Contacts of the helix formed by residues 127 - 157 (chain K) in PDB entry 3A68
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 127 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123K HIS* 2.9 19.9 + - - -
124K ALA 4.1 0.4 + - - -
125K ASP 3.4 2.2 + - - -
126K LYS* 1.3 79.9 - - - +
128K ASP* 1.3 66.8 + - - -
129K ALA 3.4 2.6 + - - -
130K LEU 3.5 1.4 + - - -
131K HIS* 3.1 22.9 + - - +
193K LYS* 3.9 17.6 - - - +
197K VAL* 6.5 0.2 - - - -
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Residues in contact with ASP 128 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D ARG* 3.0 41.5 + - - -
69K TYR* 4.2 8.2 + - + +
70K PHE* 3.6 15.4 - - + -
75K VAL* 3.7 15.2 - - - +
77K LEU* 3.8 1.7 - - - +
121K PHE 3.6 20.6 - - - +
122K ASP* 3.9 21.0 + - - +
123K HIS 4.3 0.7 - - - +
127K GLY* 1.3 72.8 - - - +
129K ALA* 1.3 80.4 + - - +
131K HIS* 3.7 0.4 - - - +
132K ALA* 3.0 26.0 + - - +
197K VAL* 4.9 0.3 - - - +
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Residues in contact with ALA 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70K PHE* 4.3 0.2 - - - -
77K LEU* 4.0 3.6 - - + -
80K LEU* 3.7 27.7 - - + +
127K GLY 3.4 0.8 - - - -
128K ASP* 1.3 84.1 + - - +
130K LEU* 1.3 63.2 + - - +
132K ALA* 3.4 1.9 + - - +
133K MET* 3.0 28.2 + - - +
188K LEU* 4.0 15.5 - - + -
197K VAL* 3.6 33.2 - - + -
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Residues in contact with LEU 130 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126K LYS* 3.6 36.1 - - + +
127K GLY 3.5 1.4 + - - -
128K ASP 3.4 0.6 - - - -
129K ALA* 1.3 78.4 - - - +
131K HIS* 1.3 64.5 + - - +
133K MET* 3.3 1.4 + - - -
134K GLU* 2.9 50.8 + - - +
185K VAL* 3.9 34.1 - - + +
188K LEU* 4.0 20.3 - - + +
189K ARG* 3.9 22.9 - - + +
197K VAL* 5.7 2.6 - - + +
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Residues in contact with HIS 131 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118K LEU* 6.0 1.8 - - - +
120K ASP 5.5 0.6 + - - -
121K PHE* 3.4 29.9 - - + +
122K ASP 3.9 8.6 + - - -
123K HIS* 3.5 33.9 + + + -
126K LYS* 4.2 16.5 + - + +
127K GLY 3.1 19.3 + - - +
128K ASP 3.7 2.5 - - - +
130K LEU* 1.3 76.9 - - - +
132K ALA* 1.3 55.8 + - - +
134K GLU* 3.3 5.2 + - - +
135K LEU* 2.9 59.1 + - + +
25U LEU* 4.6 14.5 - - + +
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Residues in contact with ALA 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66K MET* 3.3 26.5 - - + +
70K PHE* 3.3 41.5 - - + -
80K LEU* 4.7 0.2 - - + -
84K PHE* 4.1 6.1 - - + -
121K PHE* 4.6 4.9 - - + -
128K ASP 3.0 8.0 + - - +
129K ALA 3.8 3.4 - - - +
131K HIS* 1.3 77.3 - - - +
133K MET* 1.3 59.0 + - - +
135K LEU* 3.3 7.5 + - - +
136K ALA* 2.9 24.1 + - - +
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Residues in contact with MET 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80K LEU* 4.3 14.6 - - + -
83K PHE* 3.7 30.7 - - + -
84K PHE* 4.2 9.2 - - + -
129K ALA 3.0 13.8 + - - +
130K LEU 3.9 3.4 - - - +
132K ALA* 1.3 74.2 - - - +
134K GLU* 1.3 59.7 + - - +
136K ALA* 4.2 0.7 - - - -
137K LEU* 2.9 28.6 + - - +
181K ILE* 3.5 15.0 - - - +
184K TYR* 3.5 38.6 - - + -
185K VAL* 3.7 15.6 - - + +
188K LEU* 3.5 27.8 - - + -
200K PHE* 4.6 1.8 - - + -
204K LEU* 3.8 18.4 - - + -
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Residues in contact with GLU 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126K LYS* 3.0 40.3 + - - +
130K LEU* 2.9 30.5 + - + +
131K HIS* 3.6 4.7 + - - +
133K MET* 1.3 74.3 - - - +
135K LEU* 1.3 59.3 + - - +
137K LEU* 3.4 5.2 + - - +
138K SER* 3.0 30.8 + - - -
185K VAL* 4.0 20.6 - - + -
189K ARG* 2.8 36.4 + - - +
25U LEU* 3.9 12.2 - - + +
28U VAL* 4.4 16.0 - - + +
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Residues in contact with LEU 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66K MET* 4.6 6.7 - - + -
118K LEU* 5.5 4.3 - - + -
121K PHE* 3.7 29.8 - - + -
131K HIS* 2.9 46.3 + - + +
132K ALA* 3.5 9.6 - - - +
134K GLU* 1.3 74.1 - - - +
136K ALA* 1.3 59.2 + - - +
138K SER* 3.1 3.9 + - - -
139K LEU* 2.8 37.8 + - + +
18U PHE* 4.7 16.2 - - + -
21U VAL* 3.9 15.9 - - + -
25U LEU* 3.3 33.2 - - + -
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Residues in contact with ALA 136 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K TYR* 3.7 26.2 + - + +
66K MET* 4.6 1.3 - - + +
83K PHE* 5.1 0.2 - - + -
84K PHE* 4.0 13.7 - - + -
132K ALA 2.9 17.1 + - - +
133K MET* 3.6 8.5 - - - +
135K LEU* 1.3 75.4 - - - +
137K LEU* 1.3 62.6 + - - +
139K LEU* 3.2 10.8 + - - +
140K GLU* 2.9 27.9 + - - +
181K ILE* 4.2 14.8 - - + -
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Residues in contact with LEU 137 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133K MET 2.9 16.8 + - - +
134K GLU* 3.5 5.6 - - - +
136K ALA* 1.3 76.8 - - - +
138K SER* 1.3 56.4 + - - +
140K GLU* 3.2 3.5 + - + -
141K LYS* 3.0 41.4 + - + +
178K ILE* 3.9 27.4 - - + +
181K ILE* 3.6 12.6 - - + +
182K SER* 3.5 30.5 - - - +
185K VAL* 4.4 13.9 - - + -
28U VAL* 4.5 21.1 - - + -
36U LEU* 3.8 23.3 - - + +
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Residues in contact with SER 138 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134K GLU 3.0 14.8 + - - -
135K LEU* 3.1 8.9 + - - -
137K LEU* 1.3 77.3 - - - +
139K LEU* 1.3 57.3 + - - +
141K LYS* 3.4 3.8 + - - +
142K LEU* 2.9 29.8 + - - +
21U VAL* 3.9 20.6 - - - +
24U GLU* 3.8 23.7 + - - +
25U LEU* 3.5 23.5 + - - +
28U VAL* 3.7 9.8 - - - +
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Residues in contact with LEU 139 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K VAL* 4.7 19.7 - - + +
62K VAL* 3.6 32.3 - - + -
63K TYR* 4.5 14.6 - - + +
66K MET* 4.3 10.5 - - - -
135K LEU* 2.8 22.1 + - + +
136K ALA* 3.5 14.8 - - - +
138K SER* 1.3 77.2 - - - +
140K GLU* 1.3 57.8 + - - +
142K LEU* 3.4 4.6 + - + +
143K THR* 2.9 32.1 + - - -
17U PRO* 4.2 19.5 - - + -
18U PHE* 5.8 3.6 - - + -
21U VAL* 3.5 28.0 - - + -
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Residues in contact with GLU 140 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K VAL* 4.6 1.1 - - - +
63K TYR* 2.6 39.9 + - - +
91K GLU* 3.5 15.5 - - - +
136K ALA 2.9 14.5 + - - +
137K LEU* 3.8 4.9 - - - +
139K LEU* 1.3 74.3 - - - +
141K LYS* 1.3 59.8 + - - +
143K THR* 3.3 5.3 + - - +
144K ASN* 2.9 25.3 + - - +
174K GLN* 2.6 46.5 + - - +
177K ALA* 4.0 12.3 - - + +
178K ILE* 3.9 13.7 - - + -
181K ILE* 3.4 20.8 - - + +
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Residues in contact with LYS 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137K LEU* 3.0 35.7 + - + +
138K SER* 3.7 5.6 - - - +
140K GLU* 1.3 74.1 - - - +
142K LEU* 1.3 59.8 + - - +
144K ASN* 3.3 0.5 + - - +
145K GLU* 2.9 17.5 + - - +
178K ILE* 4.2 8.5 - - + -
24U GLU* 3.8 25.7 + - + +
27U LEU 5.7 1.4 + - - -
28U VAL* 5.8 4.8 - - + +
29U PRO* 5.0 8.9 - - - +
35U SER 5.5 0.2 + - - -
36U LEU 2.7 30.0 + - - -
37U ALA 3.7 13.7 - - - -
38U ARG 3.3 18.3 + - - -
39U GLN* 2.9 48.1 + - + +
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Residues in contact with LEU 142 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55K VAL* 5.9 0.7 - - + -
59K VAL* 5.9 1.3 - - + -
138K SER 2.9 17.6 + - - +
139K LEU* 3.5 9.2 - - + +
140K GLU 3.3 0.2 - - - -
141K LYS* 1.3 75.4 - - - +
143K THR* 1.3 63.3 + - - +
145K GLU* 3.3 22.3 + - - +
146K LYS* 3.1 36.2 + - + +
15U PHE* 3.3 34.3 - - + -
17U PRO* 4.2 2.9 - - + +
20U GLU* 3.8 36.6 - - + +
21U VAL* 3.5 25.4 - - + -
24U GLU* 4.9 9.6 + - + +
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Residues in contact with THR 143 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52K GLN* 4.1 3.6 - - - +
55K VAL* 4.4 7.5 - - + +
56K GLU* 3.6 26.7 - - - +
59K VAL* 3.5 25.3 - - - +
91K GLU* 4.7 0.3 + - - -
139K LEU 2.9 17.8 + - - -
140K GLU* 3.6 9.2 + - - +
141K LYS 3.3 0.2 - - - -
142K LEU* 1.3 78.6 - - - +
144K ASN* 1.3 56.2 + - - +
146K LYS* 3.2 6.8 + - - +
147K LEU* 2.9 29.9 + - + +
174K GLN* 3.4 19.3 - - - +
214K CA 3.9 9.2 - - - -
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Residues in contact with ASN 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140K GLU 2.9 17.7 + - - +
141K LYS 3.6 0.7 - - - +
143K THR* 1.3 73.5 - - - +
145K GLU* 1.3 65.4 + - - +
147K LEU* 3.2 3.7 + - - +
148K LEU* 2.9 49.2 + - - +
171K LEU* 4.3 11.4 - - - +
174K GLN* 3.3 30.8 - - + +
175K VAL* 5.2 8.4 - - - +
178K ILE* 3.8 8.9 - - + +
39U GLN* 2.9 35.9 + - - +
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Residues in contact with GLU 145 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141K LYS 2.9 13.8 + - - +
142K LEU* 3.3 25.0 + - - +
144K ASN* 1.3 77.3 - - - +
146K LYS* 1.3 61.4 + - + +
148K LEU* 3.5 8.8 + - - +
149K ASN* 3.0 27.9 + - + +
24U GLU* 4.7 9.6 - - - +
39U GLN* 4.1 9.5 - - - +
40U LYS* 3.4 26.7 + - - +
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Residues in contact with LYS 146 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51K GLU* 4.1 12.2 + - - +
52K GLN* 3.3 24.5 - - - +
55K VAL* 4.2 21.1 - - + -
142K LEU* 3.1 22.8 + - + +
143K THR 3.6 6.5 - - - +
144K ASN 3.2 0.4 - - - -
145K GLU* 1.3 78.0 - - + +
147K LEU* 1.3 58.6 + - - +
149K ASN* 3.2 9.8 + - + +
150K LEU* 2.8 25.6 + - - +
14U ILE 5.8 1.0 + - - -
15U PHE* 3.8 20.1 - - - -
20U GLU* 3.3 32.7 + - - -
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Residues in contact with LEU 147 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52K GLN* 3.4 28.0 - - + +
56K GLU* 3.9 7.6 - - - +
98K LEU* 5.2 0.4 - - + -
143K THR* 2.9 23.6 + - + +
144K ASN 3.7 3.4 - - - +
146K LYS* 1.3 75.0 - - - +
148K LEU* 1.3 59.0 + - - +
150K LEU* 3.2 10.0 + - + +
151K HIS* 2.9 26.9 + - - +
166K VAL* 3.7 12.7 - - + +
170K TYR* 3.9 40.2 - - + +
171K LEU* 3.9 14.8 - - + -
174K GLN* 3.6 36.1 - - + +
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Residues in contact with LEU 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144K ASN* 2.9 43.9 + - - +
145K GLU* 3.8 6.1 - - - +
147K LEU* 1.3 75.4 - - - +
149K ASN* 1.3 57.3 + - - +
151K HIS* 3.2 7.1 + - - +
152K SER* 2.9 31.3 + - - -
171K LEU* 3.7 21.3 - - + -
40U LYS* 4.0 28.9 - - + -
160U VAL* 3.3 33.4 - - + -
161U GLN* 5.3 4.3 - - + +
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Residues in contact with ASN 149 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145K GLU* 3.0 19.1 + - + +
146K LYS* 3.5 12.3 - - + +
148K LEU* 1.3 74.5 - - - +
150K LEU* 1.3 59.5 + - - +
152K SER* 3.1 11.7 + - - -
153K VAL* 2.9 40.0 + - - +
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Residues in contact with LEU 150 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48K ALA* 3.5 38.1 - - + +
49K VAL* 4.0 13.9 - - + +
52K GLN* 3.9 31.2 - - + +
98K LEU* 4.4 12.6 - - + -
146K LYS 2.8 13.5 + - - +
147K LEU* 3.2 12.3 + - + +
149K ASN* 1.3 75.8 + - - +
151K HIS* 1.3 61.6 + - - +
153K VAL* 3.3 6.6 + - + +
154K ALA* 3.0 20.1 + - - +
162K LEU* 4.6 9.6 - - + -
166K VAL* 3.7 28.5 - - + -
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Residues in contact with HIS 151 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147K LEU 2.9 14.2 + - - +
148K LEU* 3.4 13.0 - - - +
149K ASN 3.2 0.2 - - - -
150K LEU* 1.3 77.4 - - - +
152K SER* 1.3 59.3 + - - +
154K ALA* 3.3 7.5 + - - +
155K THR* 3.0 54.6 + - + +
163K ALA* 3.3 33.2 - - + +
166K VAL* 4.3 9.8 - - + +
167K GLU* 3.2 25.5 + - + -
171K LEU* 4.4 5.6 - - + -
160U VAL* 3.3 34.0 - - + +
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Residues in contact with SER 152 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148K LEU 2.9 14.6 + - - -
149K ASN* 3.1 18.4 + - - -
151K HIS* 1.3 76.7 + - - +
153K VAL* 1.3 60.9 + - - +
155K THR* 2.7 24.9 + - - -
156K LYS* 2.8 19.0 + - - +
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Residues in contact with VAL 153 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44K GLU* 3.8 26.9 - - + +
45K SER* 4.6 3.1 - - - -
48K ALA* 3.9 26.2 - - + -
149K ASN* 2.9 33.0 + - - +
150K LEU* 3.6 8.1 - - + +
152K SER* 1.3 72.3 - - - +
154K ALA* 1.3 67.2 + - - +
156K LYS* 3.4 12.1 + - + +
157K ASN* 3.1 46.1 + - - +
162K LEU* 6.0 0.2 - - + -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K SER* 4.7 2.2 - - - -
150K LEU 3.0 11.5 + - - +
151K HIS* 3.4 9.6 - - - +
153K VAL* 1.3 77.7 - - - +
155K THR* 1.3 57.0 + - - +
157K ASN* 3.3 0.9 + - - -
158K GLY 3.0 7.6 + - - -
159K ASP* 2.8 35.4 + - - +
162K LEU* 3.7 36.3 - - + +
163K ALA* 3.7 19.5 - - - +
----------------------------------------------------------
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Residues in contact with THR 155 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K HIS* 3.0 40.6 + - + +
152K SER* 2.7 23.7 + - - -
154K ALA* 1.3 73.2 - - - +
156K LYS* 1.3 65.2 + - - +
158K GLY* 3.0 13.9 + - - +
159K ASP 4.9 0.9 - - - +
163K ALA* 4.3 9.4 - - + -
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Residues in contact with LYS 156 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44K GLU* 2.6 42.6 + - - -
152K SER 2.8 17.7 + - - +
153K VAL* 3.8 11.9 - - + +
154K ALA 3.3 0.2 - - - -
155K THR* 1.3 78.0 + - - +
157K ASN* 1.3 63.8 + - - +
158K GLY 3.3 0.6 + - - -
----------------------------------------------------------
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Residues in contact with ASN 157 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K VAL* 3.8 23.6 - - + +
44K GLU* 3.0 45.2 + - - +
45K SER* 3.5 19.0 + - - +
153K VAL* 3.1 22.2 + - - +
154K ALA 4.0 2.7 - - - +
156K LYS* 1.3 84.0 - - - +
158K GLY* 1.3 62.5 + - - +
159K ASP* 3.3 3.5 + - + +
----------------------------------------------------------
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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