Contacts of the helix formed by residues 95 - 124 (chain J) in PDB entry 5JKL
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 95 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J TYR* 3.8 3.6 + - - -
41J PHE* 3.5 13.4 - - - -
46J VAL* 6.3 0.7 - - - -
93J TRP 2.8 8.5 + - - +
94J GLU* 1.3 79.3 + - - +
96J GLY* 1.3 64.0 + - - +
97J LEU* 3.6 1.6 + - - +
98J ASN* 3.0 26.0 + - - +
99J ALA 3.1 17.7 + - - -
161J PRO* 3.6 24.5 - - - +
167J GLU* 3.6 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 96 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J PHE* 3.6 14.4 - - - -
51J PHE* 3.4 27.7 - - - -
95J SER* 1.3 72.1 - - - +
97J LEU* 1.3 60.0 + - - +
99J ALA* 3.4 2.3 + - - +
100J MET* 3.1 27.0 + - - +
155J LEU* 4.2 2.5 - - - -
167J GLU* 2.8 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J SER* 3.3 4.0 - - - +
96J GLY* 1.3 77.3 - - - +
98J ASN* 1.3 63.7 + - - +
100J MET* 3.2 2.1 + - - +
101J GLU* 3.0 36.0 + - - +
152J VAL* 3.8 42.0 - - + +
155J LEU* 3.9 18.2 - - + +
156J ARG* 4.0 15.0 - - + +
160J ALA* 3.6 30.7 - - + +
161J PRO* 3.8 13.9 - - + -
167J GLU* 2.9 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 98 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J GLU* 5.8 2.6 - - - +
93J TRP* 3.0 31.1 + - - +
94J GLU* 3.8 26.1 - - - +
95J SER* 3.0 18.5 + - - +
97J LEU* 1.3 76.2 - - - +
99J ALA* 1.3 57.8 + - - +
101J GLU* 3.2 16.9 + - - +
102J GLU* 2.9 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J MET* 3.6 18.8 - - - +
41J PHE* 3.6 37.7 - - + -
55J PHE* 3.9 11.2 - - + -
93J TRP* 3.9 13.9 + - + -
95J SER 3.1 7.1 + - - +
96J GLY 3.7 2.2 - - - +
97J LEU 3.3 0.2 - - - -
98J ASN* 1.3 77.7 - - - +
100J MET* 1.3 56.4 + - - +
102J GLU* 3.3 1.3 + - - -
103J ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 100 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J PHE* 3.8 23.3 - - + -
54J TYR* 3.9 22.7 - - + -
55J PHE* 3.8 14.8 - - + -
96J GLY 3.1 17.8 + - - +
97J LEU 3.2 8.0 + - - +
99J ALA* 1.3 75.5 - - - +
101J GLU* 1.3 57.3 + - - +
103J ALA* 3.6 3.2 - - - +
104J LEU* 2.9 28.4 + - - +
148J LEU* 3.7 26.8 - - - +
151J HIS* 3.9 23.3 - - + -
152J VAL* 3.7 20.0 - - + +
155J LEU* 3.9 16.4 - - + -
170J PHE* 4.4 4.3 - - + -
175J LEU* 4.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 101 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J LEU* 3.0 32.7 + - - +
98J ASN* 3.6 22.3 - - - +
100J MET* 1.3 73.9 - - - +
102J GLU* 1.4 63.0 + - + +
104J LEU* 3.4 8.5 + - + +
105J GLU* 3.1 29.9 + - - +
152J VAL* 4.0 21.1 - - + -
156J ARG* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J MET* 3.8 20.4 - - + -
89J ASP* 5.4 5.7 - - - +
90J GLU* 5.0 7.8 - - - +
93J TRP* 3.9 22.8 - - + -
98J ASN* 2.9 39.0 + - - +
101J GLU* 1.4 75.7 - - + +
103J ALA* 1.3 57.9 + - - +
105J GLU* 3.4 25.3 + - - +
106J LEU* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 3.9 28.2 + - + +
37J MET* 4.0 6.5 - - - +
55J PHE* 4.3 6.5 - - + -
99J ALA 2.9 18.1 + - - +
100J MET 3.6 4.7 - - - +
101J GLU 3.2 0.2 - - - -
102J GLU* 1.3 78.7 - - - +
104J LEU* 1.3 56.9 + - - +
106J LEU* 3.3 7.4 + - - +
107J GLU* 2.9 34.7 + - - +
148J LEU* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100J MET 2.9 16.8 + - - +
101J GLU* 3.5 9.2 - - + +
103J ALA* 1.3 75.6 - - - +
105J GLU* 1.3 62.8 + - + +
107J GLU* 3.3 2.6 + - - +
108J LYS* 3.0 37.7 + - + +
145J ILE* 3.7 40.8 - - + +
148J LEU* 3.7 17.4 - - + +
149J GLY* 4.3 6.7 - - - +
152J VAL* 4.6 8.3 - - + -
7L GLN* 3.7 42.0 - - + +
8L VAL* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101J GLU* 3.1 21.6 + - + +
102J GLU* 3.6 28.0 - - - +
104J LEU* 1.3 77.5 - - + +
106J LEU* 1.3 59.6 + - - +
108J LYS* 3.3 8.8 + - - +
109J ASN* 2.9 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J LEU* 5.5 1.8 - - + -
29J TYR* 4.1 27.6 - - + -
30J ALA* 4.0 25.4 - - + -
33J VAL* 4.0 28.7 - - + -
34J TYR* 4.1 25.4 - - + -
102J GLU 2.9 14.8 + - - +
103J ALA* 3.5 7.4 - - - +
105J GLU* 1.3 76.0 - - - +
107J GLU* 1.3 60.9 + - - +
109J ASN* 3.1 11.4 + - + +
110J VAL* 2.9 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J ALA* 5.1 0.9 - - - +
34J TYR* 2.6 39.2 + - - +
58J GLN* 5.7 0.2 - - - +
62J GLU* 3.2 15.8 - - - +
65J HIS* 5.9 0.2 - - - -
103J ALA 2.9 23.2 + - - +
104J LEU 3.9 2.0 - - - +
106J LEU* 1.3 78.7 - - + +
108J LYS* 1.3 57.5 + - - +
110J VAL* 4.4 5.4 - - - +
111J ASN* 2.9 26.3 + - - +
141J GLN* 2.8 40.6 + - - +
144J ALA* 4.0 15.5 - - + +
145J ILE* 3.9 19.9 - - + +
148J LEU* 3.5 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 108 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J LEU* 3.0 26.4 + - + +
105J GLU* 3.8 6.5 - - - +
107J GLU* 1.3 74.9 - - - +
109J ASN* 1.3 60.6 + - - +
111J ASN 3.3 0.2 + - - -
112J GLN* 2.9 15.9 + - - +
145J ILE* 4.0 16.2 - - + -
6L SER 4.6 1.2 + - - -
7L GLN* 2.8 30.8 + - - +
8L VAL 3.8 4.9 - - - -
9L ARG 3.0 26.9 + - - -
10L GLN* 2.9 49.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J LEU* 4.6 5.6 - - + +
105J GLU* 2.9 28.0 + - - +
106J LEU* 3.5 12.7 - - + +
108J LYS* 1.3 76.1 - - - +
110J VAL* 1.3 65.7 + - + +
112J GLN* 3.3 7.2 + - - +
113J SER* 3.1 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J GLN* 3.8 8.7 - - - +
26J LEU* 4.1 23.6 - - + +
27J GLU* 3.5 28.3 - - - +
30J ALA* 4.4 11.7 - - + -
62J GLU* 5.8 0.2 - - - +
106J LEU* 2.9 40.7 + - + +
107J GLU* 3.8 7.6 - - - +
109J ASN* 1.3 74.6 - - + +
111J ASN* 1.3 63.3 + - - +
113J SER* 3.2 4.5 + - - -
114J LEU* 3.0 22.9 + - + +
141J GLN* 3.9 19.7 - - - +
201J FE 4.4 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 111 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107J GLU 2.9 19.1 + - - +
108J LYS 3.6 0.2 - - - +
109J ASN 3.2 0.2 - - - -
110J VAL* 1.3 75.9 - - - +
112J GLN* 1.3 58.1 + - - +
114J LEU* 3.1 3.3 + - - -
115J LEU* 2.8 49.5 + - - +
138J LEU* 4.2 14.0 - - - +
141J GLN* 3.4 29.9 - - + +
142J VAL* 5.1 8.5 - - - +
145J ILE* 3.9 11.8 - - + +
10L GLN* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 112 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J LYS 2.9 17.1 + - - +
109J ASN* 3.6 9.0 - - - +
111J ASN* 1.3 74.7 - - - +
113J SER* 1.3 58.3 + - - +
115J LEU* 3.3 12.8 + - - +
116J GLU* 2.9 69.2 + - - +
10L GLN* 3.7 20.4 + - - +
11L ASN* 5.8 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 113 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J ARG 5.9 0.3 - - - -
23J GLN* 2.6 25.0 + - - -
26J LEU* 3.6 24.5 - - - +
109J ASN 3.1 10.6 + - - -
110J VAL 3.2 7.8 + - - -
112J GLN* 1.3 76.9 - - - +
114J LEU* 1.3 55.9 + - - +
116J GLU* 3.2 12.6 + - - +
117J LEU* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J GLN* 3.4 31.2 - - + +
27J GLU* 4.5 2.7 - - - +
69J LEU* 5.7 1.3 - - + -
110J VAL* 3.0 23.4 + - + +
111J ASN* 3.1 5.3 + - - +
113J SER* 1.3 74.9 - - - +
115J LEU* 1.3 58.7 + - - +
117J LEU* 3.3 13.1 + - + +
118J HIS* 2.8 28.8 + - - +
133J ILE* 4.1 10.6 - - + +
137J TYR* 4.0 36.3 - - + +
138J LEU* 3.9 16.2 - - + -
141J GLN* 3.5 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J ASN* 2.8 46.8 + - - +
112J GLN* 3.7 19.5 - - - +
114J LEU* 1.3 72.7 - - - +
116J GLU* 1.3 63.8 + - - +
118J HIS* 3.3 3.9 + - - +
119J LYS* 3.0 23.0 + - - +
138J LEU* 4.0 16.8 - - + -
10L GLN* 4.7 3.1 - - + +
11L ASN* 3.9 31.2 - - + +
126L ASP* 6.1 0.2 - - - +
127L PRO* 3.7 34.1 - - + +
128L HIS* 5.2 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J GLN* 2.9 51.6 + - - +
113J SER* 3.6 10.6 - - - +
115J LEU* 1.3 77.8 - - - +
117J LEU* 1.3 62.6 + - - +
119J LYS* 3.3 11.3 + - + +
120J LEU* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J SER* 4.7 2.0 - - - +
19J ALA* 3.4 35.4 - - + +
20J ILE* 3.8 29.8 - - + +
23J GLN* 4.2 28.0 - - + +
69J LEU* 5.2 1.6 - - + -
113J SER 2.9 16.8 + - - +
114J LEU* 3.5 11.9 - - + +
116J GLU* 1.3 76.8 - - - +
118J HIS* 1.4 55.4 + - - +
120J LEU* 3.3 8.5 + - + +
121J ALA* 2.9 26.9 + - - +
129J LEU* 4.9 7.0 - - + -
133J ILE* 3.6 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 118 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114J LEU 2.8 20.1 + - - +
115J LEU* 3.3 6.3 + - - +
117J LEU* 1.4 70.6 - - - +
119J LYS* 1.3 60.7 + - - +
121J ALA* 3.3 2.8 + - - +
122J THR* 2.9 49.9 + - - -
130J CYS* 3.6 29.7 - - + +
133J ILE* 4.0 20.1 - - + +
134J GLU* 2.6 34.2 + - + -
138J LEU* 4.3 1.3 - - + -
127L PRO* 3.4 37.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J LEU 3.0 16.3 + - - +
116J GLU* 3.7 10.1 - - + +
117J LEU 3.3 0.2 - - - -
118J HIS* 1.3 77.8 + - - +
120J LEU* 1.3 58.3 + - - +
122J THR* 3.2 8.1 + - - -
123J ASP* 2.9 64.5 + - - +
125L ASN* 5.6 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J ASP* 3.6 38.4 - - + +
16J SER* 4.1 10.3 - - - +
19J ALA* 3.8 19.1 - - + -
22J ARG* 5.4 2.7 - - - +
116J GLU 3.0 16.3 + - - +
117J LEU* 3.6 6.7 - - + +
119J LYS* 1.3 76.5 - - - +
121J ALA* 1.4 62.7 + - - +
123J ASP* 3.1 10.6 + - + +
124J LYS* 3.0 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J SER* 4.7 4.0 + - - -
117J LEU* 2.9 17.6 + - - +
118J HIS* 3.7 6.3 - - - +
120J LEU* 1.4 78.5 - - - +
122J THR* 1.3 59.5 + - - +
124J LYS* 3.5 4.1 + - - +
125J ASN 3.2 3.3 + - - -
126J ASP* 3.0 33.3 + - + +
129J LEU* 3.8 35.2 - - + -
130J CYS* 3.8 16.6 - - - +
133J ILE* 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118J HIS* 2.9 39.0 + - - -
119J LYS* 3.4 12.5 - - - +
121J ALA* 1.3 75.2 - - - +
123J ASP* 1.3 63.5 + - - +
125J ASN* 3.0 27.2 + - - +
130J CYS* 3.6 8.4 - - - -
125L ASN* 6.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J LYS* 2.9 52.8 + - - +
120J LEU* 3.1 11.6 + - + +
122J THR* 1.3 81.1 - - - +
124J LYS* 1.3 69.3 + - + +
125J ASN* 3.6 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ASN* 4.3 7.6 - - - +
13J HIS* 3.7 54.5 + - + +
15J ASP* 3.7 19.0 + - - -
16J SER* 4.3 8.7 - - - +
120J LEU* 3.0 34.2 + - + +
121J ALA* 3.5 3.8 + - - +
122J THR 3.2 0.2 - - - -
123J ASP* 1.3 84.8 - - + +
125J ASN* 1.3 71.6 + - - +
126J ASP* 3.2 6.9 + - + +
----------------------------------------------------------
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