Contacts of the helix formed by residues 67 - 98 (chain A) in PDB entry 1YDI
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 67 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 2.9 15.8 + - - +
66A GLU* 1.3 73.6 - - - +
68A GLN* 1.3 58.7 + - - +
69A ILE* 3.0 10.9 + - - +
70A LEU* 2.9 29.5 + - + +
71A LYS* 2.9 28.7 + - - +
129A ALA* 3.9 9.5 - - - +
132A ARG* 2.9 28.0 + - - -
136A ARG* 4.8 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR 4.3 0.2 - - - +
66A GLU* 2.9 30.7 + - - +
67A ASP* 1.3 72.0 + - - +
69A ILE* 1.3 62.8 + - + +
71A LYS* 3.5 35.8 - - - +
72A ARG* 3.4 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 3.0 8.1 + - - +
68A GLN* 1.3 78.1 - - + +
70A LEU* 1.3 67.0 + - - +
71A LYS 3.2 0.2 - - - -
72A ARG* 3.1 7.2 + - + +
73A ASP* 3.1 37.3 + - - +
132A ARG* 3.6 43.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 4.6 0.7 - - + -
65A THR* 3.9 14.1 - - + +
67A ASP* 2.9 30.8 + - + +
69A ILE* 1.3 74.5 - - - +
71A LYS* 1.3 66.4 + - - +
72A ARG 3.0 1.4 + - - -
73A ASP* 4.7 2.9 - - - +
74A MET* 3.2 56.5 + - + +
125A THR* 3.9 26.0 - - - +
126A PHE* 4.0 16.4 - - + -
129A ALA* 4.5 6.7 - - + -
132A ARG* 3.8 4.2 - - - +
764B ARG* 3.7 37.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 2.7 45.8 + - + +
63A GLN 5.6 1.1 - - - -
64A THR 4.7 0.6 - - - +
65A THR* 2.7 45.7 + - - +
67A ASP 2.9 12.0 + - - +
68A GLN* 3.5 35.0 - - - +
69A ILE 3.2 0.2 - - - -
70A LEU* 1.3 77.9 - - - +
72A ARG* 1.3 56.2 + - - +
75A PRO* 3.4 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN 3.4 11.8 + - - +
69A ILE* 3.1 6.7 + - + +
70A LEU 3.1 1.0 - - - -
71A LYS* 1.3 79.8 - - - +
73A ASP* 1.3 71.4 + - - +
74A MET 3.4 0.2 - - - -
75A PRO* 3.8 7.9 - - - +
76A PRO* 3.8 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 3.1 32.9 + - - +
70A LEU* 4.3 2.5 - - - +
72A ARG* 1.3 85.0 - - - +
74A MET* 1.3 65.0 + - - +
75A PRO 3.7 0.2 - - - -
76A PRO* 3.4 13.2 - - - +
77A ALA* 4.3 3.8 + - - +
125A THR* 3.7 28.6 - - + +
128A GLU* 4.5 12.7 - - - +
132A ARG* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY* 3.8 9.9 - - - +
61A THR* 3.8 16.6 - - + -
62A VAL* 3.7 21.5 - - + -
65A THR* 5.8 0.2 - - - -
70A LEU* 3.2 46.0 + - + +
71A LYS* 5.5 0.2 - - - -
73A ASP* 1.3 76.7 - - - +
75A PRO* 1.3 75.2 - - + +
77A ALA* 3.0 14.7 + - - +
78A PHE* 3.0 52.5 + - + -
122A LEU* 4.6 1.6 - - + -
125A THR* 3.8 14.4 - - - +
126A PHE* 3.7 22.4 - - + -
761B ILE* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 4.2 17.0 - - + -
71A LYS 3.4 19.5 - - - +
72A ARG* 3.8 4.7 - - - +
73A ASP 3.8 0.7 - - - -
74A MET* 1.3 94.3 - - + +
76A PRO* 1.3 65.5 - - + +
78A PHE* 3.1 9.3 + - + +
79A ILE* 2.8 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG 3.8 9.6 - - - +
73A ASP* 3.4 18.6 - - - +
75A PRO* 1.3 98.7 - - + +
77A ALA* 1.3 55.9 + - - +
79A ILE* 3.5 9.0 - - + +
80A LYS* 3.0 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASP 4.3 4.9 + - - +
74A MET 3.0 11.8 + - - +
76A PRO* 1.3 76.8 - - - +
78A PHE* 1.3 66.5 + - - +
80A LYS* 3.2 8.1 + - - +
81A VAL* 3.1 25.2 + - - +
118A GLY 3.7 6.8 - - - +
121A ASP* 3.9 14.1 - - + +
122A LEU* 3.6 39.9 - - + +
125A THR* 5.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.6 36.8 - - + -
55A VAL* 4.2 23.2 - - + +
58A GLY* 3.4 21.3 - - - -
62A VAL* 5.5 1.6 - - + -
74A MET* 3.0 52.8 + - + -
75A PRO* 3.1 9.0 + - + +
77A ALA* 1.3 79.1 - - - +
79A ILE* 1.3 63.5 + - + +
81A VAL* 3.2 7.2 + - + +
82A GLU* 2.9 34.0 + - - +
122A LEU* 3.3 37.9 - - + -
761B ILE* 4.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO* 2.8 31.0 + - + +
76A PRO* 3.5 9.2 - - + +
78A PHE* 1.3 81.2 - - + +
80A LYS* 1.3 59.1 + - + +
82A GLU* 3.4 21.1 + - + +
83A ASN* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PRO* 3.0 18.1 + - + +
77A ALA* 3.5 8.7 - - - +
79A ILE* 1.3 78.8 - - + +
81A VAL* 1.3 60.5 + - - +
83A ASN* 3.9 5.5 + - - +
84A ALA* 3.1 24.3 + - - +
114A GLY* 4.2 7.9 - - - +
117A SER* 2.8 29.5 + - - -
118A GLY* 4.0 14.6 - - - +
121A ASP* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 3.9 29.4 - - + -
54A LEU* 4.7 12.6 - - + -
55A VAL* 5.9 1.1 - - + -
77A ALA 3.1 15.9 + - - +
78A PHE* 3.2 10.3 + - + +
80A LYS* 1.3 76.4 - - - +
82A GLU* 1.3 63.2 + - - +
84A ALA* 3.2 7.0 + - - +
85A CYS* 3.0 21.1 + - - +
114A GLY 4.7 2.5 - - - -
115A ILE* 3.9 12.6 - - + +
118A GLY* 3.5 26.2 - - - +
119A THR* 3.7 12.3 - - - +
122A LEU* 5.5 2.7 - - + -
754B ILE* 4.6 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 4.0 13.4 - - + +
52A SER* 5.7 1.6 + - - -
55A VAL* 3.3 45.4 - - + +
59A LYS* 5.4 3.5 + - - -
78A PHE* 2.9 13.4 + - - +
79A ILE* 3.8 23.9 - - + +
81A VAL* 1.3 77.5 - - - +
83A ASN* 1.3 64.1 + - - +
85A CYS* 3.1 12.9 + - - +
86A THR* 3.1 19.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 2.9 21.9 + - + +
80A LYS* 3.9 6.7 + - - +
82A GLU* 1.3 75.5 - - - +
84A ALA* 1.3 62.5 + - - +
86A THR* 2.6 32.0 + - - +
87A LYS* 3.5 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LYS 3.1 18.7 + - - +
81A VAL 3.6 4.0 - - - +
82A GLU 3.2 0.2 - - - -
83A ASN* 1.3 77.5 - - - +
85A CYS* 1.3 63.5 + - - +
87A LYS* 3.0 27.6 + - - +
88A LEU* 3.4 4.9 + - - +
110A ASP 4.7 0.4 - - - +
111A GLY* 3.3 33.9 - - - +
114A GLY* 3.5 9.6 - - - -
115A ILE* 3.5 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 5.4 0.7 - - - -
47A VAL* 4.3 7.2 - - - -
48A GLN* 3.7 40.8 - - - -
51A VAL* 4.1 23.3 - - + -
81A VAL 3.0 12.6 + - - +
82A GLU* 3.1 13.2 + - - +
84A ALA* 1.3 76.9 - - - +
86A THR* 1.3 62.5 + - + +
88A LEU* 3.0 16.9 + - - +
89A VAL* 3.1 15.4 + - - +
115A ILE* 4.2 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 3.1 17.4 + - + +
83A ASN* 2.6 25.9 + - - +
85A CYS* 1.3 76.5 - - + +
87A LYS* 1.3 59.9 + - - +
89A VAL* 3.4 10.1 + - - +
90A GLN* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASN* 3.7 35.2 - - - +
84A ALA* 3.0 11.4 + - - +
86A THR* 1.3 79.0 + - - +
88A LEU* 1.3 59.8 + - - +
90A GLN* 3.4 3.1 + - - +
91A ALA 2.9 23.7 + - - -
107A TYR* 3.5 49.8 - - + +
110A ASP* 2.9 40.3 + - + +
111A GLY* 4.1 7.0 - - - +
114A GLY* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 3.7 25.0 - - + +
47A VAL* 4.0 17.7 - - + -
84A ALA 3.4 8.9 + - - +
85A CYS* 3.0 8.5 + - - +
87A LYS* 1.3 76.7 - - - +
89A VAL* 1.3 63.1 + - - +
91A ALA* 3.2 6.1 + - - +
92A ALA* 3.0 19.6 + - - +
108A LEU* 3.6 41.1 - - + +
111A GLY* 3.9 4.0 - - - -
112A SER* 3.8 14.1 - - - +
115A ILE* 3.6 28.9 - - + -
747B LEU* 4.1 18.8 - - + -
750B ILE* 4.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 3.7 19.7 - - + -
48A GLN* 3.7 38.4 - - + +
85A CYS* 3.1 16.2 + - - +
86A THR* 3.7 11.2 - - - +
88A LEU* 1.3 76.7 - - - +
90A GLN* 1.3 64.6 + - - +
92A ALA* 3.3 3.7 + - - +
93A GLN* 3.2 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR 3.0 18.3 + - - +
87A LYS* 3.7 6.1 - - - +
89A VAL* 1.3 76.5 - - - +
91A ALA* 1.3 64.0 + - - +
93A GLN* 3.1 29.2 + - - +
94A MET* 3.0 37.4 + - - +
107A TYR* 3.9 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS 2.9 14.5 + - - +
88A LEU 3.2 8.5 + - - +
90A GLN* 1.3 78.0 - - - +
92A ALA* 1.3 61.9 + - - +
94A MET* 3.2 9.7 + - - +
95A LEU* 2.9 29.6 + - - +
104A ALA* 3.4 27.5 - - + +
107A TYR* 3.7 7.5 - - + -
108A LEU* 3.6 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASP* 5.0 0.9 - - - +
40A LEU* 4.0 30.8 + - + +
41A THR* 4.0 13.7 + - + +
44A VAL* 4.1 11.4 - - + +
88A LEU 3.0 16.2 + - - +
89A VAL* 3.3 4.9 + - - +
91A ALA* 1.3 76.2 - - - +
93A GLN* 1.3 64.1 + - + +
95A LEU* 3.4 11.7 + - - +
96A GLN* 3.3 26.5 + - - +
108A LEU* 5.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 3.2 31.9 + - + +
90A GLN* 3.1 35.6 + - - +
92A ALA* 1.3 78.6 - - + +
94A MET* 1.3 60.7 + - - +
96A GLN* 3.4 27.2 + - - +
97A SER* 4.0 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLN* 3.0 25.4 + - - +
91A ALA 3.2 5.8 + - - +
93A GLN* 1.3 77.4 - - - +
95A LEU* 1.3 58.5 + - - +
97A SER* 3.2 10.4 + - - -
98A ASP* 3.0 28.0 + - - +
101A SER* 4.0 7.9 - - - +
103A PRO* 3.7 31.4 - - + -
104A ALA* 3.9 15.0 - - + +
107A TYR* 3.7 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.9 30.6 - - + +
38A PRO 4.7 7.8 - - - +
39A ASP* 5.9 3.8 - - - -
40A LEU* 4.0 14.1 - - + +
91A ALA 2.9 23.4 + - - +
92A ALA* 3.8 6.7 - - - +
93A GLN 3.3 0.2 - - - -
94A MET* 1.3 75.7 - - - +
96A GLN* 1.3 63.5 + - - +
97A SER 3.2 0.2 - - - -
98A ASP 3.6 16.6 - - - +
99A PRO* 3.4 42.3 - - + +
101A SER* 4.4 3.4 - - - +
104A ALA* 3.6 18.6 - - + -
108A LEU* 3.9 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASP* 4.0 20.2 + - - +
41A THR* 2.8 34.1 + - - +
92A ALA 3.3 14.3 + - - +
93A GLN* 3.5 16.9 - - - +
94A MET 3.2 0.4 - - - -
95A LEU* 1.3 80.2 - - - +
97A SER* 1.3 59.6 + - - +
99A PRO* 5.1 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLN 4.0 4.1 + - - -
94A MET* 3.2 12.2 + - - -
96A GLN* 1.3 81.7 - - - +
98A ASP* 1.3 63.4 + - - +
99A PRO* 4.0 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A MET 3.0 9.6 + - - +
95A LEU* 3.6 10.1 - - - +
97A SER* 1.3 82.5 - - - +
99A PRO* 1.3 63.5 - - - +
100A TYR* 2.9 28.4 + - - +
101A SER* 3.0 37.9 + - - -
----------------------------------------------------------
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