Contacts of the helix formed by residues 93 - 120 (chain F) in PDB entry 4P9U
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 93 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ASP* 3.0 25.5 + - - +
92F GLU* 1.3 105.0 + - - +
94F ALA* 1.3 56.5 + - - +
95F THR* 2.9 8.6 - - - +
96F SER* 2.9 43.0 + - - +
97F ILE* 3.4 9.7 + - + +
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Residues in contact with ALA 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F MET* 3.5 35.0 - - + +
90F ASP 3.5 2.6 + - - -
91F ALA* 2.9 21.3 + - - +
93F ASN* 1.3 79.2 - - - +
95F THR* 1.3 61.3 + - - +
97F ILE* 3.5 5.5 + - - -
98F VAL* 3.3 29.4 + - - +
270F LEU* 6.0 3.8 - - + -
274F PHE* 5.3 3.4 - - + -
275F THR* 4.0 14.8 - - + -
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Residues in contact with THR 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ALA 4.3 1.1 + - - -
92F GLU 4.2 10.5 + - - -
93F ASN* 3.8 4.7 - - - +
94F ALA* 1.3 80.3 - - - +
96F SER* 1.3 63.3 + - - +
98F VAL* 3.8 4.2 + - - +
99F GLU* 3.2 40.3 + - - +
263F TRP* 4.9 5.9 + - - +
267F LYS* 4.3 21.8 - - + +
270F LEU* 5.4 8.4 - - - +
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Residues in contact with SER 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F ASN* 2.9 32.5 + - - +
95F THR* 1.3 78.2 - - - +
97F ILE* 1.3 79.7 + - - +
99F GLU* 2.9 24.8 + - - +
100F ASP* 3.1 18.8 + - - +
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Residues in contact with ILE 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E GLN* 5.4 3.4 - - - +
83F LEU* 4.1 20.7 - - + +
86F LEU* 3.8 19.3 - - + +
87F MET* 3.6 57.2 - - + +
90F ASP* 4.8 4.3 - - - +
93F ASN* 3.5 15.3 - - + +
94F ALA* 3.8 2.5 - - - +
95F THR 3.4 0.2 - - - -
96F SER* 1.3 84.6 + - - +
98F VAL* 1.3 63.3 + - - +
100F ASP* 2.9 22.0 + - - +
101F LEU* 3.1 10.9 + - - +
211F LEU* 4.0 19.7 - - + +
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Residues in contact with VAL 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F MET* 4.1 15.0 - - + -
94F ALA 3.3 17.5 + - - +
95F THR 4.2 2.7 - - - +
96F SER 3.3 0.4 - - - -
97F ILE* 1.3 76.2 - - + +
99F GLU* 1.3 57.6 - - - +
101F LEU* 2.9 10.8 + - + +
102F LEU* 2.9 35.8 + - + +
211F LEU* 5.6 0.4 - - - -
215F VAL* 3.8 39.3 - - + -
263F TRP* 3.5 42.0 - - + +
274F PHE* 4.8 3.4 - - + -
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Residues in contact with GLU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F THR* 3.2 38.6 - - - +
96F SER* 2.9 10.8 + - - +
98F VAL* 1.3 75.7 - - - +
100F ASP* 1.3 61.4 + - - +
102F LEU* 4.0 9.4 - - - +
103F ALA* 3.1 26.5 + - - +
263F TRP* 4.4 16.1 + - + +
264F ASN* 5.9 2.5 - - - +
267F LYS* 3.7 15.6 + - - +
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Residues in contact with ASP 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E GLY 3.9 13.7 - - - +
198E ASN* 3.3 31.3 + - - +
199E GLN* 3.9 23.7 + - + +
200E ILE* 3.9 8.5 - - + -
83F LEU* 5.8 4.0 - - + +
96F SER* 3.1 18.1 + - - +
97F ILE* 2.9 15.6 + - + +
99F GLU* 1.3 78.7 - - - +
101F LEU* 1.3 61.0 + - - +
103F ALA* 2.9 1.6 + - - +
104F ALA* 2.9 31.5 + - - +
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Residues in contact with LEU 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E ILE* 3.7 8.7 - - + +
97F ILE 3.1 10.1 + - - +
98F VAL* 2.9 10.0 + - + +
100F ASP* 1.3 75.7 - - - +
102F LEU* 1.3 65.3 + - + +
104F ALA* 4.4 0.9 - - - +
105F ARG* 3.4 25.5 + - + +
205F PHE* 6.5 0.4 - - + -
208F LEU* 3.9 31.0 - - + -
211F LEU* 3.7 39.0 - - + +
212F TYR* 4.0 39.5 - - + -
215F VAL* 4.1 17.7 - - + -
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Residues in contact with LEU 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F VAL* 2.9 27.8 + - + +
99F GLU* 4.2 7.0 - - - +
101F LEU* 1.3 82.2 - - + +
103F ALA* 1.3 57.0 + - - +
105F ARG* 3.7 31.7 + - - +
106F THR* 2.5 35.8 + - - +
215F VAL* 5.4 8.1 - - + -
219F TYR* 6.4 2.0 - - + -
259F SER* 5.2 8.5 - - - +
260F GLY* 5.5 5.4 - - - -
263F TRP* 3.9 38.8 - - + -
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Residues in contact with ALA 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E ASN* 3.7 11.9 - - - +
99F GLU 3.1 20.3 + - - +
100F ASP* 2.9 5.2 + - - +
102F LEU* 1.3 73.2 - - - +
104F ALA* 1.3 68.2 + - - +
106F THR* 2.9 7.7 + - - -
107F ASN* 2.9 33.8 + - - +
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Residues in contact with ALA 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E ASN* 3.6 8.2 - - - +
200E ILE* 3.7 34.1 - - + -
201E TYR* 3.8 19.7 - - + +
100F ASP 2.9 15.0 + - - +
101F LEU 4.4 0.9 - - - +
103F ALA* 1.3 75.2 - - - +
105F ARG* 1.3 58.9 + - - +
107F ASN* 2.9 4.7 + - - +
108F ILE* 2.9 39.7 + - + +
208F LEU* 6.0 0.7 - - + -
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Residues in contact with ARG 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F LEU* 3.4 19.6 + - + +
102F LEU* 3.8 31.1 + - - +
103F ALA 3.2 0.4 - - - -
104F ALA* 1.3 78.8 - - - +
106F THR* 1.3 59.4 + - - +
108F ILE* 4.3 8.3 - - - +
109F SER* 2.2 47.0 + - - +
185F ASP* 3.8 6.9 + - - -
189F PHE* 3.6 32.2 - - + -
205F PHE* 4.0 13.0 - - + -
212F TYR* 2.6 52.1 + - + -
219F TYR* 6.4 0.6 - - - -
220F PHE* 6.1 0.4 - - - -
255F TYR* 3.9 24.8 + - - -
256F GLY* 6.2 0.4 - - - -
259F SER* 4.6 8.7 + - - -
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Residues in contact with THR 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F LEU* 2.5 24.6 + - - +
103F ALA* 2.9 8.5 + - - -
105F ARG* 1.3 83.1 + - - +
107F ASN* 1.3 64.2 + - - +
109F SER* 4.4 0.9 - - - -
110F PRO* 3.3 17.8 - - - +
252F ILE* 3.9 17.8 - - + +
253F ARG* 4.1 15.5 - - + +
256F GLY* 4.0 28.9 + - - -
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Residues in contact with ASN 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E ILE* 3.7 24.1 - - + +
115E TYR* 3.8 32.4 + - - -
198E ASN* 4.9 0.8 - - - +
201E TYR* 2.7 34.4 + - - +
103F ALA* 2.9 26.6 + - - +
104F ALA* 2.9 3.5 + - - +
106F THR* 1.3 84.3 - - - +
108F ILE* 1.3 60.0 + - + +
109F SER 3.4 0.2 - - - -
110F PRO* 3.3 14.2 - - - +
111F ILE* 4.0 9.0 - - - +
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Residues in contact with ILE 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E ILE* 4.4 17.3 - - + -
111E ILE* 5.4 2.5 - - + -
200E ILE* 6.3 0.7 - - + -
201E TYR* 4.2 24.5 - - + +
204E ILE* 5.8 3.6 - - + -
104F ALA* 2.9 27.3 + - + +
105F ARG* 4.2 5.8 - - - +
107F ASN* 1.3 77.5 - - + +
109F SER* 1.3 66.1 + - - +
110F PRO 3.4 1.1 - - - -
111F ILE* 3.1 24.7 + - + +
112F PHE* 3.1 23.1 - - + -
201F TYR* 4.8 11.2 - - + +
204F ILE* 4.5 32.1 - - + -
205F PHE* 4.6 14.1 - - + -
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Residues in contact with SER 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F ARG* 2.2 29.8 + - - +
106F THR* 4.4 0.3 - - - -
108F ILE* 1.3 76.3 - - - +
110F PRO* 1.4 71.1 - - - +
111F ILE 3.1 0.7 + - - -
112F PHE* 3.7 10.9 - - - -
113F MET* 3.1 39.8 + - - +
189F PHE* 3.6 20.8 - - - -
252F ILE* 3.5 22.6 - - - +
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Residues in contact with PRO 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F THR 3.3 16.2 - - - +
107F ASN 3.3 18.4 - - - +
109F SER* 1.4 93.0 - - - +
111F ILE* 1.3 62.9 + - + +
114F ARG* 3.3 24.2 + - - +
248F LEU* 3.7 11.3 - - + +
249F PRO* 4.3 23.1 - - + +
252F ILE* 3.6 23.8 - - + -
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Residues in contact with ILE 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E ASN* 3.7 35.4 - - + +
108E ILE* 5.4 1.3 - - + -
111E ILE* 4.9 12.1 - - + -
107F ASN 4.0 7.2 - - - +
108F ILE* 3.2 26.2 - - + +
109F SER 3.0 1.2 - - - -
110F PRO* 1.3 84.8 - - + +
112F PHE* 1.3 62.5 + - - +
114F ARG* 3.7 3.1 - - - +
115F TYR* 3.1 31.9 + - + -
201F TYR* 3.2 33.7 - - + +
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Residues in contact with PHE 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F ILE* 3.1 30.9 + - + -
109F SER* 3.7 18.6 - - - -
111F ILE* 1.3 76.7 - - - +
113F MET* 1.3 87.6 - - + +
114F ARG 3.1 1.8 - - - -
115F TYR* 3.0 5.0 + - - +
116F ALA* 2.7 36.4 + - - +
189F PHE* 3.8 18.8 - + - -
192F LEU* 3.6 10.1 - - + -
193F ALA* 3.5 28.9 - - + -
196F SER* 3.7 23.5 - - - +
201F TYR* 3.9 31.6 - + + -
205F PHE* 3.8 28.3 - + - -
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Residues in contact with MET 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F SER* 3.1 16.6 + - - +
112F PHE* 1.3 99.0 - - + +
114F ARG* 1.3 60.5 + - - +
116F ALA* 4.2 5.4 - - - -
117F PHE* 3.0 41.4 + - + -
188F LEU* 4.4 2.5 - - + -
189F PHE* 3.7 37.2 - - + -
192F LEU* 4.1 23.3 - - + -
232F PHE* 4.8 1.1 - - + -
236F LEU* 3.9 33.7 - - + -
248F LEU* 4.1 10.3 - - + -
252F ILE* 3.7 23.6 - - - -
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Residues in contact with ARG 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E ARG* 5.5 9.1 - - - +
110F PRO 3.3 21.7 + - - +
111F ILE* 3.7 5.2 - - - +
112F PHE 3.1 0.2 - - - -
113F MET* 1.3 77.8 - - - +
115F TYR* 1.3 106.0 + - - +
117F PHE* 3.0 16.0 + - - +
118F LYS* 3.2 32.9 + - + +
245F ARG* 3.4 48.0 - - + +
248F LEU* 4.4 8.2 - - + +
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Residues in contact with TYR 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E ASN* 4.2 29.4 + - - -
253E ARG* 4.8 12.1 + - - -
111F ILE* 3.1 28.6 + - + -
112F PHE* 3.0 7.6 + - - +
114F ARG* 1.3 109.9 + - - +
116F ALA* 1.3 58.8 + - - +
118F LYS* 3.0 11.3 + - + +
119F LEU* 2.9 47.8 + - + +
196F SER* 3.7 23.1 - - - +
201F TYR* 5.8 2.9 - + - -
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Residues in contact with ALA 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F PHE 2.7 21.0 + - - +
113F MET* 4.0 7.4 - - - +
115F TYR* 1.3 71.8 - - - +
117F PHE* 1.3 67.1 + - + +
120F ASN* 3.2 30.3 + - - +
124F ALA* 3.9 1.6 - - + +
192F LEU* 3.5 28.7 - - + +
195F HIS* 3.3 28.2 - - + +
196F SER* 3.9 1.0 - - - +
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Residues in contact with PHE 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F MET* 3.0 31.6 + - + +
114F ARG* 3.0 7.8 + - - +
116F ALA* 1.3 80.9 - - + +
118F LYS* 1.3 59.4 + - + +
121F LYS* 3.5 23.5 - - - +
124F ALA* 4.0 9.6 - - + -
128F MET* 4.0 19.3 - - - -
192F LEU* 4.3 12.3 - - + -
236F LEU* 3.7 32.5 - - + -
239F VAL* 3.9 13.2 - - + -
240F CYS* 3.6 39.5 - - + +
243F GLY* 6.1 1.4 - - - -
245F ARG* 5.6 8.1 - - + -
248F LEU* 3.8 25.1 - - + -
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Residues in contact with LYS 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F ARG* 3.3 47.1 - - - +
115F TYR* 3.0 13.5 + - + +
117F PHE* 1.3 81.1 - - - +
119F LEU* 1.3 73.8 + - + +
121F LYS* 4.4 5.1 + - - +
245F ARG* 3.7 45.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F TYR* 2.9 43.2 + - + +
118F LYS* 1.3 88.2 - - + +
120F ASN* 1.3 72.8 + - - +
121F LYS 3.8 1.7 + - - -
122F GLU* 4.6 1.4 - - - +
195F HIS 4.7 5.4 - - - +
196F SER 4.5 11.0 - - - +
197F GLY* 5.5 4.0 - - - +
----------------------------------------------------------
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Residues in contact with ASN 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F ALA 3.2 9.2 + - - +
119F LEU* 1.3 89.7 - - - +
121F LYS* 1.3 53.7 + - - +
122F GLU* 2.8 24.6 - - - +
123F SER* 4.0 11.9 - - - +
124F ALA* 2.9 29.5 + - - +
195F HIS* 3.5 41.7 + - + +
197F GLY* 5.3 3.4 - - - +
----------------------------------------------------------
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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