Contacts of the helix formed by residues 110 - 140 (chain E) in PDB entry 1UMN
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 THR 110 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E ARG 4.4 2.7 - - - -
108E ASN 4.9 4.3 - - - +
109E VAL* 1.3 73.9 - - - +
111E ILE* 1.3 66.1 + - - +
112E GLU* 3.5 8.1 + - - +
113E GLU* 2.8 44.1 + - - +
114E GLN* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ARG* 3.7 26.0 - - - +
50E MET* 3.4 38.4 - - + -
51E ARG 3.4 17.7 + - - +
52E GLY* 3.7 18.4 - - - +
53E ARG 3.4 16.4 - - - +
54E GLY 4.2 0.4 - - - -
55E PHE* 3.9 8.5 - - - +
58E TRP* 4.5 8.1 - - + -
110E THR* 1.3 72.9 - - - +
112E GLU* 1.3 59.4 + - + +
114E GLN* 3.0 9.8 + - - +
115E LEU* 2.9 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ARG* 2.9 44.1 + - - +
110E THR* 3.2 7.3 + - - +
111E ILE* 1.3 78.0 - - + +
113E GLU* 1.3 62.2 + - + +
115E LEU* 4.6 0.7 - - + -
116E ALA* 3.1 22.7 + - - +
166E LEU* 3.9 31.0 - - + +
1174E EPE 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E ASN 4.4 1.6 - - - +
109E VAL* 3.4 23.9 - - + +
110E THR* 2.8 48.2 + - + +
112E GLU* 1.3 73.5 - - + +
114E GLN* 1.3 67.8 + - - +
116E ALA* 3.3 6.9 + - - +
117E ARG* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E GLN* 5.7 1.5 - - - +
46E VAL* 3.6 43.2 - - + +
49E TYR* 4.4 21.2 + - - +
50E MET* 4.5 10.7 - - + +
51E ARG 5.9 0.2 - - - +
106E ASP 4.3 8.9 + - - -
109E VAL* 3.6 31.0 + - + +
110E THR 2.9 25.9 + - - +
111E ILE* 3.3 9.9 - - - +
113E GLU* 1.3 76.5 - - - +
115E LEU* 1.3 65.3 + - + +
117E ARG* 3.0 13.1 + - - +
118E VAL* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ARG* 5.4 1.3 - - - +
50E MET* 5.2 2.5 - - + -
58E TRP* 3.7 56.1 - - + +
62E MET* 4.0 16.6 - - + -
111E ILE* 2.9 31.5 + - + +
112E GLU* 4.0 4.3 - - - +
114E GLN* 1.3 79.1 - - + +
116E ALA* 1.3 58.3 + - - +
118E VAL* 2.9 7.6 + - - +
119E VAL* 2.8 32.2 + - - +
162E LEU* 4.0 11.8 - - + +
165E GLU* 3.9 17.5 - - + -
166E LEU* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E GLU 3.1 18.9 + - - +
113E GLU* 3.3 8.0 + - - +
115E LEU* 1.3 75.5 - - - +
117E ARG* 1.3 57.4 - - - +
119E VAL* 3.2 7.4 + - - +
120E GLU* 2.9 37.5 + - - +
163E GLN* 5.6 0.4 - - - +
166E LEU* 3.9 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ILE* 3.7 42.1 - - + +
45E GLN* 5.1 5.5 + - - -
46E VAL* 4.5 10.5 - - + -
100E LEU* 6.0 2.4 - - - +
101E LYS 3.0 30.1 + - - +
102E GLU* 4.0 7.1 - - - +
103E VAL* 4.3 18.3 - - - +
113E GLU 2.9 13.3 + - - +
114E GLN* 3.1 18.2 - - - +
116E ALA* 1.3 76.5 - - - +
118E VAL* 1.3 61.2 + - - +
120E GLU* 3.2 25.9 + - - +
121E VAL* 3.1 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ILE* 6.2 0.9 - - + -
43E LEU* 4.1 13.7 - - + -
46E VAL* 4.2 13.7 - - + -
62E MET* 3.9 27.8 - - + -
65E TYR* 4.2 7.0 - - + -
114E GLN 2.9 21.7 + - - +
115E LEU* 2.9 8.7 + - - +
117E ARG* 1.3 78.8 - - + +
119E VAL* 1.3 56.3 + - - +
121E VAL* 3.1 8.6 + - - +
122E PHE* 2.8 49.1 + - + -
162E LEU* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E LEU 2.8 19.8 + - - +
116E ALA* 3.2 10.7 + - - +
118E VAL* 1.3 76.6 - - - +
120E GLU* 1.3 53.3 + - + +
122E PHE* 3.1 7.9 + - - +
123E ARG* 2.7 64.0 + - + +
159E ILE* 4.4 9.4 - - + +
162E LEU* 3.6 31.0 - - + -
163E GLN* 3.5 30.3 - - + +
166E LEU* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E LEU* 5.9 0.2 - - - -
116E ALA* 2.9 21.0 + - - +
117E ARG* 3.2 26.7 + - - +
119E VAL* 1.3 77.6 - - + +
121E VAL* 1.3 65.4 + - + +
123E ARG* 3.2 10.9 + - - +
124E TYR* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ALA* 3.6 32.5 - - + +
42E ILE* 4.2 32.5 - - + -
43E LEU* 5.9 3.8 - - + -
100E LEU* 3.8 18.6 - - + -
117E ARG* 3.1 25.2 + - - +
118E VAL* 3.6 9.2 - - - +
120E GLU* 1.3 75.4 - - + +
122E PHE* 1.3 64.6 + - + +
124E TYR* 3.2 8.2 + - - +
125E LEU* 2.9 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LEU* 4.3 17.5 - - + -
65E TYR* 3.8 35.0 - + + -
69E ILE* 4.4 8.5 - - + -
118E VAL* 2.8 32.6 + - + +
119E VAL 3.6 4.5 - - - +
121E VAL* 1.3 80.1 - - + +
123E ARG* 1.3 65.8 + - - +
125E LEU* 3.2 8.2 + - + +
126E ALA* 2.8 25.6 + - - +
155E ILE* 3.5 30.9 - - + +
158E HIS* 3.8 31.4 - + + -
159E ILE* 3.6 17.3 - - + -
162E LEU* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E VAL* 2.7 39.4 + - + +
120E GLU* 3.6 9.6 - - - +
122E PHE* 1.3 72.1 - - - +
124E TYR* 1.3 64.0 + - - +
126E ALA* 3.3 3.8 + - - +
127E ALA* 3.0 23.3 + - - +
159E ILE* 3.8 19.5 - - + +
163E GLN* 3.2 27.9 + - - +
170E PRO 2.9 24.2 + - - -
171E LYS* 2.9 33.0 + - - +
172E LEU* 3.9 9.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E GLN* 3.8 2.3 + - - +
35E ASP* 2.7 47.3 + - + -
99E GLN* 3.5 39.9 + - + +
100E LEU* 3.6 28.5 - - + -
120E GLU 3.0 12.3 + - - +
121E VAL 3.4 8.1 - - - +
123E ARG* 1.3 77.1 - - - +
125E LEU* 1.3 71.3 + - + +
127E ALA* 3.1 9.9 + - + +
128E LEU* 2.9 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E ALA* 6.4 0.2 - - - -
35E ASP* 4.3 22.2 - - + +
36E LEU* 4.2 20.2 - - + -
39E ALA* 4.1 15.0 - - + -
69E ILE* 3.8 28.7 - - + -
100E LEU* 5.0 0.4 - - + -
121E VAL* 2.9 24.0 + - + +
122E PHE* 3.2 17.7 + - + +
124E TYR* 1.3 89.3 - - + +
126E ALA* 1.3 52.5 + - - +
128E LEU* 3.1 8.0 + - + +
129E PHE* 2.8 56.1 + - + -
155E ILE* 4.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E PHE 2.8 20.4 + - - +
123E ARG* 3.5 7.9 - - - +
125E LEU* 1.3 72.8 - - - +
127E ALA* 1.3 62.0 + - - +
129E PHE* 3.2 12.8 + - - +
130E GLN* 3.0 22.5 + - - +
152E LYS* 4.2 8.7 - - + +
155E ILE* 4.2 13.3 - - + +
156E GLU* 4.3 24.2 - - + +
159E ILE* 4.6 3.8 - - + -
172E LEU* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E ARG 3.0 13.8 + - - +
124E TYR* 3.4 13.7 - - + +
126E ALA* 1.3 72.7 - - - +
128E LEU* 1.3 67.0 + - - +
130E GLN* 3.1 9.9 + - - +
131E LYS* 3.1 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E LEU* 5.9 3.8 - - + -
28E VAL* 4.2 13.2 - - + -
31E GLN* 3.7 28.0 - - + -
32E ALA* 3.9 21.3 - - + -
35E ASP* 4.1 13.7 - - + +
124E TYR* 2.9 26.3 + - + +
125E LEU* 3.4 12.1 - - + +
127E ALA* 1.3 76.2 - - - +
129E PHE* 1.3 84.3 + - + +
131E LYS* 3.1 11.4 + - + +
132E GLY 3.0 18.5 + - - -
148E PHE* 4.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E ALA* 4.7 2.0 - - + -
36E LEU* 4.2 15.5 - - + -
72E TYR* 4.1 17.5 - + - -
76E MET* 3.7 21.8 - - + -
125E LEU* 2.8 36.2 + - + +
126E ALA* 3.2 6.3 + - - +
128E LEU* 1.3 91.2 - - + +
130E GLN* 1.3 56.9 + - - +
132E GLY 3.3 0.5 + - - -
133E PHE* 2.9 25.7 + - - +
148E PHE* 3.5 38.1 - + + +
151E ALA* 3.5 14.8 - - + -
152E LYS* 3.6 28.7 - - + -
155E ILE* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY 5.0 8.7 + - - +
142A SER* 4.9 6.7 + - - -
126E ALA 3.0 13.4 + - - +
127E ALA* 3.1 11.6 + - - +
129E PHE* 1.3 76.5 - - - +
131E LYS* 1.3 59.4 + - - +
133E PHE* 3.1 18.3 + - - +
134E ASP* 2.8 56.1 + - - +
152E LYS* 3.3 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E LEU* 6.1 6.1 - - + -
28E VAL* 4.4 6.5 - - + -
127E ALA 3.1 11.3 + - - +
128E LEU* 3.3 15.7 - - + +
130E GLN* 1.3 76.9 - - - +
132E GLY* 1.3 57.2 + - - +
134E ASP* 3.2 8.2 + - - +
135E VAL* 2.8 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E VAL* 3.4 26.9 - - - +
128E LEU 3.0 10.7 + - - -
129E PHE 3.3 1.8 + - - -
130E GLN 3.3 0.4 - - - -
131E LYS* 1.3 76.8 - - - +
133E PHE* 1.3 50.6 + - - +
135E VAL* 3.9 0.3 - - - +
136E SER* 2.8 39.3 + - - -
148E PHE* 3.4 22.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY 5.8 1.8 - - - -
142A SER* 3.3 35.0 - - - -
129E PHE 2.9 14.7 + - - +
130E GLN* 3.2 21.1 - - - +
132E GLY* 1.3 76.1 - - - +
134E ASP* 1.3 71.4 + - - +
136E SER* 2.9 6.7 + - - -
137E ASP* 2.8 44.8 + - - +
145E ASN* 3.0 47.4 + - - +
148E PHE* 3.9 7.5 - - + -
149E ASN* 3.7 24.5 - - + +
152E LYS* 6.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E GLN* 2.8 46.3 + - - +
131E LYS* 3.7 7.1 - - - +
133E PHE* 1.3 80.7 - - - +
135E VAL* 1.3 63.8 + - + +
137E ASP* 3.3 4.9 + - - +
138E GLU* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E LEU* 4.1 16.6 - - + +
23E ALA 4.3 5.2 - - - +
24E ASP* 3.4 38.8 - - - +
25E SER* 3.6 2.9 - - - +
28E VAL* 4.4 10.5 - - + -
131E LYS* 2.8 29.2 + - + +
132E GLY 3.9 2.5 - - - +
134E ASP* 1.3 74.2 - - + +
136E SER* 1.3 63.6 + - - +
138E GLU* 3.3 6.0 + - - +
139E GLU* 3.1 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E SER* 3.4 20.8 + - - -
132E GLY 2.8 26.6 + - - -
133E PHE 2.9 12.3 + - - -
135E VAL* 1.3 74.9 - - - +
137E ASP* 1.3 57.0 + - - +
139E GLU* 3.3 1.4 + - - +
140E GLY 2.9 23.2 + - - -
141E ASP 3.0 29.7 + - - +
144E THR* 4.1 8.5 - - - -
145E ASN* 3.1 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E PHE* 2.8 34.1 + - + +
134E ASP* 3.5 7.2 - - - +
135E VAL 3.2 0.2 - - - -
136E SER* 1.3 74.7 + - - +
138E GLU* 1.3 66.1 + - - +
140E GLY* 3.0 14.0 + - - -
141E ASP 5.9 0.2 - - - -
145E ASN* 3.7 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E ASP 3.0 12.7 + - - +
135E VAL* 3.6 10.1 - - - +
137E ASP* 1.3 76.3 - - - +
139E GLU* 1.3 62.6 + - + +
140E GLY* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ALA 5.5 1.6 - - - +
24E ASP* 2.8 21.0 - - - +
25E SER* 2.5 48.8 + - - +
135E VAL* 3.1 15.9 + - + +
136E SER 3.6 8.5 - - - +
137E ASP 3.1 0.2 - - - -
138E GLU* 1.3 79.6 - - + +
140E GLY* 1.3 58.7 + - - +
141E ASP* 3.6 9.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E SER 2.9 4.6 + - - -
137E ASP* 3.0 13.2 + - - -
138E GLU 3.3 0.6 - - - -
139E GLU* 1.3 79.7 - - - +
141E ASP* 1.3 61.1 + - - +
142E SER* 3.2 10.5 + - - -
130I GLN* 5.1 10.0 + - - +
133I PHE* 5.7 2.6 - - - -
----------------------------------------------------------
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