Contacts of the helix formed by residues 136 - 168 (chain A) in PDB entry 2BU6
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 ASP 136 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TYR 4.3 6.2 - - - +
134A GLY 3.7 10.3 + - - +
135A ASP* 1.3 75.3 - - - +
137A PRO* 1.3 78.3 - - + +
138A VAL* 3.9 11.7 + - - +
139A SER* 2.9 37.7 + - - -
140A ASN 2.9 18.9 + - - -
299A MET* 3.5 2.5 - - - +
300A TYR* 4.1 3.6 - - - -
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Residues in contact with PRO 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASP 4.7 0.7 - - - +
136A ASP* 1.3 88.7 - - + +
138A VAL* 1.3 54.9 + - + +
140A ASN* 3.2 5.8 + - + +
141A GLN* 2.7 39.5 + - - +
300A TYR* 4.0 15.7 - - - +
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASP* 3.3 9.9 + - - +
137A PRO* 1.3 80.4 - - + +
139A SER* 1.3 57.3 + - - +
141A GLN* 3.6 6.9 - - - +
142A ASN* 2.7 51.3 + - - +
376A THR* 3.7 31.6 - - + +
378A GLN* 3.4 38.8 - - + +
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 2.8 42.3 + - - -
133A TYR 5.4 0.2 + - - -
134A GLY 4.3 0.9 - - - -
136A ASP* 2.9 37.0 + - - -
138A VAL* 1.3 78.1 - - - +
140A ASN* 1.3 63.8 + - - +
142A ASN* 4.0 6.6 - - - +
143A ILE* 3.0 31.8 + - - +
299A MET* 4.3 4.3 - - - -
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Residues in contact with ASN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASP 2.9 6.5 + - - +
137A PRO* 3.4 10.1 + - - +
139A SER* 1.3 78.3 - - - +
141A GLN* 1.3 55.4 + - - +
143A ILE* 3.8 1.5 - - - +
144A GLN* 2.8 45.2 + - - +
297A SER* 2.5 31.1 + - - -
299A MET* 3.2 33.0 - - + +
300A TYR* 3.4 26.2 + - - +
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Residues in contact with GLN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PRO* 2.7 22.7 + - - +
138A VAL* 3.6 7.7 - - - +
140A ASN* 1.3 79.7 - - - +
142A ASN* 1.3 58.7 + - - +
144A GLN* 3.4 5.4 - - - +
145A TYR* 2.8 32.0 + - + +
373A HIS 5.3 1.4 + - - +
376A THR* 3.2 37.2 + - - +
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Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 2.7 35.4 + - - +
139A SER* 4.0 5.4 - - - +
141A GLN* 1.3 74.5 - - - +
143A ILE* 1.3 61.4 + - + +
145A TYR* 3.3 6.2 + - - +
146A PHE* 2.8 33.0 + - - +
373A HIS 4.1 8.1 - - - +
374A TYR* 4.3 22.0 + - + -
376A THR* 3.6 25.0 + - - -
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 6.4 1.3 - - + -
126A VAL* 4.4 16.8 - - + -
129A TYR* 4.2 33.4 - - + -
139A SER* 3.0 23.0 + - - +
140A ASN* 3.8 3.6 - - - +
142A ASN* 1.3 75.4 - - + +
144A GLN* 1.3 57.5 + - - +
146A PHE* 4.6 6.1 - - + -
147A LEU* 2.7 66.3 + - + +
298A TYR* 4.6 7.6 - - + -
299A MET* 4.0 27.6 - - + +
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Residues in contact with GLN 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASN* 2.8 28.4 + - - +
141A GLN* 3.4 7.2 - - - +
143A ILE* 1.3 73.4 - - - +
145A TYR* 1.3 63.3 + - - +
148A ASP* 2.9 46.7 + - - +
296A PHE* 3.1 22.4 + - - +
297A SER* 3.3 11.9 + - - -
298A TYR* 3.0 49.4 + - - +
299A MET 4.7 0.2 + - - -
323A PRO* 4.8 0.6 - - - +
326A ARG* 5.0 7.9 - - - +
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Residues in contact with TYR 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLN* 2.8 22.2 + - + +
142A ASN* 3.5 6.5 - - - +
144A GLN* 1.3 75.1 - - - +
146A PHE* 1.3 60.9 + - - +
148A ASP* 3.9 4.5 - - - +
149A ARG* 3.3 69.5 + - + +
370A ALA* 3.6 12.6 - - - -
373A HIS* 3.3 55.9 + + + +
374A TYR* 3.4 37.5 - + - -
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Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 4.9 3.6 - - + -
59A GLU* 4.2 8.7 - - + -
60A ILE* 3.7 36.6 - - + -
63A LEU* 3.9 28.3 - - + -
67A VAL* 6.1 2.7 - - + -
73A VAL* 6.1 1.8 - - + -
122A MET* 3.7 28.5 - - + -
142A ASN 2.8 20.4 + - - +
143A ILE* 3.8 4.7 - - + +
145A TYR* 1.3 72.2 - - - +
147A LEU* 1.3 70.5 + - + +
149A ARG* 3.3 2.6 + - - +
150A PHE* 2.7 53.7 + + + +
374A TYR* 3.7 29.8 - + + +
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A MET* 3.9 18.2 - - + -
126A VAL* 3.8 17.3 - - + -
143A ILE* 2.7 45.2 + - + +
146A PHE* 1.3 91.7 - - + +
148A ASP* 1.3 64.9 + - - +
150A PHE* 4.2 4.5 - - + -
151A TYR* 2.8 53.6 + - + +
298A TYR* 3.6 38.1 - - + -
320A TYR* 5.1 0.9 - - - +
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Residues in contact with ASP 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLN* 2.9 39.1 + - - +
145A TYR* 3.9 5.4 - - - +
147A LEU* 1.3 75.9 - - - +
149A ARG* 1.3 58.3 + - + +
152A LEU* 2.9 32.1 + - - +
298A TYR* 2.9 29.0 + - - -
323A PRO* 4.8 2.6 - - - +
326A ARG* 5.2 8.6 + - - -
327A LEU* 3.5 23.0 - - + +
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 4.5 2.7 - - + -
59A GLU* 2.8 39.8 + - - +
145A TYR* 3.3 59.0 + - + +
146A PHE 3.3 5.9 + - - +
148A ASP* 1.3 76.3 - - + +
150A PHE* 1.3 59.4 + - - +
152A LEU* 3.3 3.3 + - - +
153A SER* 2.8 33.5 + - - -
364A PRO* 3.6 32.5 - - + +
365A VAL 2.8 37.2 + - - +
370A ALA* 3.5 6.8 - - - +
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Residues in contact with PHE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 3.3 33.5 - - + +
60A ILE* 3.7 25.4 - - + -
76A VAL* 4.5 3.4 - - + -
80A TYR* 3.6 32.8 - + - -
118A VAL* 3.5 28.7 - - + -
122A MET* 3.8 26.0 - - + -
146A PHE* 2.7 36.7 + + + +
147A LEU* 3.8 6.7 - - + +
149A ARG* 1.3 72.5 - - - +
151A TYR* 1.3 76.5 + + - +
153A SER* 3.2 3.8 + - - -
154A ARG* 2.9 27.7 + - - +
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Residues in contact with TYR 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 4.8 1.1 - - + -
119A VAL* 3.5 46.8 + - + +
122A MET* 3.4 21.7 - - + +
123A ALA 4.2 0.2 + - - -
147A LEU* 2.8 46.3 + - + +
150A PHE* 1.3 90.1 - + - +
152A LEU* 1.3 66.4 + - - +
154A ARG* 3.0 13.1 + - - +
155A ILE* 2.8 28.8 + - + +
298A TYR* 3.6 36.1 - + - -
320A TYR* 4.1 9.5 - + - -
324A ILE* 4.4 12.3 - - + -
327A LEU* 3.4 15.9 - - + -
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASP 2.9 18.5 + - - +
149A ARG* 3.7 5.8 - - - +
151A TYR* 1.3 74.6 - - - +
153A SER* 1.3 63.9 + - - +
155A ILE* 2.9 23.0 + - + +
156A SER* 3.0 12.9 + - - -
327A LEU* 3.9 25.7 - - + +
330A LYS* 5.2 4.7 - - + -
331A TYR* 3.8 34.3 - - + +
362A ARG* 3.3 46.7 - - + +
364A PRO* 4.4 12.6 - - + -
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 4.3 4.3 + - - +
56A ILE* 3.4 32.6 - - - +
80A TYR* 5.7 0.3 - - - -
149A ARG 2.8 13.5 + - - -
150A PHE 3.2 10.8 - - - -
152A LEU* 1.3 76.1 - - - +
154A ARG* 1.3 62.9 + - - +
156A SER* 2.6 26.3 + - - -
157A ILE* 3.0 17.2 + - - +
364A PRO* 4.0 19.0 - - - +
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Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 4.1 18.8 - - - +
115A HIS* 2.9 35.6 + - + +
116A ASN* 3.7 17.0 + - - +
118A VAL* 3.6 25.9 - - - +
119A VAL* 3.6 23.9 - - - +
150A PHE* 2.9 15.4 + - + +
151A TYR* 3.0 17.8 + - + +
153A SER* 1.3 77.0 + - - +
155A ILE* 1.3 66.7 + - + +
157A ILE* 3.1 11.2 + - + +
158A ARG* 2.9 59.5 + - + +
328A TYR* 5.6 3.0 + - - -
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Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A TYR* 2.8 23.6 + - + +
152A LEU* 2.9 10.7 + - + +
154A ARG* 1.3 75.1 - - + +
156A SER* 1.3 59.0 + - - +
158A ARG* 3.3 8.8 + - - +
159A MET* 2.9 26.7 + - - +
236A HIS* 4.2 4.4 + - + +
324A ILE* 4.7 3.8 - - + +
327A LEU* 3.9 30.5 - - + +
328A TYR* 4.0 55.0 - - + +
331A TYR* 3.8 30.3 - - + -
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 3.3 37.6 + - - +
152A LEU 3.0 10.0 + - - -
153A SER* 2.6 23.8 + - - -
155A ILE* 1.3 77.3 - - - +
157A ILE* 1.3 60.4 + - - +
159A MET* 3.3 3.5 + - - +
160A LEU* 3.2 17.7 + - - +
331A TYR* 3.4 29.1 + - - -
361A GLU* 3.7 0.9 - - - -
362A ARG 5.6 0.7 - - - -
363A LEU* 4.3 13.3 - - - +
364A PRO* 5.7 0.4 - - - +
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Residues in contact with ILE 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.8 21.9 - - + +
52A ARG* 3.9 30.7 - - + +
53A LEU* 3.8 33.0 - - + +
80A TYR* 4.7 9.9 - - + +
111A ILE* 6.2 1.3 - - + -
153A SER* 3.0 26.5 + - - +
154A ARG* 3.1 10.1 + - + +
156A SER* 1.3 79.2 + - - +
158A ARG* 1.3 68.9 + - + +
159A MET 3.3 0.3 + - - -
160A LEU* 3.3 7.0 + - - +
161A ILE* 3.1 35.3 + - + +
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Residues in contact with ARG 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 3.5 37.7 + - + +
115A HIS* 5.6 2.9 - - + +
116A ASN* 4.0 14.0 + - - -
154A ARG* 2.9 65.3 + - + +
155A ILE* 3.7 7.6 - - - +
157A ILE* 1.3 79.6 - - + +
159A MET* 1.3 58.5 + - - +
161A ILE* 3.4 9.8 + - + +
162A ASN* 2.8 52.5 + - - +
328A TYR* 5.2 7.9 + - - -
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Residues in contact with MET 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 3.8 29.6 - - + -
155A ILE 2.9 9.5 + - - +
156A SER 3.4 4.7 - - - +
157A ILE 3.2 0.4 - - - -
158A ARG* 1.3 73.0 - - - +
160A LEU* 1.3 69.9 + - + +
162A ASN* 3.2 8.0 + - - +
163A GLN* 2.9 32.5 + - + +
182A SER* 3.7 21.3 - - - -
183A ILE* 4.3 9.6 - - + -
233A VAL* 4.1 14.4 - - + -
236A HIS* 4.1 15.0 - - + +
331A TYR* 3.1 38.1 - - + +
332A PHE* 3.5 27.4 - - + -
361A GLU* 4.7 0.2 - - - +
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.7 2.5 - - + -
28A PHE* 3.7 20.4 - - + -
44A PHE* 4.8 1.1 - - + -
45A LEU* 4.0 23.3 - - + -
48A GLU* 4.0 11.4 - - + -
49A LEU* 4.6 10.5 - - + -
52A ARG* 3.2 42.4 - - - +
156A SER 3.2 12.5 + - - +
157A ILE 3.7 5.4 - - - +
159A MET* 1.3 75.4 - - - +
161A ILE* 1.3 65.0 + - - +
163A GLN 3.1 1.9 + - - -
164A HIS* 2.9 21.4 + - - +
361A GLU* 4.2 1.1 - - - +
1386A TF2 3.0 41.3 - - - -
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Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 5.6 0.2 - - - -
49A LEU* 4.3 11.7 - - + -
108A LEU* 4.1 37.7 - - + +
111A ILE* 4.6 20.4 - - + -
112A ARG* 4.2 31.4 - - + +
157A ILE* 3.1 30.1 + - + +
158A ARG* 3.7 11.2 - - + +
160A LEU* 1.3 78.0 - - - +
162A ASN* 1.3 59.7 + - - +
164A HIS* 3.4 0.7 + - - +
165A THR* 2.8 46.1 + - + +
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Residues in contact with ASN 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 3.0 33.3 + - - -
158A ARG* 2.8 49.6 + - - +
159A MET* 3.8 5.8 - - - +
161A ILE* 1.3 72.8 - - - +
163A GLN* 1.3 60.6 + - - +
165A THR* 3.5 4.9 - - - -
166A LEU* 2.9 46.5 + - + +
182A SER* 4.9 10.9 - - - +
236A HIS* 5.9 2.4 + - - -
----------------------------------------------------------
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Residues in contact with GLN 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 4.1 29.6 + - + -
159A MET* 2.9 28.8 + - + +
160A LEU 3.4 2.9 - - - +
162A ASN* 1.3 78.6 - - - +
164A HIS* 1.3 59.6 + - - +
167A ILE* 2.8 45.7 + - - +
180A ILE 2.9 21.1 + - - -
181A GLY* 3.1 4.0 - - - -
182A SER* 2.5 40.0 + - - +
183A ILE* 4.0 16.5 - - - +
1386A TF2 3.3 20.8 - - + +
----------------------------------------------------------
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Residues in contact with HIS 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 4.0 15.4 + - + +
41A SER* 2.6 32.7 + - - +
42A PHE* 4.2 4.9 - - + +
45A LEU* 3.6 21.3 - - + +
101A LEU* 5.0 1.8 + - - +
104A PHE* 3.9 13.1 - + - -
105A THR* 3.9 22.6 + - - -
108A LEU* 3.6 23.3 - - + -
160A LEU 2.9 10.5 + - - +
161A ILE 3.8 3.1 - - - +
162A ASN 3.3 0.2 - - - -
163A GLN* 1.3 73.8 - - - +
165A THR* 1.3 66.6 + - - +
167A ILE 3.2 1.9 + - - -
168A PHE* 3.0 54.8 + + - +
1386A TF2 3.9 5.3 - - - +
----------------------------------------------------------
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Residues in contact with THR 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A THR* 4.2 17.4 - - + +
108A LEU* 4.0 24.2 - - + -
109A VAL* 3.7 30.5 - - + -
112A ARG* 3.5 19.9 + - - +
161A ILE* 2.8 25.3 + - + +
162A ASN 3.4 4.2 + - - -
164A HIS* 1.3 73.7 - - - +
166A LEU* 1.3 62.2 + - - +
168A PHE 3.9 0.6 - - - -
169A ASP* 3.1 28.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 4.4 9.0 - - - +
162A ASN* 2.9 35.5 + - + +
165A THR* 1.3 90.2 + - - +
167A ILE* 1.3 64.6 + - - +
169A ASP* 3.7 16.8 + - - +
181A GLY* 3.2 37.7 - - - +
182A SER* 3.9 10.8 - - - +
----------------------------------------------------------
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Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.6 20.6 - - + -
36A ALA 6.1 0.9 - - - +
163A GLN* 2.8 39.7 + - - +
164A HIS 3.2 2.7 + - - +
166A LEU* 1.3 77.4 - - - +
168A PHE* 1.3 88.2 + - + +
169A ASP* 3.6 5.8 + - - +
180A ILE* 4.4 13.5 - - + -
181A GLY* 3.9 19.3 - - - +
1386A TF2 3.7 21.8 - - + -
----------------------------------------------------------
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Residues in contact with PHE 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.5 11.2 - + - -
36A ALA 4.9 11.0 - - - -
37A CYS 4.1 6.1 - - - -
38A GLU* 3.3 62.4 - - + +
41A SER* 4.0 7.2 - - - -
105A THR* 4.8 12.7 + - - +
164A HIS* 3.0 56.4 + + - +
165A THR 3.9 1.8 - - - -
167A ILE* 1.3 102.8 - - + +
169A ASP* 1.3 71.7 + - - +
1386A TF2 5.3 0.9 - - - -
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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