Contacts of the helix formed by residues 134 - 162 (chain A) in PDB entry 5VEY
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 ALA 134 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 4.6 25.1 - - + +
106A ARG* 5.7 8.3 - - - +
120A HIS* 4.3 8.5 - - + +
133A GLY* 1.3 71.4 - - - -
135A GLY* 1.3 64.6 + - - +
136A ALA 3.1 1.8 - - - -
137A PRO* 3.2 9.6 - - - +
138A VAL* 3.0 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 4.3 9.0 - - - -
94A VAL* 3.7 23.2 - - - +
97A TYR* 6.3 1.5 - - - -
133A GLY* 4.6 0.4 - - - -
134A ALA* 1.3 78.6 - - - +
136A ALA* 1.3 56.9 + - - +
138A VAL* 3.8 6.5 - - - +
139A TYR* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 3.9 26.5 - - + +
66A THR* 4.2 6.0 - - - +
67A SER 4.4 5.1 - - - +
70A ILE* 3.1 32.3 - - + +
123A LEU* 4.9 2.9 - - + -
132A VAL* 4.7 4.5 - - + -
133A GLY* 4.2 4.4 - - - +
134A ALA 3.1 0.2 - - - -
135A GLY* 1.3 74.9 - - - +
137A PRO* 1.3 68.9 - - + +
139A TYR* 3.0 4.8 + - - +
140A LEU* 2.8 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 3.8 15.0 - - + +
119A VAL* 3.8 14.6 - - + +
120A HIS* 3.4 46.9 - - + +
123A LEU* 4.0 8.2 - - + -
132A VAL* 4.2 1.6 - - + -
133A GLY 2.8 28.9 - - - +
134A ALA 3.2 8.1 - - - +
136A ALA* 1.3 89.7 - - + +
138A VAL* 1.3 51.0 + - - +
140A LEU* 3.8 0.8 - - + -
141A ALA* 2.8 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 3.5 39.5 - - + +
94A VAL* 4.0 4.0 - - - +
97A TYR* 4.1 23.1 - - + -
110A ALA* 3.9 14.4 - - + -
112A LEU* 3.5 5.5 - - + +
116A VAL* 3.5 23.8 - - + -
134A ALA* 3.0 20.2 + - + +
135A GLY* 3.8 7.9 - - - +
136A ALA 3.1 0.2 - - - -
137A PRO* 1.3 77.9 - - - +
139A TYR* 1.3 61.8 + - - +
141A ALA* 3.4 2.5 + - - -
142A ALA* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 2.9 20.4 - - - +
70A ILE* 3.7 20.6 - - + -
71A GLN* 3.3 40.9 - - + +
74A VAL* 3.9 18.9 - - + +
86A ALA 3.6 2.7 + - - -
87A VAL* 3.4 27.9 + - - +
90A GLY* 3.4 42.3 - - - +
91A THR* 3.7 3.8 - - - -
94A VAL* 4.5 2.2 - - + -
135A GLY 2.9 19.9 + - - +
136A ALA* 3.4 6.1 - - - +
138A VAL* 1.3 77.4 - - - +
140A LEU* 1.3 62.1 + - - +
142A ALA* 3.3 5.0 + - - +
143A VAL* 3.2 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.2 44.2 - - + +
49A ILE* 3.4 50.0 - - + -
50A ALA 5.8 0.7 - - - +
70A ILE* 4.6 12.5 - - + +
74A VAL* 5.4 0.2 - - + -
119A VAL* 4.0 8.3 - - + -
123A LEU* 4.7 9.0 - - + -
136A ALA 2.8 14.8 + - - +
137A PRO* 3.9 4.7 - - + +
139A TYR* 1.3 78.1 - - - +
141A ALA* 1.3 66.6 + - - +
143A VAL* 3.1 8.9 + - + +
144A LEU* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.6 19.9 - - + +
114A PHE* 4.8 12.0 - - + +
116A VAL* 4.3 11.0 - - + -
119A VAL* 4.4 13.9 - - + +
137A PRO 2.8 24.8 + - - +
138A VAL* 3.6 5.4 - - - +
139A TYR 3.3 0.2 - - - -
140A LEU* 1.3 72.8 - - - +
142A ALA* 1.3 63.0 + - - +
144A LEU* 3.3 12.3 + - - +
145A GLU* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 3.3 37.1 - - + +
90A GLY* 3.9 0.2 - - - -
93A ALA* 3.8 10.3 - - + -
112A LEU* 3.9 15.6 - - + +
138A VAL 3.0 13.6 + - - +
139A TYR 3.5 9.4 - - - +
140A LEU 3.2 0.2 - - - -
141A ALA* 1.3 75.7 - - - +
143A VAL* 1.3 62.8 + - - +
145A GLU* 3.4 4.2 + - - +
146A TYR* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 4.9 11.4 - - + -
74A VAL* 4.3 26.0 - - + -
78A LEU* 4.7 11.4 - - + -
86A ALA* 4.5 13.0 - - + +
89A GLU* 4.1 7.9 - - - +
90A GLY 5.1 0.2 - - - +
139A TYR* 3.2 38.4 - - + +
140A LEU* 3.1 12.3 + - + +
142A ALA* 1.3 78.8 - - + +
144A LEU* 1.3 62.4 + - + +
146A TYR* 3.2 4.0 + - + +
147A LEU* 3.0 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 5.4 2.5 - - + -
42A VAL* 4.0 37.4 - - + +
45A ILE* 3.7 36.6 - - + -
46A PHE* 4.7 10.5 - - + +
114A PHE* 5.0 12.3 - - + -
119A VAL* 5.1 9.6 - - + -
140A LEU* 3.0 40.9 + - + +
141A ALA* 3.6 11.2 - - - +
142A ALA 3.3 0.2 - - - -
143A VAL* 1.3 77.9 - - + +
145A GLU* 1.3 56.4 + - - +
147A LEU* 3.3 7.2 + - + +
148A THR* 2.7 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.7 5.6 - - + +
111A GLY 5.1 0.9 - - - +
112A LEU* 3.2 27.6 - - + +
113A GLN* 3.3 32.6 + - - +
114A PHE* 4.1 21.0 - - + +
141A ALA 3.1 15.9 + - - +
142A ALA* 3.7 4.8 - - - +
144A LEU* 1.3 76.8 - - - +
146A TYR* 1.3 62.4 + - - +
148A THR* 3.3 6.6 + - - -
149A ALA* 3.1 22.7 + - - +
697C TYR* 3.3 31.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 5.2 4.3 - - + -
82A LEU* 4.5 14.5 - - + -
85A HIS* 3.6 17.1 - - + +
86A ALA* 5.1 0.9 - - - -
89A GLU* 2.8 46.0 - - + +
142A ALA 3.1 8.8 + - - +
143A VAL* 3.4 7.4 - - + +
145A GLU* 1.3 77.7 - - - +
147A LEU* 1.3 65.9 + - + +
149A ALA* 3.3 5.2 + - + +
150A GLU* 2.9 50.5 + - + +
697C TYR* 6.2 1.1 - - - -
698C LEU* 3.0 45.3 - - + -
699C LEU* 3.8 0.8 - - - -
700C ARG* 3.4 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.5 28.9 - - + -
45A ILE* 4.1 22.7 - - + -
78A LEU* 4.5 22.7 - - + -
82A LEU* 4.9 5.6 - - + -
143A VAL* 3.0 32.0 + - + +
144A LEU* 3.7 7.9 - - + +
146A TYR* 1.3 78.9 - - + +
148A THR* 1.3 62.2 + - - +
150A GLU* 3.4 14.3 + - - +
151A ILE* 3.0 32.9 + - + +
182A LEU* 5.0 6.1 - - + -
185A LEU* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.6 28.7 - - + -
20A VAL* 4.9 4.9 - - + -
38A MET* 3.5 28.4 - - + +
41A PHE* 5.3 2.7 - - - -
42A VAL* 4.6 9.8 - - + +
114A PHE* 3.8 21.1 - - + -
144A LEU 2.7 24.0 + - - -
145A GLU* 3.6 7.4 - - - -
146A TYR 3.3 0.2 - - - -
147A LEU* 1.3 78.1 - - - +
149A ALA* 1.3 60.0 + - - +
151A ILE* 3.6 1.1 + - - -
152A LEU* 3.1 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.7 23.5 - - + +
24A VAL* 4.5 5.5 - - + +
145A GLU 3.1 17.2 + - - +
146A TYR* 3.7 5.8 - - - +
148A THR* 1.3 75.5 - - - +
150A GLU* 1.3 65.4 + - - +
152A LEU* 3.4 4.0 + - - +
153A GLU* 3.0 26.0 + - - +
697C TYR* 3.9 28.7 - - + -
698C LEU 5.2 4.0 - - - +
699C LEU* 5.5 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.8 20.2 - - - +
146A TYR* 2.9 45.1 + - + +
147A LEU* 3.7 9.7 - - + +
148A THR 3.4 0.2 - - - -
149A ALA* 1.3 78.0 - - - +
151A ILE* 1.3 62.3 + - + +
153A GLU* 3.4 5.7 + - - +
154A LEU* 3.1 34.6 + - + +
182A LEU* 4.1 14.3 - - + +
698C LEU 5.5 0.8 + - - +
699C LEU* 5.1 10.8 - - + -
700C ARG* 3.0 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A MET* 4.0 18.2 - - + -
41A PHE* 3.5 43.5 - - + -
147A LEU* 3.0 19.8 + - + +
148A THR 3.9 3.6 - - - +
150A GLU* 1.3 76.7 - - + +
152A LEU* 1.3 59.1 + - - +
154A LEU* 3.4 9.2 + - - +
155A ALA* 3.0 27.4 + - - +
172A LEU* 3.6 28.3 - - + +
175A ALA* 4.8 2.2 - - + +
176A ILE* 4.3 26.9 - - + -
182A LEU* 4.8 11.4 - - + -
186A LEU* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.7 28.7 - - + +
20A VAL* 3.9 22.7 - - + -
21A LEU* 4.2 29.7 - - + +
24A VAL* 4.6 6.3 - - + -
30A ILE* 3.9 28.5 - - + -
38A MET* 4.3 8.7 - - + -
148A THR 3.1 20.0 + - - +
149A ALA* 3.7 4.5 - - - +
151A ILE* 1.3 77.9 - - - +
153A GLU* 1.3 60.9 + - - +
155A ALA* 3.4 5.4 + - - +
156A GLY* 3.0 19.8 + - - -
167A ILE* 4.1 12.2 - - + +
172A LEU* 5.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 3.6 29.1 - - + +
25A HIS* 4.9 15.8 - - + +
149A ALA 3.0 14.5 + - - +
150A GLU 3.7 4.9 - - - +
151A ILE 3.3 0.2 - - - -
152A LEU* 1.3 77.4 - - - +
154A LEU* 1.3 63.5 + - + +
156A GLY* 3.2 11.4 + - - -
157A ASN* 3.0 24.3 + - - -
699C LEU* 4.0 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A GLU* 3.1 25.8 + - + +
151A ILE* 3.8 2.9 - - - +
153A GLU* 1.3 77.2 - - + +
155A ALA* 1.3 63.7 + - - +
157A ASN* 3.1 24.6 + - + +
158A ALA* 3.3 9.9 + - - +
175A ALA* 3.7 25.1 - - + +
179A ASP* 4.3 5.6 - - + +
182A LEU* 3.3 33.9 - - + -
700C ARG* 3.3 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE 3.0 17.1 + - - +
152A LEU* 3.5 7.2 - - - +
154A LEU* 1.3 76.9 - - - +
156A GLY* 1.3 56.7 + - - +
158A ALA* 3.2 4.1 + - - +
159A ALA* 2.8 29.7 + - - +
167A ILE* 3.5 29.6 - - + -
171A HIS* 4.2 13.6 - - - +
172A LEU* 3.9 13.9 - - + -
175A ALA* 3.8 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 4.7 17.3 - - - +
152A LEU 3.0 14.1 + - - -
153A GLU* 3.2 7.1 + - - -
155A ALA* 1.3 78.0 - - - +
157A ASN* 1.3 55.6 + - - +
159A ALA* 3.2 8.7 + - - +
160A ARG* 2.9 37.9 + - - +
167A ILE* 4.6 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLU* 3.0 38.6 + - - -
154A LEU* 3.1 17.9 + - + +
156A GLY* 1.3 75.7 - - - +
158A ALA* 1.3 62.7 + - - +
160A ARG* 3.3 15.8 + - - +
161A ASP* 3.2 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU 3.3 7.6 + - - +
155A ALA* 3.2 9.3 + - - +
157A ASN* 1.3 76.1 - - - +
159A ALA* 1.3 62.8 + - - +
161A ASP* 3.0 11.3 + - - +
162A ASN* 2.7 36.9 + - - +
171A HIS* 4.2 15.5 - - + +
174A LEU* 3.6 31.2 - - + -
175A ALA* 5.0 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 5.7 1.8 - - + -
155A ALA 2.8 14.0 + - - +
156A GLY* 3.4 13.2 - - - +
158A ALA* 1.3 76.9 - - - +
160A ARG* 1.3 62.3 + - + +
162A ASN 3.0 8.0 + - - -
164A LYS* 2.8 43.3 + - - +
165A THR* 4.8 4.9 - - - +
166A ARG 4.1 13.9 - - - +
167A ILE* 4.8 3.8 - - + -
171A HIS* 3.8 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A HIS* 5.2 14.0 - - - -
156A GLY 2.9 20.9 + - - +
157A ASN* 3.5 16.2 - - - +
158A ALA 3.2 0.2 - - - -
159A ALA* 1.3 75.4 - - + +
161A ASP* 1.3 63.5 + - - +
163A LYS* 3.0 17.5 + - - +
164A LYS 4.3 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASN* 3.2 19.7 + - - +
158A ALA* 3.0 14.1 + - - +
160A ARG* 1.3 76.9 - - - +
162A ASN* 1.3 61.3 + - - +
163A LYS* 3.5 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ALA* 2.7 27.5 + - - +
159A ALA 3.0 3.1 + - - +
161A ASP* 1.3 79.5 - - - +
163A LYS* 1.3 70.6 + - - +
164A LYS* 3.2 20.8 + - + +
171A HIS* 3.4 34.2 + - - +
174A LEU* 4.6 13.9 - - - +
----------------------------------------------------------
Back to top of page
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