Contacts of the helix formed by residues 111 - 138 (chain M) in PDB entry 7PRC
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 GLY 111 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104M ILE* 5.9 1.1 - - - -
105M PRO* 3.4 25.1 + - - +
106M PRO 2.8 18.9 + - - -
107M LEU* 3.5 15.7 - - - -
109M ASP 3.5 0.2 - - - -
110M GLY* 1.3 72.1 - - - +
112M TRP* 1.3 61.8 + - - +
113M TRP 3.2 0.2 + - - -
114M LEU* 3.2 13.2 + - - +
115M MET* 3.2 14.3 + - - +
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Residues in contact with TRP 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M ILE* 3.5 32.0 - - + +
72M ASN* 3.5 34.8 - - - +
93M LEU* 4.0 7.8 - - + +
107M LEU* 3.0 57.9 + - + +
110M GLY 3.2 1.0 - - - -
111M GLY* 1.3 75.1 - - - +
113M TRP* 1.3 62.2 + - - +
115M MET* 3.1 39.8 - - + +
116M ALA* 3.1 7.3 + - - +
706M LDA 3.4 57.8 - - + +
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Residues in contact with TRP 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93M LEU* 3.3 34.8 - - + +
94M TYR 3.1 19.3 - - - +
95M PRO* 3.6 23.1 - - + -
96M PRO* 4.5 2.9 - - + -
110M GLY 3.0 10.0 + - - +
112M TRP* 1.3 76.9 - - - +
114M LEU* 1.3 78.1 + - + +
116M ALA* 3.3 4.2 + - - +
117M GLY* 2.7 32.1 + - - -
159M GLY 3.6 20.6 - - - -
169M TRP* 4.0 31.4 - + + -
172M GLY* 3.9 12.3 - - - -
173M VAL 2.8 41.6 + - - -
174M PRO* 3.8 0.2 - - - +
175M PHE* 3.5 21.6 - + - -
600M NS5 3.9 19.3 - - + -
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Residues in contact with LEU 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104M ILE* 4.9 10.8 - - + -
105M PRO* 3.7 31.6 - - + -
110M GLY 3.1 8.5 + - - +
111M GLY* 3.6 9.4 - - - +
113M TRP* 1.3 88.4 - - + +
115M MET* 1.3 57.1 + - - +
117M GLY* 3.5 1.6 - - - +
118M LEU* 2.8 31.0 + - - +
169M TRP* 3.8 36.1 - - + +
600M NS5 3.7 50.8 - - + +
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Residues in contact with MET 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M ILE* 4.5 7.4 - - + -
107M LEU* 4.9 5.4 - - + -
111M GLY 3.2 14.6 + - - +
112M TRP* 3.1 39.5 - - + +
114M LEU* 1.3 79.8 - - - +
116M ALA* 1.3 62.0 + - - +
118M LEU* 3.3 12.2 + - + +
119M PHE* 2.9 56.3 + - + -
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Residues in contact with ALA 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M ALA* 4.0 11.6 - - + +
68M ILE* 4.2 17.9 - - + +
69M ILE* 4.0 21.1 - - + -
93M LEU* 4.3 2.0 - - + -
112M TRP 3.1 9.0 + - - +
113M TRP 3.7 7.0 - - - +
115M MET* 1.3 76.3 - - - +
117M GLY* 1.3 64.9 + - - +
119M PHE* 3.9 1.0 - - - +
120M MET* 2.9 27.2 + - - +
175M PHE* 3.9 17.7 - - + -
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Residues in contact with GLY 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M TRP 2.7 18.7 + - - -
114M LEU* 3.5 4.3 - - - -
115M MET 3.1 0.4 - - - -
116M ALA* 1.3 75.2 - - - +
118M LEU* 1.3 62.3 + - - +
120M MET* 3.3 2.6 + - - +
121M THR* 2.9 22.5 + - - -
175M PHE* 4.0 8.5 - - - -
600M NS5 3.5 35.2 - - - +
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Residues in contact with LEU 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M LEU 2.8 15.2 + - - +
115M MET* 3.5 16.4 - - + +
117M GLY* 1.3 72.5 - - - +
119M PHE* 1.3 74.9 + - + +
121M THR* 3.2 9.0 - - + -
122M LEU* 3.1 44.5 + - + +
600M NS5 3.8 38.9 - - + +
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Residues in contact with PHE 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M PHE* 3.6 33.5 - + - +
64M THR* 3.8 30.5 - - + -
65M ALA* 4.0 17.3 - - + +
68M ILE* 4.2 9.9 - - + -
115M MET* 2.9 56.6 + - + +
116M ALA 3.3 3.1 + - - +
118M LEU* 1.3 85.4 - - + +
120M MET* 1.3 58.6 + - - +
122M LEU* 3.0 12.8 + - + +
123M SER* 2.8 28.6 + - - -
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Residues in contact with MET 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M ALA* 3.9 7.0 - - + +
116M ALA 2.9 17.3 + - - +
117M GLY 3.7 1.6 - - - +
119M PHE* 1.3 74.9 - - - +
121M THR* 1.3 51.2 + - - +
123M SER* 3.1 10.0 - - - -
124M LEU* 2.8 50.3 + - + +
155M VAL* 3.4 33.4 - - + -
156M LEU* 6.4 0.2 - - + -
175M PHE* 3.6 27.8 - - + -
600M NS5 3.4 24.0 - - + -
805M BCB 4.4 15.3 - - - +
806M BCB 4.1 34.8 - - + -
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Residues in contact with THR 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M GLY 2.9 14.0 + - - -
118M LEU* 3.2 15.7 - - + -
120M MET* 1.3 75.9 - - - +
122M LEU* 1.3 65.8 + - + +
124M LEU* 3.4 10.3 + - + +
125M GLY* 3.0 22.7 + - - -
152M ILE* 5.9 0.7 - - + +
156M LEU* 4.2 22.6 - - + +
600M NS5 3.6 33.9 - - + +
704M LDA 5.7 0.3 - - - +
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Residues in contact with LEU 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M PHE* 3.7 39.5 - - + -
118M LEU* 3.3 38.6 - - + +
119M PHE* 3.0 14.2 + - + +
121M THR* 1.3 77.5 - - + +
123M SER* 1.3 60.6 + - - +
125M GLY* 3.1 1.9 + - - -
126M SER* 2.6 35.3 + - - -
704M LDA 3.8 25.6 - - + +
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Residues in contact with SER 123 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401L BPB 2.9 35.0 - - - +
58M ALA* 3.5 10.7 + - - +
61M PHE* 3.7 5.8 - - - +
62M GLY* 3.5 24.7 - - - -
119M PHE 2.8 12.2 + - - -
120M MET* 3.1 13.6 + - - -
122M LEU* 1.3 78.1 - - - +
124M LEU* 1.3 62.4 + - - +
126M SER* 3.4 5.9 + - - -
127M TRP* 3.1 18.2 + - - +
806M BCB 4.7 2.5 - - - +
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Residues in contact with LEU 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401L BPB 3.2 27.4 - - - +
120M MET* 2.8 42.6 + - + +
121M THR* 3.6 10.5 - - - +
123M SER* 1.3 74.4 - - - +
125M GLY* 1.3 57.3 + - - +
127M TRP* 3.3 4.5 + - - +
128M TRP* 2.9 26.7 + - - +
148M PHE* 4.3 1.8 - - + -
152M ILE* 4.0 35.3 - - + +
155M VAL* 4.7 5.4 - - + -
156M LEU* 5.9 2.0 - - + -
806M BCB 3.9 50.3 - - + -
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Residues in contact with GLY 125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M THR 3.0 13.8 + - - -
122M LEU 3.1 2.7 + - - -
124M LEU* 1.3 74.0 - - - +
126M SER* 1.3 66.5 + - - +
128M TRP* 2.8 20.3 + - - +
129M ILE* 3.0 16.0 + - - +
152M ILE* 5.4 2.2 - - - +
704M LDA 3.9 13.7 - - - -
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Residues in contact with SER 126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M SER* 3.2 35.3 - - - +
57M ALA* 3.8 10.3 - - - -
58M ALA* 3.5 9.6 - - - -
61M PHE* 3.6 14.2 - - - -
122M LEU 2.6 22.8 + - - -
123M SER 3.4 3.3 + - - -
125M GLY* 1.3 70.4 - - - +
127M TRP* 1.3 61.7 + - - +
129M ILE* 3.3 7.8 + - - +
130M ARG* 3.1 17.0 + - - +
704M LDA 3.5 17.7 - - - +
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Residues in contact with TRP 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219L VAL* 3.6 21.5 - - + -
220L VAL* 4.7 6.1 - - + -
401L BPB 2.7 67.4 + + + +
49M ILE* 6.2 0.2 - - + -
55M GLY* 4.8 7.0 - - - -
58M ALA* 3.7 21.2 - - + +
59M PHE* 5.7 1.1 - - + -
123M SER 3.1 13.3 + - - +
124M LEU 3.5 9.0 - - - +
125M GLY 3.0 0.6 - - - -
126M SER* 1.3 75.2 - - - +
128M TRP* 1.3 59.6 + - - +
130M ARG* 3.2 38.9 + - - +
131M VAL* 2.9 31.6 + - + +
148M PHE* 3.5 20.6 - + - -
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Residues in contact with TRP 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M LEU 2.9 12.6 + - - +
125M GLY* 2.8 12.0 + - - +
127M TRP* 1.3 75.5 - - - +
129M ILE* 1.3 71.8 + - + +
131M VAL* 3.1 2.6 + - - +
132M TYR* 2.8 61.0 + + + +
145M ALA* 2.8 38.3 + - + -
146M TRP* 3.8 35.2 - + - -
148M PHE* 3.6 28.2 - + - -
149M ALA* 3.5 14.3 - - + +
152M ILE* 3.8 17.3 - - + -
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Residues in contact with ILE 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M SER* 3.6 14.8 - - - -
125M GLY 3.0 14.2 + - - +
126M SER* 3.4 15.3 - - - +
128M TRP* 1.3 90.6 - - + +
130M ARG* 1.3 52.1 + - - +
132M TYR* 3.5 4.8 - - + +
133M SER* 2.5 41.3 + - - +
704M LDA 3.7 57.2 - - + -
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Residues in contact with ARG 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218L ASP 3.1 18.1 + - - -
219L VAL* 2.8 36.7 + - + +
49M ILE* 3.7 10.7 - - - +
50M TYR* 3.1 19.9 + - - -
51M LEU 2.7 29.9 + - - -
54M SER* 3.3 19.1 + - - +
55M GLY* 4.0 12.5 - - - +
126M SER 3.1 10.6 + - - +
127M TRP* 3.3 44.1 - - + +
129M ILE* 1.3 74.5 - - - +
131M VAL* 1.3 63.5 + - - +
133M SER* 4.3 2.2 - - - -
134M ARG* 3.0 34.0 + - + +
804M SO4 4.3 6.5 - - - +
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Residues in contact with VAL 131 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215L TYR* 2.6 37.3 + - - +
219L VAL* 4.1 14.6 - - + -
401L BPB 3.5 29.4 - - + +
127M TRP* 2.9 46.2 + - + +
128M TRP 3.6 4.5 - - - +
130M ARG* 1.3 74.6 - - - +
132M TYR* 1.3 61.9 + - - +
135M ALA* 4.0 2.8 + - - +
144M ILE* 4.1 1.6 - - + -
145M ALA* 3.6 31.3 + - + +
148M PHE* 4.3 7.6 - - + -
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Residues in contact with TYR 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128M TRP* 2.8 45.7 + + + +
129M ILE* 3.5 5.6 - - + +
131M VAL* 1.3 75.3 - - - +
133M SER* 1.3 71.5 + - - +
135M ALA* 3.3 8.7 + - - +
136M ARG* 3.3 36.1 + - + +
142M THR* 3.5 28.7 - - + +
145M ALA* 3.6 25.4 - - + -
146M TRP* 4.2 10.7 - + - -
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Residues in contact with SER 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M TRP* 3.8 12.5 - - - -
129M ILE* 2.5 28.1 + - - +
130M ARG* 3.9 3.4 - - - -
132M TYR* 1.3 74.9 - - - +
134M ARG* 1.3 57.2 + - - +
135M ALA 3.0 2.2 - - - -
136M ARG* 3.0 6.0 + - - +
137M ALA* 2.6 37.4 + - - +
704M LDA 2.8 34.1 - - - -
804M SO4 3.7 11.9 - - - -
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Residues in contact with ARG 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215L TYR* 3.8 20.2 - - + -
218L ASP* 3.0 44.4 + - + -
219L VAL* 4.0 12.6 - - + +
21M GLY* 4.7 2.6 - - - -
23M TRP* 3.0 52.9 + - - +
28M ARG* 3.5 15.0 - - - +
50M TYR* 3.4 42.2 - - + -
130M ARG* 3.0 23.1 + - + +
133M SER* 1.3 75.7 - - - +
135M ALA* 1.3 62.0 + - - +
137M ALA* 3.4 19.8 - - - +
138M LEU* 3.0 31.9 + - + +
804M SO4 5.2 1.2 + - - +
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Residues in contact with ALA 135 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196L SER* 5.8 0.4 - - - -
215L TYR* 3.4 21.6 - - + -
131M VAL 4.2 4.0 - - - +
132M TYR 3.3 11.3 + - - +
133M SER 3.0 0.8 - - - -
134M ARG* 1.3 79.1 - - - +
136M ARG* 1.3 55.1 + - - +
138M LEU 3.1 1.4 + - - -
139M GLY 2.9 9.5 + - - -
140M LEU* 2.7 41.0 + - + +
141M GLY 3.6 25.6 - - - +
142M THR* 4.6 6.3 - - + -
144M ILE* 6.5 1.1 - - + -
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Residues in contact with ARG 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200L PRO 3.1 26.0 + - - -
201L GLY* 5.6 1.2 - - - -
202L ASP* 4.6 12.1 + - - -
204L ASP* 4.2 13.1 + - - -
22M GLU* 4.5 10.7 - - - +
23M TRP* 4.5 12.8 - - + -
132M TYR* 3.3 32.5 + - + +
133M SER* 3.0 9.7 + - - +
135M ALA* 1.3 77.8 - - - +
137M ALA* 1.3 65.2 + - - +
139M GLY* 2.8 18.9 + - - -
140M LEU 3.2 21.3 + - - +
141M GLY* 5.2 0.9 - - - -
142M THR* 4.0 21.1 - - + +
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Residues in contact with ALA 137 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M SER 4.5 0.5 - - - +
21M GLY* 3.2 3.4 - - - -
22M GLU* 2.7 42.6 + - - +
23M TRP* 4.0 14.9 - - + +
133M SER 2.6 19.6 + - - +
134M ARG* 3.4 39.7 - - - +
136M ARG* 1.3 73.4 - - - +
138M LEU* 1.3 59.5 + - - +
139M GLY 3.2 0.6 + - - -
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Residues in contact with LEU 138 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207L LYS* 4.1 2.3 - - - -
211L HIS* 3.3 29.3 + - + +
214L GLN* 3.8 21.8 - - + -
215L TYR* 3.8 36.8 - - + +
218L ASP* 3.9 17.3 - - - +
19M VAL* 3.8 27.8 - - + +
20M SER 4.0 10.2 - - - +
21M GLY* 4.0 7.2 - - - +
28M ARG* 4.3 2.0 - - - +
134M ARG* 3.0 24.9 + - - +
135M ALA 4.0 1.8 - - - +
137M ALA* 1.3 76.8 - - - +
139M GLY* 1.3 62.6 + - - +
140M LEU* 3.5 12.6 - - + -
----------------------------------------------------------
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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