Contacts of the helix formed by residues 109 - 137 (chain A) in PDB entry 2AXT
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 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 3.1 23.5 - - - +
83A VAL 4.5 2.9 - - - -
84A PRO 4.4 0.2 - - - -
85A SER* 3.5 22.2 - - - -
106A LEU 3.1 10.9 + - - -
108A ASN* 1.3 80.2 - - - +
110A GLY* 1.3 65.4 + - - +
111A PRO* 3.2 6.5 - - - -
112A TYR* 3.1 15.3 + - - +
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Residues in contact with GLY 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 5.2 1.1 - - - -
94A TYR* 3.9 13.8 - - - +
105A TRP* 2.6 54.4 + - - -
108A ASN 3.5 1.6 + - - -
109A GLY* 1.3 70.7 - - - +
111A PRO* 1.3 64.8 - - - +
112A TYR 3.1 1.2 + - - -
113A GLN* 3.3 14.7 + - - +
114A LEU 3.4 6.1 + - - -
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Residues in contact with PRO 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A CYS* 4.5 6.3 - - - -
51A ALA* 4.4 20.0 - - + -
58A VAL* 5.7 1.1 - - + -
82A VAL* 4.5 7.0 - - + -
83A VAL 5.9 0.2 - - - +
105A TRP* 3.4 39.5 - - + +
106A LEU* 3.8 20.2 - - + +
109A GLY* 3.3 7.4 - - - -
110A GLY* 1.3 89.1 - - - +
112A TYR* 1.3 62.6 + - - +
114A LEU* 3.4 2.0 + - + +
115A ILE* 2.9 30.0 + - - +
566A BCR 4.5 7.4 - - + -
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Residues in contact with TYR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A VAL* 4.3 10.5 - - + +
83A VAL 3.4 19.2 + - - +
84A PRO* 3.5 26.0 - - + -
85A SER* 3.6 9.0 - - - +
109A GLY 3.1 10.6 + - - +
111A PRO* 1.3 78.3 - - - +
113A GLN* 1.3 66.7 + - - +
115A ILE* 2.9 6.0 + - - +
116A ILE* 2.8 50.6 + - + +
158A PHE* 3.8 15.8 + - - -
162A PRO* 5.8 0.6 - - + +
168A PHE* 3.9 23.6 - + + -
170A ASP 4.9 0.4 + - - -
171A GLY* 3.1 13.8 + - - -
172A MET 2.8 27.1 + - - -
173A PRO* 4.1 2.0 - - + -
174A LEU* 3.9 27.1 - - + -
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 3.9 23.8 + - - +
89A ILE* 4.6 2.0 - - - +
92A HIS 3.2 17.2 + - - -
93A PHE* 3.8 0.5 - - - +
94A TYR* 2.7 40.8 + - + +
109A GLY 4.1 0.2 + - - -
110A GLY* 3.3 9.1 + - - +
112A TYR* 1.3 78.4 - - + +
114A LEU* 1.3 65.2 + - - +
116A ILE* 4.0 9.2 - - - -
117A PHE* 3.0 51.1 + - + -
168A PHE* 3.0 37.2 - - + -
563A CLA 4.2 5.5 - - - +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA* 5.4 2.5 - - + +
47A CYS* 3.2 39.0 - - + -
96A ILE* 5.0 1.3 - - + -
105A TRP* 4.1 11.2 - - + -
110A GLY 3.4 9.1 + - - +
111A PRO 3.4 6.2 + - - +
112A TYR 3.2 0.4 - - - -
113A GLN* 1.3 79.5 - - - +
115A ILE* 1.3 62.2 + - - +
118A HIS* 3.0 48.6 + - + +
563A CLA 3.2 54.1 + - + +
566A BCR 3.9 30.5 - - + -
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 3.8 12.1 - - + +
47A CYS* 3.8 21.8 - - + +
48A PHE* 3.2 38.6 - - + +
51A ALA* 4.4 2.2 - - + -
82A VAL* 4.2 20.6 - - + -
111A PRO 2.9 20.1 + - - +
112A TYR 2.9 5.9 + - - +
114A LEU* 1.3 77.9 - - - +
116A ILE* 1.3 57.6 + - - +
119A PHE* 3.0 24.4 + - - +
174A LEU* 3.4 22.7 - - + -
561A PHO 3.6 23.6 - - + -
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Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A TYR* 2.8 64.5 + - + +
113A GLN* 3.6 7.9 - - - +
115A ILE* 1.3 70.6 - - + +
117A PHE* 1.3 93.4 + - + +
118A HIS 3.1 1.6 - - - -
119A PHE* 4.2 3.8 - - - +
120A LEU* 2.8 31.2 + - + +
158A PHE* 3.5 46.9 - - + +
159A LEU* 5.9 0.2 - - + -
168A PHE* 4.1 8.1 - - + -
174A LEU* 4.3 12.8 - - + -
561A PHO 5.4 0.4 - - + -
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Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PHE* 3.9 27.1 - + - -
113A GLN* 3.0 35.4 + - + +
114A LEU 4.5 1.3 - - - +
116A ILE* 1.3 98.3 - - + +
118A HIS* 1.3 62.7 + - - +
120A LEU* 4.0 6.3 - - + +
121A LEU* 3.1 23.7 + - - +
159A LEU* 5.1 5.4 - - + -
168A PHE* 3.6 31.0 - + - -
563A CLA 3.7 28.6 - - + +
218C PHE* 3.6 24.9 - + - -
201I MGE 3.8 33.5 - - + +
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Residues in contact with HIS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR* 2.7 56.4 - - + +
43A ALA* 3.7 16.6 - - + +
44A ALA* 3.7 18.8 - - + -
114A LEU* 3.0 36.7 + - + +
116A ILE 3.1 0.4 - - - -
117A PHE* 1.3 78.6 - - - +
119A PHE* 1.3 64.9 + - - +
121A LEU* 3.3 0.6 + - - -
122A GLY* 3.1 6.9 + - - -
563A CLA 2.6 75.2 + + + +
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Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.4 7.8 - - + +
44A ALA* 3.9 5.3 - - - +
115A ILE 3.0 19.9 + - - +
116A ILE* 3.1 2.4 + - - +
118A HIS* 1.3 76.1 - - - +
120A LEU* 1.3 70.3 + - + +
123A ALA* 2.9 42.3 + - + +
154A ALA* 4.0 22.0 - - + -
158A PHE* 4.4 7.4 - + - -
558A CLA 3.5 52.7 - - + -
559A CLA 4.7 1.1 - - + -
561A PHO 3.6 65.7 - - + -
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 2.8 24.4 + - + +
117A PHE* 4.0 5.8 - - + +
119A PHE* 1.3 92.7 - - + +
121A LEU* 1.3 60.2 + - - +
123A ALA* 4.1 1.3 - - - -
124A SER* 2.8 29.1 + - - -
151A LEU* 5.1 1.3 - - + -
154A ALA* 3.7 22.9 - - + +
155A PHE* 3.8 34.3 - - + -
158A PHE* 4.2 16.2 - - + +
159A LEU* 3.7 37.5 - - + -
201I MGE 4.3 10.9 - - + +
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 4.6 8.3 - - + -
40A THR* 3.7 14.4 - - + +
117A PHE 3.1 16.1 + - - +
119A PHE 3.2 0.2 - - - -
120A LEU* 1.3 77.0 - - - +
122A GLY* 1.3 63.5 + - - +
124A SER* 3.2 13.6 + - - -
125A CYS* 3.2 19.0 + - - -
563A CLA 3.8 50.5 - - + -
495C CLA 4.2 35.4 - - + -
201I MGE 3.6 35.8 - - + +
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Residues in contact with GLY 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A MET* 3.6 29.0 - - - +
40A THR* 3.5 8.3 - - - +
41A LEU* 4.2 11.2 - - - -
118A HIS 3.1 12.1 + - - -
119A PHE 4.1 0.2 - - - -
121A LEU* 1.3 78.7 - - - +
123A ALA* 1.3 51.2 + - - +
124A SER 3.0 0.2 - - - -
125A CYS* 3.2 1.8 + - - -
126A TYR* 2.7 36.8 + - - +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.4 4.6 - - - +
119A PHE* 2.9 43.7 + - + +
120A LEU 4.1 1.6 - - - +
122A GLY* 1.3 74.8 - - - +
124A SER* 1.3 60.2 + - - +
126A TYR* 3.5 8.7 - - - +
127A MET 3.4 12.0 + - - -
147A TYR* 3.4 24.9 + - - +
151A LEU* 3.5 24.0 - - + +
561A PHO 5.2 2.2 - - - +
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Residues in contact with SER 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU 2.8 16.8 + - - -
121A LEU* 3.2 11.6 + - - -
122A GLY 3.0 0.6 - - - -
123A ALA* 1.3 75.7 - - - +
125A CYS* 1.3 57.3 + - - +
126A TYR 3.0 1.1 - - - -
127A MET* 2.6 31.8 + - - +
128A GLY* 2.9 4.3 + - - -
151A LEU* 3.9 10.3 - - - +
155A PHE* 3.3 24.9 - - - -
495C CLA 3.7 31.7 - - - +
507C DGD 5.5 0.5 - - - +
201I MGE 4.2 4.9 - - - +
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Residues in contact with CYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.6 33.6 - - + +
36A ILE* 3.9 30.3 - - - -
37A MET* 3.9 9.6 - - + -
121A LEU* 3.5 12.8 - - - -
122A GLY 3.2 6.2 + - - +
124A SER* 1.3 79.2 - - - +
126A TYR* 1.3 52.8 + - - +
128A GLY* 3.3 2.6 - - - +
129A ARG* 2.5 39.5 + - - +
495C CLA 4.3 25.6 - - - -
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A MET* 3.4 30.9 - - + -
122A GLY 2.7 17.5 + - - +
123A ALA* 3.5 11.7 - - - +
125A CYS* 1.3 77.0 - - - +
127A MET* 1.3 56.8 + - - +
129A ARG* 3.7 10.5 - - - +
130A GLN* 3.1 56.5 + - + +
147A TYR* 3.4 23.3 - + - -
561A PHO 2.6 63.5 + - + +
256D ILE* 3.4 18.1 + - + -
257D PHE* 3.3 18.8 - + - -
360D MGE 5.0 9.0 - - + -
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Residues in contact with MET 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA 3.4 3.6 + - - +
124A SER* 2.6 21.0 + - - +
126A TYR* 1.3 73.5 - - - +
128A GLY* 1.3 63.1 + - - +
130A GLN* 3.2 9.5 + - - -
144A CYS* 3.2 49.7 - - + +
147A TYR* 3.7 22.4 - - + -
148A SER* 4.0 15.7 - - - -
151A LEU* 3.9 20.9 - - + -
438C LEU* 5.3 0.4 - - + -
442C LEU* 3.6 21.8 - - + -
495C CLA 3.5 47.3 - - + -
507C DGD 4.8 5.6 - - + -
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 3.0 34.4 - - - -
124A SER 2.9 11.1 + - - -
125A CYS 3.0 1.3 + - - -
127A MET* 1.3 75.7 - - - +
129A ARG* 1.3 65.3 + - - +
131A TRP* 2.9 23.0 + - - +
132A GLU 3.2 4.7 + - - -
495C CLA 3.7 14.3 - - - +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 4.6 6.3 - - - +
29A TYR* 2.6 51.6 + - + +
30A VAL* 4.1 3.6 - - - +
31A GLY* 4.6 4.0 - - - +
33A PHE* 3.4 9.2 - - + -
34A GLY* 4.0 20.9 - - - +
37A MET* 3.8 34.5 - - - +
38A ILE* 5.8 2.0 - - - +
125A CYS 2.5 20.3 + - - +
126A TYR* 3.7 9.8 - - - +
128A GLY* 1.3 70.5 - - - +
130A GLN* 1.3 54.3 + - - +
131A TRP 2.6 12.8 + - - -
132A GLU* 3.1 12.8 + - - +
133A LEU* 3.2 11.8 + - - +
255D GLN 3.5 5.4 + - - -
256D ILE* 2.9 57.6 + - + +
257D PHE 4.1 0.2 - - - +
360D MGE 4.7 10.3 - - - +
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Residues in contact with GLN 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TYR* 3.1 50.4 + - + +
127A MET 3.4 11.4 - - - +
128A GLY 3.1 0.8 - - - -
129A ARG* 1.3 72.4 - - - +
131A TRP* 1.3 56.8 + - - +
134A SER* 4.6 2.4 + - - -
141A PRO 5.2 1.4 - - - +
143A ILE* 3.8 11.5 + - - +
144A CYS* 3.5 20.2 + - + +
147A TYR* 3.4 26.1 - - - +
561A PHO 3.1 30.0 + - - +
252D PHE* 3.9 18.5 - - + -
253D TRP* 3.4 16.1 - - - -
256D ILE* 3.3 22.1 - - + +
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Residues in contact with TRP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 4.0 13.7 - + - -
128A GLY* 3.2 19.1 - - - +
129A ARG 2.6 6.3 + - - -
130A GLN* 1.3 77.4 - - - +
132A GLU* 1.3 112.6 + - + +
133A LEU 3.2 1.1 - - - -
134A SER* 2.6 32.2 + - - -
135A TYR* 2.9 22.2 + + + +
141A PRO* 4.6 11.2 - - + -
144A CYS* 4.2 18.6 - - - -
446C GLY* 4.4 15.9 + - - -
449C ARG* 4.0 39.5 - - + +
495C CLA 3.2 57.4 - + + +
23I PHE* 4.3 8.7 - + - -
27I ASP* 4.5 0.9 - - - -
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 5.4 0.2 - - - +
22A THR* 5.2 0.3 + - - -
29A TYR* 2.4 30.8 + - + +
31A GLY* 3.3 4.0 - - - -
32A TRP* 2.9 39.8 + - - +
33A PHE* 3.3 22.3 + - - +
128A GLY 3.2 2.0 + - - +
129A ARG* 3.1 8.6 + - - +
131A TRP* 1.3 110.2 - - + +
133A LEU* 1.3 63.6 + - - +
135A TYR* 3.1 2.6 + - - +
136A ARG* 2.8 50.0 + - - +
23I PHE* 3.9 3.2 - - - -
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 5.1 3.8 - - + +
29A TYR* 3.3 38.4 - - + -
129A ARG 3.2 8.6 + - - +
131A TRP 3.2 0.6 - - - -
132A GLU* 1.3 77.7 - - - +
134A SER* 1.3 65.1 + - - +
136A ARG* 3.1 6.9 + - + +
137A LEU* 2.8 47.2 + - + +
252D PHE* 3.2 57.4 - - + +
255D GLN* 4.0 17.3 - - + +
256D ILE* 4.0 13.5 - - + -
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Residues in contact with SER 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLN 4.6 2.5 - - - -
131A TRP* 2.6 31.4 + - - -
133A LEU* 1.3 74.7 - - - +
135A TYR* 1.3 56.4 + - - +
137A LEU 3.0 2.1 + - - -
138A GLY 2.9 8.5 + - - -
139A MET* 2.8 58.5 + - - +
140A ARG 3.7 15.3 + - - -
141A PRO* 3.9 11.8 - - - +
143A ILE* 6.2 0.9 - - - -
252D PHE* 3.8 14.7 - - - -
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Residues in contact with TYR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TRP* 2.9 24.1 + + + +
132A GLU* 3.2 9.9 - - - +
134A SER* 1.3 77.4 + - - +
136A ARG* 1.3 79.1 + - - +
137A LEU 2.9 4.3 - - - -
138A GLY* 2.7 26.2 + - - +
139A MET 4.7 2.0 - - - -
265C ILE* 4.9 1.2 - - - +
449C ARG* 2.8 60.1 + - + -
450C ALA* 4.7 2.7 - - + -
452C ALA* 5.8 0.9 - - - +
453C ALA* 4.1 18.3 + - + +
455C PHE* 3.8 19.8 - + - -
27I ASP 4.1 0.7 - - - -
28I PRO* 2.8 32.7 + - - +
30I ARG 3.6 16.4 - - - -
31I ASN* 3.9 5.0 + - + +
32I PRO* 3.9 5.7 - - - +
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 3.0 41.5 + - - +
24A THR* 3.5 30.0 + - + +
29A TYR* 3.7 13.0 - - + +
32A TRP* 4.5 0.8 - - - -
131A TRP* 4.6 0.6 - - - -
132A GLU* 2.8 55.7 + - - +
133A LEU* 3.5 9.6 - - + +
135A TYR* 1.3 92.5 - - - +
137A LEU* 1.3 57.7 + - - +
138A GLY 3.4 0.8 + - - -
449C ARG* 4.1 1.2 - - - +
469C MET* 4.5 2.4 - - - +
27I ASP* 2.5 47.4 + - - +
30I ARG* 3.4 25.1 + - - -
31I ASN* 4.8 3.3 - - - +
32I PRO* 3.9 11.9 - - - +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 3.3 30.7 - - + -
133A LEU* 2.8 32.5 + - + +
134A SER 3.6 4.3 - - - +
135A TYR 2.9 0.4 - - - -
136A ARG* 1.3 77.2 - - - +
138A GLY* 1.3 60.5 + - - +
139A MET* 3.1 22.9 + - + +
459C ILE* 5.5 2.4 - - - +
465C PRO* 4.0 15.0 - - - +
466C VAL* 4.3 13.3 - - + +
469C MET* 3.7 18.2 - - + -
248D THR* 4.5 4.8 - - + +
251D ARG* 3.8 24.7 - - + -
252D PHE* 3.9 20.6 - - - +
255D GLN* 4.3 6.5 - - - +
32I PRO* 4.3 4.7 - - - -
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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