Contacts of the helix formed by residues 127 - 157 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122L ASP* 5.1 0.7 - - - -
123L HIS* 2.8 21.4 + - - -
124L ALA 4.4 0.2 - - - -
125L ASP 3.3 2.2 - - - -
126L LYS* 1.3 83.6 - - - +
128L ASP* 1.3 66.4 + - - -
129L ALA 3.4 2.5 - - - -
130L LEU 3.6 0.6 + - - -
131L HIS* 3.1 20.4 + - - +
193L LYS* 3.8 17.2 - - - +
197L VAL* 6.6 0.2 - - - -
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Residues in contact with ASP 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E ARG* 3.1 40.4 + - - -
69L TYR* 4.1 10.3 + - + +
70L PHE* 3.6 17.3 - - + -
75L VAL* 3.7 13.0 - - - +
77L LEU* 3.8 1.6 - - - +
121L PHE 3.5 21.8 - - - +
122L ASP* 4.0 17.9 + - - +
123L HIS 4.3 0.7 - - - +
127L GLY* 1.3 72.6 - - - +
129L ALA* 1.3 75.4 + - - +
132L ALA* 2.9 32.2 + - - +
197L VAL* 4.9 0.3 - - - +
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Residues in contact with ALA 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70L PHE* 4.3 9.6 - - - -
77L LEU* 4.2 8.7 - - + -
80L LEU* 4.7 14.6 - - + +
127L GLY 3.4 0.8 - - - -
128L ASP* 1.3 83.6 + - - +
130L LEU* 1.3 62.6 + - - +
132L ALA* 3.4 2.1 + - - +
133L MET* 3.0 24.3 + - - +
188L LEU* 3.8 17.9 - - + +
197L VAL* 3.7 32.3 - - + -
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Residues in contact with LEU 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126L LYS* 3.6 36.8 - - + +
127L GLY 3.6 1.8 + - - -
128L ASP 3.4 0.2 - - - -
129L ALA* 1.3 79.1 - - - +
131L HIS* 1.3 58.8 + - - +
133L MET 3.3 0.9 + - - -
134L GLU* 2.9 57.5 + - + +
185L VAL* 3.9 31.9 - - + +
188L LEU* 4.1 21.0 - - + +
189L ARG* 3.9 26.0 - - + +
197L VAL* 5.7 2.7 - - + +
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Residues in contact with HIS 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L LEU* 6.2 2.0 - - - +
120L ASP 5.4 1.0 + - - -
121L PHE* 3.5 34.2 - + + +
122L ASP 3.8 13.5 + - - -
123L HIS* 3.5 31.6 + + + -
126L LYS* 4.2 14.8 - - + +
127L GLY 3.1 18.5 + - - +
128L ASP 3.7 2.7 - - - +
130L LEU* 1.3 78.1 - - - +
132L ALA* 1.3 57.3 + - - +
134L GLU* 3.3 4.2 + - - +
135L LEU* 2.9 36.2 + - + +
25T LEU* 4.2 25.7 - - + +
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Residues in contact with ALA 132 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66L MET* 4.4 6.5 - - - +
70L PHE* 3.4 42.0 - - + -
84L PHE* 4.1 14.0 - - + -
121L PHE* 4.6 10.3 - - + -
128L ASP 2.9 7.4 + - - +
129L ALA 3.8 2.7 - - - +
131L HIS* 1.3 79.1 - - - +
133L MET* 1.3 58.0 + - - +
135L LEU* 3.3 7.8 + - - +
136L ALA* 2.9 28.4 + - - +
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Residues in contact with MET 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80L LEU* 3.2 33.2 - - + -
83L PHE* 4.1 17.3 - - + -
84L PHE* 4.3 6.3 - - - -
129L ALA 3.0 17.5 + - - +
130L LEU 3.9 3.1 - - - +
132L ALA* 1.3 74.4 - - - +
134L GLU* 1.3 60.9 + - - +
136L ALA* 3.3 2.4 + - - -
137L LEU* 2.9 24.4 + - - +
181L ILE* 3.5 19.9 - - + +
184L TYR* 3.5 49.4 - - + -
185L VAL* 3.7 14.9 - - + +
188L LEU* 3.9 10.8 - - + -
200L PHE* 4.3 6.7 - - + -
204L LEU* 4.2 9.9 - - + -
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Residues in contact with GLU 134 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126L LYS* 2.9 37.8 + - - +
130L LEU* 2.9 37.3 + - + +
131L HIS* 3.7 4.2 + - - +
133L MET* 1.3 73.6 - - - +
135L LEU* 1.3 61.8 + - - +
137L LEU* 3.4 6.0 + - - +
138L SER* 3.0 31.0 + - - -
185L VAL* 4.1 15.7 - - + -
189L ARG* 2.9 34.8 + - - -
25T LEU* 3.7 17.6 - - + +
28T VAL* 4.4 13.9 - - + +
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Residues in contact with LEU 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66L MET* 3.2 27.6 - - + -
118L LEU* 5.2 2.7 - - + -
121L PHE* 3.5 25.8 - - + -
131L HIS* 2.9 24.6 + - + +
132L ALA 3.4 9.4 - - - +
133L MET 3.2 0.2 - - - -
134L GLU* 1.3 74.8 - - - +
136L ALA* 1.3 59.5 + - - +
138L SER* 3.1 3.0 + - - -
139L LEU* 2.8 30.7 + - + +
18T PHE* 3.6 17.0 - - + -
21T VAL* 3.8 33.4 - - + -
25T LEU* 4.0 16.7 - - + +
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Residues in contact with ALA 136 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63L TYR* 3.9 29.6 - - + +
66L MET* 4.5 1.3 - - - +
83L PHE* 5.3 0.4 - - + -
84L PHE* 4.1 12.6 - - + -
132L ALA 2.9 16.7 + - - +
133L MET* 3.5 9.9 - - - +
135L LEU* 1.3 76.3 - - - +
137L LEU* 1.3 62.4 + - - +
139L LEU* 3.2 7.9 + - - +
140L GLU* 2.9 28.4 + - - +
181L ILE* 4.2 13.0 - - + -
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Residues in contact with LEU 137 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133L MET 2.9 16.7 + - - +
134L GLU* 3.5 6.5 - - - +
135L LEU 3.3 0.2 - - - -
136L ALA* 1.3 77.9 - - - +
138L SER* 1.3 62.1 + - - +
140L GLU* 3.2 4.3 + - + -
141L LYS* 3.0 34.3 + - + +
178L ILE* 3.8 28.3 - - + +
181L ILE* 3.6 12.5 - - + +
182L SER* 3.4 26.7 - - - +
185L VAL* 4.4 14.4 - - + -
28T VAL* 4.5 22.0 - - + -
36T LEU* 3.8 27.4 - - + +
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Residues in contact with SER 138 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134L GLU 3.0 14.8 + - - -
135L LEU* 3.5 7.4 - - - -
137L LEU* 1.3 78.1 - - - +
139L LEU* 1.3 58.2 + - - +
141L LYS* 3.3 2.0 + - - -
142L LEU* 2.9 32.2 + - - +
21T VAL* 3.4 23.3 - - - -
24T GLU* 3.7 18.4 + - - +
25T LEU* 3.3 27.2 + - - +
28T VAL* 3.6 8.9 - - - +
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Residues in contact with LEU 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L VAL* 4.8 18.9 - - + +
62L VAL* 3.4 34.1 - - + -
63L TYR* 4.5 14.6 - - + +
66L MET* 3.7 16.6 - - + -
135L LEU* 2.8 16.6 + - + +
136L ALA* 3.2 11.2 + - - +
138L SER* 1.3 77.4 - - - +
140L GLU* 1.3 58.1 + - - +
142L LEU* 3.3 8.8 + - + +
143L THR* 2.9 31.6 + - - -
15T PHE* 6.1 1.1 - - + -
17T PRO* 4.2 27.8 - - + +
18T PHE* 5.7 1.8 - - + -
21T VAL* 4.1 17.7 - - + -
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Residues in contact with GLU 140 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L VAL* 4.2 4.2 - - - +
63L TYR* 2.5 36.2 + - - +
91L GLU* 3.6 14.0 - - - +
136L ALA 2.9 20.7 + - - +
137L LEU* 3.8 4.7 - - - +
139L LEU* 1.3 74.2 - - - +
141L LYS* 1.3 61.1 + - - +
143L THR* 3.4 5.9 + - - +
144L ASN* 2.9 18.0 + - - +
174L GLN* 2.7 52.0 + - - +
177L ALA* 4.3 12.4 - - + +
178L ILE* 4.0 15.0 - - + +
181L ILE* 3.4 19.7 - - + -
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Residues in contact with LYS 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L LEU* 3.0 34.3 + - + +
138L SER* 3.3 5.1 + - - +
140L GLU* 1.3 74.8 - - - +
142L LEU* 1.3 64.5 + - - +
144L ASN* 3.3 0.7 + - - +
145L GLU* 3.0 12.6 + - - +
178L ILE* 4.2 8.7 - - + -
24T GLU* 3.7 28.9 + - + +
27T LEU 5.3 2.0 + - - -
28T VAL* 5.7 2.7 - - + +
29T PRO* 4.9 10.7 - - - +
35T SER 5.4 0.2 + - - -
36T LEU 2.7 28.6 + - - -
37T ALA* 3.6 15.9 - - - +
38T ARG 3.4 17.0 + - - -
39T GLN* 2.9 46.5 + - + +
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Residues in contact with LEU 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L VAL* 5.8 0.2 - - - -
138L SER 2.9 16.7 + - - +
139L LEU* 3.6 10.1 - - + +
140L GLU 3.3 0.2 - - - -
141L LYS* 1.3 76.6 - - - +
143L THR* 1.3 64.0 + - - +
145L GLU* 3.2 22.8 + - - +
146L LYS* 3.0 27.8 + - + +
15T PHE* 5.4 10.5 - - + -
17T PRO* 4.0 4.7 - - + +
20T GLU* 3.3 35.0 - - + +
21T VAL* 3.3 42.0 - - + +
24T GLU* 4.1 16.6 - - + +
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Residues in contact with THR 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L GLN* 4.0 5.8 - - - +
55L VAL* 4.2 7.7 - - + +
56L GLU* 3.5 27.8 - - - +
59L VAL* 3.4 24.7 - - + +
91L GLU* 5.3 0.2 + - - -
139L LEU 2.9 18.3 + - - -
140L GLU* 3.6 8.0 + - - -
141L LYS 3.3 0.2 - - - -
142L LEU* 1.3 76.2 - - - +
144L ASN* 1.3 58.6 + - - +
146L LYS* 3.1 7.7 + - - +
147L LEU* 2.8 29.8 + - + +
174L GLN* 4.0 18.4 - - - +
214L CA 4.0 8.1 - - - -
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Residues in contact with ASN 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140L GLU 2.9 14.2 + - - +
141L LYS 3.5 8.5 - - - +
142L LEU 3.3 0.2 - - - -
143L THR* 1.3 76.8 - - - +
145L GLU* 1.3 57.3 + - - +
147L LEU* 3.2 2.8 + - - +
148L LEU* 2.9 56.2 + - - +
171L LEU* 4.4 10.2 - - - +
174L GLN* 3.4 30.7 - - + +
175L VAL* 5.2 9.5 + - - +
178L ILE* 3.8 9.4 - - + +
39T GLN* 3.0 30.9 + - - +
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Residues in contact with GLU 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141L LYS 3.0 13.1 + - - +
142L LEU* 3.2 25.6 + - - +
144L ASN* 1.3 76.6 - - - +
146L LYS* 1.3 58.9 + - + +
148L LEU* 3.5 2.8 + - - +
149L ASN* 3.0 27.8 + - + +
39T GLN* 4.2 7.5 - - - +
40T LYS* 3.5 36.4 + - - +
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Residues in contact with LYS 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51L GLU* 3.8 23.5 + - + +
52L GLN* 3.4 24.7 - - - +
55L VAL* 4.0 19.7 - - + -
142L LEU* 3.0 19.2 + - + +
143L THR 3.1 7.6 + - - +
145L GLU* 1.3 76.1 - - + +
147L LEU* 1.3 60.6 + - - +
149L ASN* 3.2 12.0 + - + +
150L LEU* 2.9 24.8 + - - +
15T PHE* 3.8 21.9 - - + +
20T GLU* 3.3 27.0 + - - -
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Residues in contact with LEU 147 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L GLN* 3.4 30.7 - - + +
56L GLU* 3.9 5.6 - - - +
98L LEU* 5.4 0.7 - - + -
143L THR* 2.8 27.7 + - + +
144L ASN 3.7 3.6 - - - +
146L LYS* 1.3 73.4 - - - +
148L LEU* 1.3 58.9 + - - +
150L LEU* 3.2 9.0 + - + +
151L HIS* 2.9 28.1 + - - +
166L VAL* 3.8 11.6 - - + +
170L TYR* 3.8 41.3 - - + +
171L LEU* 3.8 14.1 - - + -
174L GLN* 3.8 36.1 - - + +
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Residues in contact with LEU 148 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144L ASN* 2.9 43.5 + - - +
145L GLU* 3.9 4.3 - - - +
147L LEU* 1.3 76.5 - - - +
149L ASN* 1.3 57.8 + - - +
151L HIS* 3.4 6.0 + - - +
152L SER* 2.9 26.7 + - - -
171L LEU* 3.9 21.5 - - + -
39T GLN 6.0 0.2 - - - +
40T LYS* 3.7 34.1 - - + -
160T VAL* 3.5 30.5 - - + -
161T GLN* 5.1 6.5 - - + +
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Residues in contact with ASN 149 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L ALA* 6.0 1.2 - - - +
51L GLU* 6.4 0.2 - - - +
145L GLU* 3.0 14.8 + - + +
146L LYS* 3.2 16.7 + - + +
148L LEU* 1.3 74.8 - - - +
150L LEU* 1.3 60.8 + - - +
152L SER* 3.1 11.7 + - - -
153L VAL* 2.9 40.2 + - - +
156L LYS* 5.2 4.7 + - - -
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Residues in contact with LEU 150 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L ALA* 3.5 40.2 - - + +
49L VAL* 3.8 14.1 - - + +
52L GLN* 3.9 30.1 - - + +
98L LEU* 4.3 13.9 - - + -
146L LYS 2.9 12.0 + - - +
147L LEU* 3.2 11.4 + - + +
149L ASN* 1.3 76.6 - - - +
151L HIS* 1.3 64.2 + - - +
153L VAL* 3.2 6.3 + - + +
154L ALA* 3.0 21.0 + - - +
162L LEU* 4.4 9.2 - - + -
166L VAL* 3.6 28.0 - - + -
170L TYR* 6.4 0.2 - - + -
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Residues in contact with HIS 151 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147L LEU 2.9 14.0 + - - +
148L LEU* 3.5 12.3 + - - +
150L LEU* 1.3 76.2 - - - +
152L SER* 1.3 59.1 + - - +
154L ALA* 3.3 6.5 + - - +
155L THR* 2.9 56.5 + - + +
163L ALA* 3.4 29.3 - - + +
166L VAL* 4.2 12.5 - - + +
167L GLU* 2.7 33.1 + - + -
171L LEU* 4.2 6.1 - - + -
160T VAL* 3.3 33.8 - - + +
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Residues in contact with SER 152 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148L LEU 2.9 14.3 + - - -
149L ASN* 3.1 17.5 + - - -
151L HIS* 1.3 76.4 + - - +
153L VAL* 1.3 60.3 + - - +
155L THR* 2.7 23.1 + - - -
156L LYS* 2.8 49.0 + - - +
----------------------------------------------------------
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Residues in contact with VAL 153 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L GLU* 3.7 30.3 - - + +
45L SER* 4.2 5.1 + - - -
48L ALA* 3.9 18.4 - - + -
149L ASN* 2.9 34.0 + - - +
150L LEU* 3.6 7.4 - - + +
152L SER* 1.3 75.6 - - - +
154L ALA* 1.3 63.3 + - - +
156L LYS* 3.4 11.3 + - + +
157L ASN* 2.8 42.4 + - - +
162L LEU* 5.9 0.2 - - + -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L SER* 4.6 1.8 - - - -
150L LEU 3.0 10.4 + - - +
151L HIS* 3.4 8.7 - - - +
153L VAL* 1.3 76.5 - - - +
155L THR* 1.3 61.0 + - - +
157L ASN* 3.1 6.6 + - - -
159L ASP* 2.8 37.4 + - - +
162L LEU* 3.6 34.3 - - + +
163L ALA* 3.6 21.1 - - - +
----------------------------------------------------------
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Residues in contact with THR 155 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151L HIS* 2.9 44.0 + - + +
152L SER* 2.7 23.9 + - - -
154L ALA* 1.3 74.4 - - - +
156L LYS* 1.3 60.3 + - - +
157L ASN 3.0 0.2 - - - -
158L GLY* 3.0 19.8 + - - +
159L ASP 4.9 2.0 - - - +
163L ALA* 4.3 9.2 - - + -
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Residues in contact with LYS 156 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L ASN* 5.2 5.1 + - - -
152L SER* 2.8 44.2 + - - +
153L VAL* 3.8 11.3 - - + +
154L ALA 3.3 0.4 - - - -
155L THR* 1.3 76.9 + - - +
157L ASN* 1.3 64.3 + - - +
158L GLY 3.5 0.2 - - - -
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Residues in contact with ASN 157 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L VAL* 3.6 28.2 - - + +
44L GLU* 3.0 29.9 + - - +
45L SER* 4.2 6.4 + - - +
153L VAL* 2.8 37.4 + - - +
154L ALA 3.1 3.4 + - - +
155L THR 3.0 1.0 - - - -
156L LYS* 1.3 84.7 - - - +
158L GLY* 1.3 65.1 + - - +
159L ASP* 3.1 5.7 + - + +
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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