Contacts of the helix formed by residues 134 - 157 (chain L) in PDB entry 5XS0
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 SER 134 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L PHE* 3.9 1.8 - - - -
132L LEU* 3.4 2.9 - - - +
133L LYS* 1.3 75.3 - - - +
135L LYS* 1.3 63.1 + - - +
136L ALA 3.6 1.0 + - - -
137L LEU* 3.3 30.4 + - - +
138L SER* 2.9 26.3 + - - -
130M GLU* 3.3 29.7 + - - -
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Residues in contact with LYS 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L VAL* 4.2 15.9 - - + -
103L PHE* 3.5 51.3 - - + -
105L VAL* 6.1 0.2 - - + -
133L LYS 3.6 0.2 + - - -
134L SER* 1.3 72.1 + - - +
136L ALA* 1.3 63.7 + - - +
138L SER* 3.2 4.7 + - - -
139L LEU* 2.9 30.4 + - + +
95M PHE* 3.6 36.6 - - + +
97M ASP* 2.9 33.1 + - - -
130M GLU* 5.2 1.8 + - - -
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Residues in contact with ALA 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134L SER* 3.3 6.0 + - - +
135L LYS* 1.3 79.8 - - - +
137L LEU* 1.3 56.8 + - - +
139L LEU 3.4 0.3 + - - -
140L GLU* 2.9 24.9 + - - +
95M PHE* 3.5 26.4 - - + -
105M VAL 4.4 3.8 - - - +
126M TYR* 3.3 15.9 - - + -
128M VAL* 3.6 36.8 - - + -
130M GLU* 4.4 6.8 + - - +
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Residues in contact with LEU 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132L LEU* 4.1 25.6 - - + -
134L SER* 3.3 23.3 + - - +
136L ALA* 1.3 76.2 - - - +
138L SER* 1.3 61.3 + - - +
140L GLU* 3.5 23.6 - - + +
141L LYS* 2.9 35.5 + - + +
128M VAL* 5.2 1.5 - - + +
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Residues in contact with SER 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L PHE* 3.7 15.2 + - - +
105L VAL* 3.9 19.3 - - - -
129L SER* 3.2 29.0 + - - -
132L LEU* 3.4 16.7 - - - +
134L SER 2.9 15.7 + - - -
135L LYS* 3.5 9.0 - - - -
137L LEU* 1.3 76.6 - - - +
139L LEU* 1.3 58.0 + - - +
141L LYS 3.4 0.2 + - - -
142L ALA* 2.9 31.1 + - - +
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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
----------------------------------------------------------
93L VAL* 4.4 10.1 - - + -
96L VAL* 4.0 26.9 - - + -
105L VAL* 4.1 13.9 - - + -
107L VAL* 4.9 1.3 - - + -
135L LYS* 2.9 20.9 + - + +
136L ALA 3.8 0.4 - - - +
138L SER* 1.3 75.6 - - - +
140L GLU* 1.3 63.8 + - - +
142L ALA* 3.3 2.5 + - - +
143L ARG* 2.9 42.2 + - + +
94M ASP* 3.5 22.2 - - + +
95M PHE* 3.6 25.6 - - + -
126M TYR* 3.3 25.6 - - + +
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Residues in contact with GLU 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136L ALA 2.9 11.0 + - - +
137L LEU* 3.5 25.5 - - + +
139L LEU* 1.3 76.6 - - - +
141L LYS* 1.3 64.0 + - - +
143L ARG* 4.0 1.2 - - - +
144L LYS* 3.0 57.7 + - + +
126M TYR* 3.4 46.1 - - + +
128M VAL* 4.3 12.2 - - - +
149M ASP* 4.5 0.9 - - - +
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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
----------------------------------------------------------
128L VAL 3.4 23.0 + - - +
129L SER* 4.1 14.2 - - - +
130L GLU 5.5 0.6 - - - +
132L LEU* 5.0 9.6 - - + -
137L LEU* 2.9 20.8 + - + +
138L SER* 3.8 3.4 - - - +
140L GLU* 1.3 78.4 - - - +
142L ALA* 1.3 58.4 + - - +
144L LYS* 4.2 2.8 - - - +
145L GLU* 2.9 51.9 + - - +
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Residues in contact with ALA 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L VAL* 3.7 15.7 - - + -
107L VAL* 3.7 24.9 - - + -
127L GLY* 3.3 28.4 - - - +
128L VAL 4.2 7.0 - - - +
129L SER* 4.7 0.2 - - - -
138L SER 2.9 18.3 + - - +
139L LEU 3.9 1.8 - - - +
141L LYS* 1.3 77.3 - - - +
143L ARG* 1.3 57.6 + - - +
146L ALA* 2.9 27.5 + - - +
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Residues in contact with ARG 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L GLN* 2.5 53.8 + - - +
93L VAL* 3.4 30.7 - - - +
107L VAL* 4.1 11.9 - - + -
139L LEU* 2.9 25.8 + - - +
140L GLU* 4.0 3.1 - - - +
142L ALA* 1.3 76.6 - - - +
144L LYS* 1.3 62.9 + - - +
146L ALA 3.2 1.7 + - - -
147L VAL* 3.0 21.3 + - - +
90M GLN* 6.1 0.6 - - - +
92M ASN* 5.1 4.8 + - - +
94M ASP* 2.8 33.1 + - - -
108M CYS* 3.4 39.5 - - - +
110M PHE* 4.5 4.9 - - - -
124M VAL* 4.2 11.4 - - + -
126M TYR* 4.1 9.0 - - + -
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Residues in contact with LYS 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140L GLU* 3.0 51.8 + - + +
141L LYS* 4.2 3.1 - - - +
143L ARG* 1.3 74.6 - - - +
145L GLU* 1.3 63.1 + - - +
147L VAL* 3.3 4.7 + - - +
148L THR* 3.0 29.8 + - - +
124M VAL* 4.1 13.9 - - + +
125M GLY* 4.6 0.2 - - - -
126M TYR* 4.2 7.0 - - - +
149M ASP* 2.7 34.5 + - - -
153M ARG* 3.4 45.1 + - - +
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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
----------------------------------------------------------
126L TYR 3.5 5.0 - - - +
127L GLY* 3.7 6.9 - - - -
128L VAL* 3.5 27.6 + - - +
141L LYS* 2.9 52.0 + - - +
142L ALA 3.7 3.6 - - - +
144L LYS* 1.3 76.3 - - - +
146L ALA* 1.3 56.9 + - - +
148L THR* 3.9 4.2 - - - -
149L ASP* 2.9 34.0 + - + +
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Residues in contact with ALA 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107L VAL* 3.4 34.5 - - + +
109L ALA* 3.7 22.7 - - + +
125L GLY* 3.4 8.8 - - - -
126L TYR 3.4 12.7 + - - +
127L GLY 3.6 0.2 - - - +
142L ALA 2.9 15.8 + - - +
143L ARG 3.5 4.9 - - - +
145L GLU* 1.3 77.9 - - - +
147L VAL* 1.3 57.0 + - - +
150L GLY 2.9 24.4 + - - -
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Residues in contact with VAL 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86L HIS* 5.3 4.9 - - + +
88L ILE* 3.7 26.7 - - + -
91L GLN* 3.5 24.7 - - - +
109L ALA* 4.0 10.5 - - + -
111L VAL* 3.6 8.9 - - + +
143L ARG 3.0 11.3 + - - +
144L LYS* 3.8 4.3 - - - +
146L ALA* 1.3 75.8 - - - +
148L THR* 1.3 64.4 + - - +
150L GLY 3.2 0.9 + - - -
151L LEU* 2.9 22.3 + - + +
122M GLU 4.9 1.8 - - - +
123M ASP* 3.6 29.6 - - - +
124M VAL* 3.6 20.6 - - + -
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Residues in contact with THR 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L GLY* 4.4 23.6 - - - +
144L LYS 3.0 17.8 + - - -
145L GLU* 4.0 4.3 - - - -
147L VAL* 1.3 78.5 - - - +
149L ASP* 1.3 62.9 + - - +
151L LEU* 3.2 10.6 + - + +
152L LYS* 3.0 34.6 + - + +
123M ASP* 5.3 2.4 + - - -
153M ARG* 4.1 12.5 + - - -
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Residues in contact with ASP 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125L GLY* 3.4 0.4 - - - -
126L TYR 3.2 20.3 + - - +
145L GLU* 2.9 19.3 + - + +
146L ALA 3.8 2.2 - - - +
148L THR* 1.3 76.4 - - - +
150L GLY* 1.3 57.6 + - - +
152L LYS* 3.3 21.0 + - - +
153L ARG* 2.9 45.9 + - - +
156L ARG* 5.6 1.9 + - - -
144V LYS* 3.0 39.4 + - - -
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Residues in contact with GLY 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L VAL* 3.8 16.8 - - - +
123L ASP* 4.4 3.1 - - - +
124L VAL 3.9 4.5 - - - -
125L GLY* 3.3 22.8 - - - -
146L ALA 2.9 13.6 + - - -
147L VAL 3.2 3.6 + - - -
149L ASP* 1.3 75.9 - - - +
151L LEU* 1.3 57.7 + - - +
153L ARG* 3.4 1.4 + - - +
154L ALA* 2.9 31.4 + - - +
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Residues in contact with LEU 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L VAL* 5.6 2.5 - - + -
72L ILE* 4.7 17.5 - - + -
84L TRP* 3.7 30.1 - - + -
86L HIS* 3.8 29.4 - - + +
111L VAL* 3.8 11.1 - - + +
113L VAL* 3.6 24.0 - - + -
147L VAL* 2.9 14.0 + - + +
148L THR* 3.2 13.4 + - + +
150L GLY* 1.3 75.7 - - - +
152L LYS* 1.3 63.9 + - + +
154L ALA* 3.3 1.3 + - - +
155L LEU* 2.9 30.8 + - + +
123M ASP* 5.7 2.9 - - - +
157M SER* 5.2 1.1 - - - +
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Residues in contact with LYS 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65L TYR* 4.5 17.2 - - - +
66L ILE* 3.2 29.8 + - + +
67L GLU* 5.2 1.4 - - - +
68L GLY* 4.6 9.8 - - - +
71L VAL* 4.1 26.5 - - + -
148L THR* 3.0 30.7 + - + +
149L ASP* 3.7 22.3 + - - +
151L LEU* 1.3 78.2 - - + +
153L ARG* 1.3 59.5 + - + +
155L LEU* 3.3 6.0 + - - +
156L ARG* 2.9 34.7 + - - +
162L LEU 4.7 2.8 - - - +
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Residues in contact with ARG 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123L ASP* 3.3 38.4 + - + +
124L VAL 2.8 25.7 + - - +
149L ASP* 2.9 38.6 + - - +
150L GLY 4.0 2.7 - - - +
152L LYS* 1.3 78.1 - - + +
154L ALA* 1.3 62.8 + - - +
156L ARG* 3.4 55.5 - - - +
157L SER* 3.9 4.9 + - - -
144V LYS* 3.3 53.4 + - - +
147V VAL* 5.1 0.2 - - - +
148V THR* 3.8 11.7 + - - -
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Residues in contact with ALA 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L VAL 3.9 12.8 - - - +
113L VAL* 3.6 24.7 - - + -
121L HIS* 3.6 26.8 - - - +
122L GLU 5.0 0.2 - - - -
123L ASP* 3.8 11.6 - - - +
150L GLY 2.9 18.7 + - - +
151L LEU* 3.8 1.8 - - - +
153L ARG* 1.3 77.2 - - - +
155L LEU* 1.3 61.8 + - - +
157L SER* 3.4 19.1 + - - -
158L PHE* 4.3 2.9 - - - -
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Residues in contact with LEU 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L VAL* 3.5 31.6 - - + +
72L ILE* 5.8 0.2 - - - -
75L ALA* 4.1 14.1 - - + -
79L PHE* 4.8 2.9 - - + -
84L TRP* 3.8 27.8 - - + -
113L VAL* 3.7 24.7 - - + -
151L LEU* 2.9 24.8 + - + +
152L LYS 3.8 3.1 - - - +
154L ALA* 1.3 72.2 - - - +
156L ARG* 1.3 65.3 + - - +
157L SER 3.1 3.9 + - - -
158L PHE* 3.2 34.6 + - + +
162L LEU* 3.4 32.3 - - + +
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Residues in contact with ARG 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L ASP* 5.6 2.2 + - - -
152L LYS* 2.9 20.0 + - - +
153L ARG* 3.4 52.8 - - - +
154L ALA 3.2 0.4 - - - -
155L LEU* 1.3 76.2 - - - +
157L SER* 1.3 58.2 + - - +
158L PHE 3.0 5.4 + - - -
159L GLY 3.3 17.0 + - - +
162L LEU 4.1 6.9 + - - -
163L GLY* 3.5 28.8 + - - +
164L ASN* 3.6 18.1 - - - +
166L ILE* 4.3 10.2 - - - +
167L LEU* 3.6 42.9 - - - +
72V ILE* 4.9 5.6 - - + -
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Residues in contact with SER 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121L HIS* 3.5 33.1 - - - -
123L ASP* 4.6 3.3 + - - -
153L ARG 3.9 7.3 + - - -
154L ALA* 3.4 8.4 + - - -
155L LEU 3.1 1.2 - - - -
156L ARG* 1.3 77.1 - - - +
158L PHE* 1.3 59.0 + - - +
159L GLY 3.4 0.4 - - - -
72V ILE* 3.9 20.6 - - - +
76V ASN* 3.3 21.0 + - - +
84V TRP* 3.6 15.8 - - - -
86V HIS* 3.6 15.5 + - - -
151V LEU* 4.9 2.1 - - - +
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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