Contacts of the helix formed by residues 93 - 120 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E ASP* 3.0 37.7 + - + +
91E ALA 3.0 0.6 - - - -
92E GLU* 1.3 86.1 + - - +
94E ALA* 1.3 62.0 + - - +
95E THR* 3.0 8.1 - - - +
96E SER* 3.0 32.4 + - - +
97E ILE* 3.4 11.2 + - + +
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Residues in contact with ALA 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E MET* 3.6 32.5 - - + +
90E ASP 3.3 4.6 + - - +
91E ALA* 2.9 19.2 + - - +
93E ASN* 1.3 77.8 - - - +
95E THR* 1.3 62.7 + - - +
96E SER 3.5 0.3 + - - -
97E ILE* 4.1 1.6 - - - -
98E VAL* 3.3 27.4 + - - +
263E TRP* 5.3 0.5 - - - -
270E LEU* 5.2 8.1 - - + -
274E PHE* 4.9 6.2 - - + -
275E THR* 3.9 15.7 - - + -
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Residues in contact with THR 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E ALA 4.6 0.8 + - - -
92E GLU 4.5 9.0 + - - -
93E ASN* 4.6 3.4 - - - -
94E ALA* 1.3 81.2 - - - +
96E SER* 1.3 63.1 + - - +
98E VAL* 4.0 2.4 + - - +
99E GLU* 2.9 43.2 + - - +
263E TRP* 4.8 5.0 + - - -
267E LYS* 4.0 26.3 - - + +
270E LEU* 5.6 6.8 - - - +
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Residues in contact with SER 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E ASN* 3.0 26.3 + - - +
95E THR* 1.3 78.8 - - - +
97E ILE* 1.3 74.7 + - - +
99E GLU* 2.9 21.8 + - - +
100E ASP* 3.0 20.4 + - - +
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Residues in contact with ILE 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E LEU* 3.7 30.8 - - + +
86E LEU* 3.6 35.0 - - + +
87E MET* 3.7 33.9 - - + +
90E ASP* 5.0 2.9 - - + +
93E ASN* 3.4 14.1 + - + +
94E ALA* 4.2 1.3 - - - +
95E THR 3.5 0.4 - - - -
96E SER* 1.3 84.3 + - - +
98E VAL* 1.3 64.0 + - - +
100E ASP* 2.9 22.2 + - - +
101E LEU* 3.0 10.9 + - - +
211E LEU* 3.9 19.7 - - + -
199F GLN* 4.9 6.5 - - - +
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Residues in contact with VAL 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E MET* 4.1 17.9 - - + -
94E ALA 3.3 17.9 + - - +
95E THR 4.3 1.6 - - - +
96E SER 3.3 0.4 - - - -
97E ILE* 1.3 75.3 - - + +
99E GLU* 1.3 58.8 + - - +
101E LEU* 2.9 11.2 + - + +
102E LEU* 2.7 40.4 + - + +
211E LEU* 5.2 1.1 - - + -
215E VAL* 3.7 41.3 - - + -
263E TRP* 3.6 39.9 - - + -
274E PHE* 4.6 2.7 - - + -
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Residues in contact with GLU 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E THR* 2.9 41.8 - - - +
96E SER* 2.9 8.0 + - - +
98E VAL* 1.3 72.1 - - - +
100E ASP* 1.3 63.6 + - - +
102E LEU* 3.8 9.9 - - + +
103E ALA* 3.0 27.9 + - - +
263E TRP* 3.9 20.2 - - + +
264E ASN* 5.2 2.5 - - - +
267E LYS* 4.2 17.9 + - - +
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Residues in contact with ASP 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E LEU* 5.7 2.6 - - + +
96E SER* 3.0 18.7 + - - +
97E ILE* 2.9 15.5 + - + +
99E GLU* 1.3 77.6 - - - +
101E LEU* 1.3 57.5 + - - +
103E ALA* 2.9 2.2 + - - +
104E ALA* 2.8 33.3 + - - +
197F GLY 3.5 15.7 - - - +
198F ASN* 3.3 31.5 + - - +
199F GLN* 3.6 26.2 + - + +
200F ILE* 3.9 9.0 - - + +
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E ILE 3.0 9.9 + - - +
98E VAL* 2.9 10.2 + - + +
100E ASP* 1.3 76.5 - - - +
102E LEU* 1.3 67.3 + - + +
104E ALA* 4.1 0.7 - - + +
105E ARG* 3.3 25.2 + - + +
208E LEU* 3.9 29.8 - - + +
211E LEU* 3.6 41.5 - - + +
212E TYR* 4.1 29.8 - - + -
215E VAL* 3.9 24.0 - - + -
200F ILE* 3.6 9.1 - - + +
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E VAL* 2.7 42.1 + - + +
99E GLU* 4.1 7.9 - - + +
101E LEU* 1.3 77.8 - - + +
103E ALA* 1.3 58.3 + - - +
105E ARG* 4.1 28.5 + - - +
106E THR* 2.5 35.0 + - - -
215E VAL* 4.9 10.8 - - + -
259E SER* 5.6 2.5 - - - +
260E GLY* 5.8 4.0 - - - -
263E TRP* 3.9 33.2 - - + -
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Residues in contact with ALA 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E GLU 3.0 18.8 + - - +
100E ASP* 2.9 5.5 + - - +
102E LEU* 1.3 75.4 - - - +
104E ALA* 1.3 61.1 + - - +
106E THR* 2.9 7.9 + - - -
107E ASN* 2.8 40.5 + - - +
198F ASN* 3.7 11.9 - - - +
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Residues in contact with ALA 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E ASP 2.8 19.3 + - - +
101E LEU* 4.1 1.3 - - + +
103E ALA* 1.3 72.3 - - - +
105E ARG* 1.3 63.6 + - - +
107E ASN* 2.9 2.8 + - - +
108E ILE* 2.9 35.4 + - + +
208E LEU* 5.7 0.9 - - + -
198F ASN* 3.5 9.3 - - - +
200F ILE* 3.6 34.1 - - + -
201F TYR* 3.9 18.2 - - + +
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Residues in contact with ARG 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E LEU* 3.3 18.9 + - + +
102E LEU* 4.1 26.5 + - - +
103E ALA 3.3 0.6 - - - -
104E ALA* 1.3 79.0 - - - +
106E THR* 1.3 63.4 + - - +
108E ILE* 4.3 8.3 - - - -
109E SER* 2.2 45.2 + - - +
185E ASP* 3.7 10.5 + - - -
189E PHE* 3.6 29.6 - - + -
205E PHE* 4.0 13.0 - - + -
212E TYR* 3.0 42.7 + - + -
219E TYR* 6.3 0.6 - - - -
220E PHE* 6.1 0.6 - - - -
255E TYR* 3.7 26.1 + - - -
256E GLY* 6.2 0.4 - - - -
259E SER* 4.7 7.7 + - - -
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Residues in contact with THR 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E LEU 2.5 24.4 + - - -
103E ALA* 2.9 8.1 + - - -
105E ARG* 1.3 83.2 + - - +
107E ASN* 1.3 63.6 + - - +
110E PRO* 3.3 17.3 - - - +
252E ILE* 3.8 31.0 - - + +
253E ARG* 4.3 18.2 - - + +
256E GLY* 4.1 18.9 - - - -
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Residues in contact with ASN 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E ALA* 2.8 28.7 + - - +
104E ALA 2.9 2.4 + - - +
106E THR* 1.3 83.5 - - - +
108E ILE* 1.3 58.9 + - - +
109E SER 3.4 0.2 - - - -
110E PRO* 3.3 14.0 - - - +
111E ILE* 4.0 9.4 - - - +
111F ILE* 3.7 26.9 - - + +
115F TYR* 4.2 24.1 + - - -
198F ASN* 4.6 0.8 - - - +
201F TYR* 2.8 37.5 + - - +
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Residues in contact with ILE 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E ALA* 2.9 26.2 + - + +
105E ARG* 4.2 4.7 - - - +
107E ASN* 1.3 76.6 - - + +
109E SER* 1.3 66.2 + - - +
110E PRO 3.4 1.3 - - - -
111E ILE* 3.1 20.9 + - + +
112E PHE* 3.0 26.8 + - + -
201E TYR* 4.8 11.9 - - + +
204E ILE* 4.4 34.8 - - + -
205E PHE* 4.7 12.6 - - + -
108F ILE* 4.4 16.6 - - + -
111F ILE* 5.4 2.5 - - + -
200F ILE* 6.3 0.9 - - + -
201F TYR* 4.0 24.9 - - + +
204F ILE* 5.8 3.4 - - + -
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Residues in contact with SER 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E ARG* 2.2 31.4 + - - +
108E ILE* 1.3 72.7 - - - +
110E PRO* 1.3 71.8 - - - +
111E ILE 3.0 1.6 - - - -
112E PHE* 3.4 17.4 - - - -
113E MET* 3.1 37.3 + - - +
189E PHE* 3.6 18.9 - - - -
252E ILE* 3.6 20.6 - - - -
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Residues in contact with PRO 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E THR 3.3 22.2 - - - +
107E ASN 3.3 12.1 - - - +
109E SER* 1.3 91.6 - - - +
111E ILE* 1.3 59.4 + - + +
114E ARG* 3.2 29.8 + - - +
248E LEU* 3.7 14.8 - - + +
249E PRO* 4.6 17.9 - - + +
252E ILE* 3.4 24.0 - - + -
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Residues in contact with ILE 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E ASN 4.0 7.6 - - - +
108E ILE* 3.2 24.7 - - + +
109E SER 3.0 1.2 - - - -
110E PRO* 1.3 81.9 - - + +
112E PHE* 1.3 60.3 + - - +
114E ARG* 3.2 23.2 - - - +
115E TYR* 3.4 16.2 - - + -
201E TYR* 3.2 32.1 - - + +
107F ASN* 3.7 34.3 - - + +
108F ILE* 5.4 1.8 - - + -
111F ILE* 4.9 12.6 - - + -
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Residues in contact with PHE 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E ILE* 3.0 23.3 + - + -
109E SER* 3.4 31.0 - - - -
111E ILE* 1.3 76.1 - - - +
113E MET* 1.3 99.4 + - + +
114E ARG 3.2 1.8 - - - -
115E TYR* 3.5 2.8 + - - -
116E ALA* 3.0 28.2 + - - +
189E PHE* 3.7 18.4 - + - -
192E LEU* 3.6 5.6 - - + -
193E ALA* 3.4 21.5 - - + -
196E SER* 3.3 20.0 - - - +
201E TYR* 3.8 33.0 - + + -
205E PHE* 3.6 32.8 - + - -
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Residues in contact with MET 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E SER* 3.1 17.4 + - - +
112E PHE* 1.3 95.5 - - + +
114E ARG* 1.3 67.2 + - - +
116E ALA* 3.0 6.5 + - - +
117E PHE* 2.8 43.5 + - + -
188E LEU* 4.4 2.2 - - + -
189E PHE* 3.6 37.7 - - + -
192E LEU* 4.1 22.4 - - + -
232E PHE* 5.0 0.7 - - + -
236E LEU* 4.0 34.1 - - + -
248E LEU* 4.5 6.7 - - + -
252E ILE* 3.8 22.4 - - + -
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Residues in contact with ARG 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E PRO 3.2 22.8 + - - +
111E ILE* 3.2 11.0 - - - +
113E MET* 1.3 82.0 - - - +
115E TYR* 1.3 84.2 + - - +
117E PHE* 3.0 13.4 + - - +
118E LYS* 3.0 49.4 + - - +
245E ARG* 3.8 36.4 - - + +
248E LEU* 4.7 9.0 - - + +
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Residues in contact with TYR 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E ILE* 3.4 23.3 + - + +
112E PHE* 3.5 7.9 + - - +
114E ARG* 1.3 104.1 - - - +
116E ALA* 1.3 58.3 + - - +
118E LYS* 3.0 15.3 + - - -
119E LEU* 2.8 45.1 + - + +
196E SER* 3.6 25.4 - - - +
198E ASN* 6.3 1.6 - - + -
201E TYR* 5.4 4.0 - + - -
107F ASN* 3.8 34.7 + - - -
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Residues in contact with ALA 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E PHE 3.0 19.0 + - - +
113E MET* 3.0 9.2 + - - +
115E TYR* 1.3 77.7 - - - +
117E PHE* 1.3 66.1 + - + +
120E ASN* 3.1 30.9 + - - +
124E ALA* 4.0 2.1 - - + +
192E LEU* 3.6 24.5 - - + +
195E HIS* 3.2 28.2 - - + +
196E SER* 4.0 0.2 - - - +
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Residues in contact with PHE 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E MET* 2.8 32.1 + - + +
114E ARG* 3.0 6.7 + - - +
116E ALA* 1.3 83.0 - - + +
118E LYS* 1.3 60.2 + - + +
121E LYS* 3.4 24.6 - - - +
124E ALA* 3.9 9.2 - - + -
128E MET* 3.8 26.9 - - + -
192E LEU* 4.1 13.9 - - + -
236E LEU* 3.9 23.1 - - + -
239E VAL* 4.1 10.8 - - + -
240E CYS* 3.5 40.1 - - + +
243E GLY* 6.1 0.7 - - - -
245E ARG* 5.4 10.1 - - + -
248E LEU* 4.0 25.4 - - + -
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Residues in contact with LYS 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E ARG* 3.0 41.8 - - - +
115E TYR* 3.0 15.3 + - - +
117E PHE* 1.3 83.0 - - - +
119E LEU* 1.3 76.3 + - + +
120E ASN 3.6 0.2 - - - -
121E LYS* 4.3 5.8 + - - +
245E ARG* 3.1 44.1 - - - +
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Residues in contact with LEU 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E TYR* 2.8 32.0 + - + +
118E LYS* 1.3 86.3 - - + +
120E ASN* 1.3 73.4 - - - +
121E LYS 3.7 1.7 + - - -
195E HIS 4.8 2.7 - - - +
196E SER 3.7 21.5 - - - +
197E GLY* 4.6 7.4 - - - -
----------------------------------------------------------
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Residues in contact with ASN 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E ALA 3.1 12.3 + - - +
119E LEU* 1.3 86.7 - - - +
121E LYS* 1.3 64.3 + - - +
122E GLU 3.5 1.8 - - - -
123E SER* 4.0 22.1 + - - +
124E ALA* 3.0 16.1 + - - +
195E HIS* 3.6 43.0 + - + +
197E GLY* 5.2 4.4 - - - +
----------------------------------------------------------
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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