Contacts of the helix formed by residues 87 - 116 (chain E) in PDB entry 5ZBX
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 GLN 87 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E TRP* 1.3 75.3 - - - +
88E ALA* 1.3 64.6 + - - +
89E GLN* 3.3 15.4 - - + +
90E ALA* 3.0 20.4 + - + +
91E LEU* 3.3 7.4 + - - +
80F THR* 4.2 8.9 - - + +
81F VAL 3.1 19.0 + - - +
82F THR* 3.5 33.0 - - - +
83F ALA* 3.5 14.9 + - - +
102I A 5.7 2.2 + - - -
195J C 4.7 1.4 + - - +
196J C 2.8 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E GLN* 5.2 2.4 + - - +
86E TRP 3.7 1.8 + - - -
87E GLN* 1.3 72.8 - - - +
89E GLN* 1.3 68.0 + - + +
91E LEU* 3.1 13.0 + - - +
92E LEU* 3.0 29.5 + - + +
196J C 3.3 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D LYS* 5.7 5.1 + - - +
87E GLN* 3.3 11.4 - - + +
88E ALA* 1.3 79.7 - - + +
90E ALA* 1.3 57.0 + - - +
92E LEU* 3.3 21.8 + - - +
93E ALA* 2.9 30.7 + - - +
83F ALA* 4.0 17.9 - - + -
99F GLY 5.4 1.2 + - - -
100F PHE* 3.4 31.2 - - + +
196J C 5.1 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E TRP* 3.8 17.7 - - + -
87E GLN* 3.0 14.1 + - + +
89E GLN* 1.3 78.0 - - - +
91E LEU* 1.3 63.7 + - - +
93E ALA* 3.3 2.9 + - - +
94E LEU* 3.0 23.9 + - - +
81F VAL 3.8 11.0 - - - +
82F THR 3.6 28.3 - - - +
83F ALA* 3.8 10.8 - - - +
86F VAL* 4.0 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E LYS* 3.3 12.3 + - - +
67E PHE* 4.1 1.6 - - + -
68E GLN* 3.6 45.8 - - + +
71E VAL* 3.7 36.8 - - + -
72E ARG* 3.8 28.5 - - + +
86E TRP* 3.7 29.8 - - + +
87E GLN 3.3 5.8 + - - +
88E ALA* 3.1 10.3 + - - +
90E ALA* 1.3 78.3 - - - +
92E LEU* 1.3 62.1 + - - +
94E LEU* 3.3 5.4 + - + +
95E GLN 3.0 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D LYS* 5.6 7.9 - - - +
60E LEU* 4.5 13.0 - - + -
64E LYS* 3.4 31.6 - - + +
68E GLN* 5.0 1.8 - - - +
88E ALA* 3.0 17.5 + - + +
89E GLN* 3.6 28.5 - - - +
91E LEU* 1.3 77.3 - - - +
93E ALA* 1.3 56.4 + - - +
95E GLN* 3.2 2.6 + - - +
96E GLU* 2.9 35.9 + - - +
100F PHE* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E GLN 2.9 18.4 + - - +
90E ALA* 3.6 7.2 - - - +
91E LEU 3.3 0.2 - - - -
92E LEU* 1.3 76.4 - - - +
94E LEU* 1.3 63.3 + - - +
96E GLU* 3.3 2.8 + - - +
97E ALA* 3.0 24.8 + - - +
83F ALA* 4.9 3.8 - - + +
86F VAL* 4.1 15.0 - - + -
97F LEU* 4.0 11.9 - - + +
100F PHE* 3.7 35.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E PHE* 3.9 6.3 - - + -
71E VAL* 3.6 39.5 - - + -
86E TRP* 4.1 9.0 - - + -
90E ALA 3.0 11.2 + - - +
91E LEU* 3.6 8.7 - - - +
93E ALA* 1.3 78.4 - - - +
95E GLN* 1.3 57.5 + - - +
97E ALA* 3.4 5.2 + - + +
98E ALA* 2.9 31.2 + - - +
61F PHE* 4.9 5.6 - - + -
62F LEU* 4.1 15.5 - - + -
65F VAL* 4.0 27.8 - - + -
66F ILE* 3.8 18.2 - - + -
86F VAL* 3.9 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E LEU* 3.4 21.2 - - + +
62E ILE* 2.8 37.4 + - - +
63E ARG 4.1 1.8 + - - -
64E LYS* 2.8 35.3 + - - +
67E PHE* 3.5 34.0 - - + -
91E LEU 3.0 14.0 + - - +
92E LEU 3.8 3.4 - - - +
94E LEU* 1.3 76.2 - - - +
96E GLU* 1.3 64.3 + - - +
98E ALA* 3.9 0.2 - - - +
99E GLU* 2.8 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C THR* 5.2 2.2 - - + -
103C ALA* 3.5 30.9 - - + +
104C GLN* 2.9 35.8 + - - +
58E THR 4.7 1.6 - - - +
60E LEU* 3.5 30.4 - - - +
92E LEU* 2.9 20.6 + - - +
93E ALA* 3.6 6.5 - - - +
95E GLN* 1.3 76.8 - - - +
97E ALA* 1.3 62.3 + - - +
99E GLU* 3.9 1.4 - - - +
100E ALA* 3.0 26.4 + - - +
97F LEU* 4.4 10.3 - - + -
100F PHE* 4.5 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C THR* 5.0 3.6 - - - +
93E ALA 3.0 16.5 + - - +
94E LEU* 3.8 5.8 - - + +
96E GLU* 1.3 76.8 - - - +
98E ALA* 1.3 58.2 + - - +
100E ALA* 3.5 4.5 + - - +
101E PHE* 2.9 30.0 + - - +
61F PHE* 4.1 5.8 - - + -
90F LEU* 3.6 38.8 - - + -
95F ARG* 6.3 0.2 - - + -
97F LEU* 4.5 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ILE* 5.8 0.2 - - + -
67E PHE* 4.0 16.8 - - + -
94E LEU 2.9 18.5 + - - +
95E GLN 3.9 2.5 - - - +
97E ALA* 1.3 76.3 - - - +
99E GLU* 1.3 60.1 + - + +
101E PHE* 3.5 3.1 + - - +
102E LEU* 3.0 34.9 + - + +
58F LEU* 3.9 24.0 - - + -
61F PHE* 3.8 19.7 - - + -
62F LEU* 4.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E GLU 4.3 0.5 - - - +
60E LEU* 3.2 21.3 - - + +
61E LEU* 2.6 29.8 + - - +
62E ILE* 2.8 44.7 + - + +
95E GLN* 2.8 35.7 + - + +
96E GLU 4.1 2.2 - - - +
98E ALA* 1.3 75.2 - - + +
100E ALA* 1.3 59.0 + - - +
102E LEU* 4.0 2.1 - - - +
103E VAL* 2.9 37.9 + - + +
37F LEU* 3.9 14.4 - - + +
40F ARG* 4.8 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C THR* 3.6 30.5 - - + +
96E GLU 3.0 18.0 + - - +
97E ALA 3.9 3.4 - - - +
99E GLU* 1.3 78.0 - - - +
101E PHE* 1.3 61.1 + - - +
103E VAL* 3.9 3.5 - - - -
104E HIS* 3.0 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E ALA 2.9 17.9 + - - +
98E ALA 3.6 5.4 - - - +
100E ALA* 1.3 77.3 - - - +
102E LEU* 1.3 78.1 + - + +
104E HIS* 3.4 4.3 + - - +
105E LEU* 2.9 26.7 + - + +
130E ARG* 4.0 2.9 - - - -
133E ARG* 3.8 12.4 + - - +
135E GLU* 3.6 26.0 - - - -
57F VAL* 3.5 32.3 - - + -
58F LEU* 5.2 1.1 - - + -
61F PHE* 3.7 44.0 - + + -
95F ARG* 3.4 41.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ILE* 4.6 6.1 - - + -
98E ALA 3.0 20.9 + - - +
99E GLU 4.0 2.7 - - - +
101E PHE* 1.3 96.3 - - + +
103E VAL* 1.3 58.8 + - - +
105E LEU* 3.3 9.6 + - + +
106E PHE* 2.9 39.5 + - + -
29F ILE* 6.0 0.7 - - + -
37F LEU* 3.6 31.6 - - + -
54F THR* 4.0 27.4 - - + -
57F VAL* 4.3 13.2 - - + -
58F LEU* 4.0 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C VAL* 3.8 29.2 - - + -
99E GLU* 2.9 22.1 + - + +
100E ALA* 3.9 5.2 - - - +
102E LEU* 1.3 76.8 - - - +
104E HIS* 1.3 59.1 + - + +
106E PHE* 3.1 8.4 + - - +
107E GLU* 2.9 33.4 + - - +
37F LEU* 3.7 34.1 - - + +
40F ARG* 3.9 27.4 - - + +
41F GLY* 4.0 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLN* 5.6 7.2 + - - -
101C THR* 6.0 0.7 - - - -
106C GLY 5.8 0.2 + - - -
107C VAL* 4.4 16.1 - - + +
100E ALA* 3.0 38.4 + - + +
101E PHE* 4.1 1.8 - - - +
103E VAL* 1.3 76.3 - - + +
105E LEU* 1.3 62.5 + - - +
107E GLU* 3.0 34.7 + - - +
108E ASP* 3.0 28.0 + - - +
133E ARG* 3.5 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E PHE* 2.9 24.7 + - + +
102E LEU* 3.6 11.7 - - + +
104E HIS* 1.3 75.4 - - - +
106E PHE* 1.3 59.2 + - + +
108E ASP* 3.5 0.8 + - - -
109E ALA* 2.9 29.0 + - - +
126E ILE* 3.7 42.8 - - + +
129E ALA* 4.4 6.7 - - + -
130E ARG* 4.4 13.2 - - + -
133E ARG* 3.3 33.2 - - - +
57F VAL* 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E LEU* 2.9 26.1 + - + -
103E VAL 3.1 7.4 + - - +
105E LEU* 1.3 74.8 - - + +
107E GLU* 1.3 59.9 + - - +
109E ALA* 4.0 1.6 - - - +
110E TYR* 2.9 31.7 + - - +
121E ILE* 4.7 9.0 - - + -
126E ILE* 3.7 28.7 - - + -
34F ILE* 4.0 13.5 - - + -
37F LEU* 3.8 17.0 - - + -
38F ALA* 3.6 39.0 - - + -
41F GLY* 4.4 9.9 - - - -
43F VAL* 4.0 16.6 - - + +
50F ILE* 4.1 11.2 - - + -
54F THR* 3.5 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 4.4 16.1 + - - +
107C VAL* 3.7 31.9 - - - +
110C ASN* 6.1 3.1 - - - +
103E VAL* 2.9 18.3 + - - +
104E HIS* 3.0 31.9 + - - +
106E PHE* 1.3 76.5 - - - +
108E ASP* 1.3 62.1 + - - +
110E TYR* 3.2 3.8 + - - +
111E LEU* 3.0 27.2 + - - +
40F ARG 4.5 1.2 - - - +
41F GLY* 3.5 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 2.9 33.7 + - - -
132A ILE* 3.5 32.1 - - + +
104E HIS* 3.0 18.0 + - - +
105E LEU 3.9 2.9 - - - +
107E GLU* 1.3 73.4 - - - +
109E ALA* 1.3 67.6 + - - +
111E LEU* 3.0 16.6 + - - +
112E LEU* 3.1 9.9 + - - +
129E ALA* 4.2 10.1 - - + -
133E ARG* 3.0 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E LEU 2.9 21.9 + - - +
106E PHE* 4.1 2.9 - - - +
108E ASP* 1.3 72.4 - - - +
110E TYR* 1.3 56.4 + - - +
112E LEU* 3.1 6.6 + - - +
113E THR* 2.9 26.9 + - - -
121E ILE* 3.6 19.1 - - + -
125E ASP* 3.6 6.5 - - - +
126E ILE* 3.7 34.1 - - + +
129E ALA* 3.9 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLN* 5.4 4.9 - - + -
115C LEU* 3.2 36.8 - - + +
106E PHE 2.9 19.6 + - - +
107E GLU* 3.6 6.1 - - - +
109E ALA* 1.3 74.1 - - - +
111E LEU* 1.3 65.5 + - - +
113E THR* 3.1 23.5 + - + -
114E LEU* 2.9 38.0 + - + +
119E VAL 2.7 29.4 + - - -
121E ILE* 3.9 7.2 - - + +
41F GLY 4.8 2.5 - - - +
42F GLY 3.6 26.0 - - - -
43F VAL* 3.7 28.0 - - + -
44F LYS* 3.2 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.9 22.0 - - + +
131A ARG* 3.6 51.8 - - + +
132A ILE* 4.4 7.2 - - + -
112C GLN* 4.0 31.9 - - + +
107E GLU 3.0 18.4 + - - +
108E ASP* 3.0 7.2 + - - +
110E TYR* 1.3 76.9 - - - +
112E LEU* 1.3 57.9 + - - +
114E LEU* 3.3 6.7 + - + +
115E HIS* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.5 26.2 - - + -
115A HIS* 3.5 22.7 - - + +
128A LEU* 3.6 21.1 - - + -
132A ILE* 4.2 11.9 - - + -
108E ASP 3.7 9.6 - - - +
109E ALA 3.1 8.5 + - - +
111E LEU* 1.3 78.8 - - - +
113E THR* 1.3 62.4 + - - +
115E HIS* 3.2 6.7 + - + +
116E ALA 3.1 17.7 + - - -
125E ASP* 3.6 10.8 - - + +
128E LEU* 3.9 20.4 - - + -
129E ALA* 3.4 37.5 - - + +
132E ILE* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E ALA 2.9 14.6 + - - -
110E TYR* 3.1 17.9 + - + -
112E LEU* 1.3 75.4 - - - +
114E LEU* 1.3 61.9 + - - +
116E ALA* 3.2 9.0 + - - +
118E ARG* 3.1 45.5 + - - +
119E VAL 3.9 2.5 - - - -
120E THR 3.3 34.8 - - - +
121E ILE* 3.1 14.6 - - - +
125E ASP* 2.9 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLN* 3.6 43.5 - - + +
114C VAL* 4.5 21.8 - - + -
115C LEU* 4.2 16.8 - - + -
110E TYR* 2.9 41.2 + - + +
111E LEU* 3.8 7.4 - - + +
113E THR* 1.3 76.2 - - - +
115E HIS* 1.3 57.1 + - - +
117E LYS* 2.8 22.5 + - - +
118E ARG 3.4 18.2 - - - +
119E VAL* 4.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.7 16.2 + - + +
115A HIS* 5.2 3.8 - - - +
116A ALA* 3.6 22.8 - - + +
118A ARG* 3.3 12.9 + - - -
124A LYS* 3.9 29.3 + - + +
125A ASP* 2.8 36.2 + - - -
128A LEU* 3.4 29.9 - - + +
111E LEU 3.0 13.9 + - - +
112E LEU* 3.3 10.8 - - - +
114E LEU* 1.3 77.6 - - - +
116E ALA* 1.3 55.5 + - - +
117E LYS* 3.1 10.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
115A HIS* 4.0 20.4 - - + +
116A ALA* 4.5 9.6 - - - +
117A LYS* 6.2 2.2 - - + -
112E LEU 3.1 11.5 + - - +
113E THR 3.6 8.7 - - - +
114E LEU 3.2 1.0 - - - -
115E HIS* 1.3 74.2 - - - +
117E LYS* 1.3 74.1 + - - +
118E ARG* 3.0 37.4 + - - +
----------------------------------------------------------
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