2 - - - +
104M PHE* 1.3 64.4 + - + +
105M GLU 3.1 5.3 + - - -
106M ASP* 3.2 3.3 + - + -
107M THR* 3.1 29.9 + - - +
124M ILE* 4.6 18.8 - - + -
127M ALA* 4.5 14.8 - - + -
128M ARG* 4.2 22.0 - - + +
131M ARG* 4.0 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 4.5 16.2 - - + -
37B LEU* 4.3 14.1 - - + -
38B ALA* 4.3 30.7 - - + -
41B GLY* 4.6 13.2 - - - +
43B VAL* 3.8 21.9 - - + +
50B ILE* 4.6 10.5 - - + -
54B THR* 4.1 24.0 - - + -
100M LEU* 3.0 36.8 + - + +
101M VAL 3.7 5.8 + - - +
103M LEU* 1.3 77.9 - - + +
105M GLU* 1.3 61.4 + - - +
107M THR* 4.1 10.6 - - - -
108M ASN* 3.8 9.7 + - - +
119M ILE* 4.4 24.7 - - + -
124M ILE* 5.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG 5.0 1.2 - - - +
41B GLY* 3.6 22.7 - - - +
107G VAL* 4.6 11.6 - - - +
101M VAL* 3.1 30.5 - - - +
102M GLY* 4.2 11.6 - - - +
103M LEU 3.1 1.2 - - - -
104M PHE* 1.3 77.9 - - - +
106M ASP* 1.3 65.3 + - - +
108M ASN* 3.9 8.8 + - - +
109M LEU* 3.8 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 106 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E ILE* 4.5 28.5 - - + +
102M GLY 4.0 3.7 - - - +
103M LEU* 3.2 6.9 + - - +
105M GLU* 1.3 78.3 - - - +
107M THR* 1.3 68.0 + - - +
108M ASN 3.2 2.1 + - - -
109M LEU* 3.4 20.9 + - - +
110M CYS* 3.5 17.3 + - - -
127M ALA* 4.2 16.6 - - + -
131M ARG* 2.3 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 107 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M LEU* 3.1 19.6 + - - +
104M PHE* 4.2 13.4 - - + -
105M GLU 3.5 0.2 - - - -
106M ASP* 1.3 77.9 - - - +
108M ASN* 1.3 61.0 + - - +
110M CYS* 3.3 5.7 + - - +
111M GLY* 3.1 18.9 + - - -
119M ILE* 4.1 28.7 - - + +
120M NLE 4.9 0.7 - - - +
123M ASP* 3.6 30.3 + - + +
124M ILE* 4.0 29.3 - - + +
127M ALA* 4.6 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLY 5.7 0.8 + - - +
42B GLY 3.8 19.6 + - - -
43B VAL* 4.0 19.1 - - + +
44B LYS 5.3 0.7 + - - -
112G GLN* 4.4 14.6 - - - +
115G LEU* 4.2 17.3 - - - +
104M PHE 3.8 15.4 + - - +
105M GLU* 4.1 7.6 - - - +
106M ASP 3.2 0.8 - - - -
107M THR* 1.3 79.9 - - - +
109M LEU* 1.3 59.0 + - + +
111M GLY* 3.3 2.0 + - - +
112M ILE* 3.0 42.6 + - - +
117M VAL 5.0 5.5 - - - +
119M ILE* 4.2 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E LEU* 4.2 20.8 - - + +
129E ARG* 3.7 47.1 - - + +
130E ILE* 5.2 6.7 - - + -
112G GLN* 4.4 27.4 - - + +
105M GLU 3.8 16.4 - - - +
106M ASP* 3.4 13.8 + - - +
107M THR 3.3 0.4 - - - -
108M ASN* 1.3 79.4 - - + +
110M CYS* 1.3 58.5 + - - +
112M ILE* 3.4 9.9 + - + +
113M HIS* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 110 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E HIS* 4.0 11.4 + - + +
126E LEU* 4.9 6.3 - - + -
130E ILE* 3.7 24.2 - - - -
106M ASP 3.6 15.0 - - - -
107M THR 3.3 6.7 + - - +
108M ASN 3.3 0.6 - - - -
109M LEU* 1.3 74.2 - - - +
111M GLY* 1.3 66.2 + - - +
113M HIS* 3.1 9.2 + - - +
114M ALA* 3.0 23.7 + - - +
123M ASP* 4.2 26.2 - - + +
126M LEU* 4.3 22.4 - - + -
127M ALA* 4.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 111 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107M THR 3.1 14.2 + - - -
108M ASN* 3.3 4.2 + - - -
110M CYS* 1.3 76.9 - - - +
112M ILE* 1.3 62.0 + - - +
114M ALA* 3.6 4.7 + - - +
116M ARG* 3.2 50.4 + - - +
117M VAL 6.1 0.7 - - - -
118M THR 4.7 6.1 - - - -
119M ILE* 5.3 3.6 - - - -
123M ASP* 4.2 7.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G GLN* 4.3 27.1 - - + +
114G VAL* 3.7 33.0 - - + -
115G LEU* 4.8 8.7 - - + -
108M ASN* 3.0 31.8 + - - +
109M LEU* 3.9 10.1 - - + +
111M GLY* 1.3 76.7 - - - +
113M HIS* 1.3 67.2 + - - +
115M LYS* 3.1 14.6 + - - +
116M ARG 4.3 12.6 - - - +
117M VAL* 5.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 113 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E CYS* 4.0 24.5 + - + +
113E HIS* 4.9 8.1 - + + -
114E ALA* 4.2 11.5 - - + +
116E ARG* 4.1 7.1 + - - -
122E LYS* 4.0 32.7 + - + +
123E ASP* 3.2 27.4 + - - -
126E LEU* 4.0 27.4 - - + +
109M LEU 2.9 15.3 + - - +
110M CYS* 3.1 13.4 + - - +
112M ILE* 1.3 77.9 - - - +
114M ALA* 1.3 57.6 + - - +
115M LYS* 3.2 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E HIS* 4.1 22.2 - - + +
114E ALA* 4.9 9.9 - - - +
115E LYS* 6.3 0.9 - - - +
110M CYS 3.0 12.7 + - - +
111M GLY 3.6 0.6 + - - +
112M ILE 3.2 0.4 - - - -
113M HIS* 1.3 75.3 - - - +
115M LYS* 1.3 71.0 + - - +
116M ARG* 3.6 35.4 + - - +
----------------------------------------------------------
Back to top of page
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