Contacts of the helix formed by residues 82 - 111 (chain A) in PDB entry 6LTJ
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 82 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 1.3 75.3 - - - +
83A SER* 1.3 63.8 + - - +
84A ALA* 3.9 19.6 - - + +
85A ALA* 2.9 23.5 + - + +
86A ILE* 3.3 5.7 + - - +
80B THR* 4.0 14.5 - - + +
81B VAL 3.2 20.2 + - - +
82B THR* 3.8 24.3 - - - +
83B ALA* 3.9 13.7 - - - +
105X G 6.2 0.3 - - - +
106X A 5.3 4.9 + - - -
53Y T 3.9 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLN* 6.1 0.9 - - - +
81A PHE 3.5 3.1 + - - -
82A GLN* 1.3 75.5 - - - +
84A ALA* 1.3 65.1 + - - +
85A ALA 3.3 0.2 + - - -
86A ILE* 3.4 10.0 + - - +
87A GLY* 3.1 17.7 + - - -
53Y T 3.4 21.9 + - - -
54Y T 5.9 2.0 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
82A GLN* 3.2 13.9 - - + +
83A SER* 1.3 82.9 + - - +
85A ALA* 1.3 57.9 + - - +
87A GLY* 3.4 2.5 + - - +
88A ALA* 2.9 28.8 + - - +
83B ALA* 3.7 18.8 - - + +
100B PHE* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 4.5 8.7 - - + -
82A GLN* 2.9 10.3 + - - +
84A ALA* 1.3 77.2 - - - +
86A ILE* 1.3 61.3 + - - +
88A ALA* 3.2 3.1 + - - +
89A LEU* 2.9 33.6 + - - +
81B VAL* 3.2 26.9 - - + +
82B THR 3.5 16.8 - - - +
83B ALA* 3.8 8.6 - - - +
86B VAL* 3.8 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS 5.1 1.1 - - - +
64A PHE* 4.3 10.0 - - + -
65A GLN* 3.4 60.1 - - + +
68A VAL* 4.5 9.4 - - + -
69A ARG* 3.7 17.9 - - - +
81A PHE* 3.8 29.2 - - + +
82A GLN 3.3 4.9 + - - +
83A SER* 3.4 8.5 + - - +
84A ALA 3.4 0.2 - - - -
85A ALA* 1.3 73.0 - - - +
87A GLY* 1.3 66.3 + - - +
89A LEU* 3.8 7.0 - - - +
90A GLN* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 6.2 1.8 - - - -
83A SER 3.1 14.4 + - - -
84A ALA* 3.4 5.1 + - - -
86A ILE* 1.3 76.9 - - - +
88A ALA* 1.3 54.8 + - - +
90A GLN* 3.2 9.7 + - - +
91A GLU* 3.0 36.9 + - - +
100B PHE* 4.1 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA 2.9 17.5 + - - +
85A ALA* 3.2 8.0 + - - +
87A GLY* 1.3 73.4 - - - +
89A LEU* 1.3 66.3 + - - +
91A GLU* 3.3 3.0 + - - +
92A ALA* 3.0 25.3 + - - +
83B ALA* 4.8 2.0 - - + -
86B VAL* 4.4 15.5 - - + -
87B VAL* 4.8 2.0 - - + -
97B LEU* 3.8 11.9 - - + +
100B PHE* 3.8 34.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 3.8 11.4 - - + -
68A VAL* 3.8 29.4 - - + -
81A PHE* 4.4 10.8 - - + -
85A ALA 2.9 16.8 + - - +
86A ILE* 3.8 4.9 - - - +
87A GLY 3.4 0.2 - - - -
88A ALA* 1.3 76.2 - - - +
90A GLN* 1.3 56.5 + - - +
92A ALA* 4.0 5.3 - - + +
93A SER* 2.5 43.5 + - - +
61B PHE* 5.8 1.6 - - + -
62B LEU* 4.8 6.1 - - + -
65B VAL* 3.9 21.8 - - + -
66B ILE* 3.7 29.6 - - + -
69B ALA* 6.3 0.2 - - + -
81B VAL* 6.2 0.2 - - + -
86B VAL* 3.7 20.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
57A LEU* 3.9 15.8 - - + +
59A ILE* 3.0 27.9 - - - +
60A ARG 4.2 0.2 - - - +
61A LYS* 3.8 32.0 + - - +
64A PHE* 3.6 35.6 - - + +
86A ILE* 2.9 21.6 + - - +
87A GLY* 3.2 7.7 + - - +
89A LEU* 1.3 75.6 - - - +
91A GLU* 1.3 67.5 + - - +
93A SER* 4.1 0.2 - - - -
94A GLU* 3.0 46.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 3.2 37.6 - - - +
87A GLY* 3.0 22.8 + - - +
88A ALA 3.7 3.4 - - - +
90A GLN* 1.3 76.9 - - - +
92A ALA* 1.3 57.2 + - - +
94A GLU* 3.9 3.1 - - - +
95A ALA* 2.9 32.2 + - - +
97B LEU* 4.0 13.9 - - + -
100B PHE* 3.5 24.2 - - + -
103G ALA* 3.6 8.7 - - + +
104G GLN* 2.5 46.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
88A ALA 3.0 17.6 + - - +
89A LEU* 4.1 5.4 - - + +
91A GLU* 1.3 77.5 - - - +
93A SER* 1.3 58.6 + - - +
95A ALA* 3.8 4.9 - - - +
96A TYR* 2.9 30.5 + - - +
61B PHE* 4.0 7.2 - - + -
90B LEU* 3.7 37.9 - - + -
95B ARG* 5.7 0.3 + - - -
97B LEU* 4.7 8.7 - - + +
101G THR* 5.2 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 3.4 19.0 - - - -
89A LEU* 2.5 25.9 + - - +
90A GLN 4.1 0.7 - - - -
92A ALA* 1.3 77.3 - - - +
94A GLU* 1.3 58.4 + - - +
96A TYR* 3.4 2.3 + - - +
97A LEU* 3.0 36.0 + - - +
58B LEU* 3.9 19.5 - - - -
61B PHE* 3.9 14.2 - - - -
62B LEU* 3.3 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU 4.7 0.3 - - - +
57A LEU* 3.2 27.1 - - + +
58A LEU* 3.3 21.4 + - - +
59A ILE* 3.2 36.5 + - + +
90A GLN* 3.0 40.5 + - + +
91A GLU* 4.0 2.9 - - - +
93A SER* 1.3 77.3 - - - +
95A ALA* 1.3 57.2 + - - +
97A LEU* 3.2 4.7 + - + +
98A VAL* 3.0 31.0 + - - +
37B LEU* 3.8 21.4 - - + +
40B ARG* 5.0 4.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU 2.9 19.3 + - - +
92A ALA 3.8 3.6 - - - +
94A GLU* 1.3 72.3 - - - +
96A TYR* 1.3 68.1 + - - +
98A VAL* 3.3 11.4 - - - +
99A GLY* 3.0 20.6 + - - -
95B ARG* 5.4 0.8 + - - -
101G THR* 4.2 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ALA 2.9 18.6 + - - +
93A SER* 3.6 2.9 - - - +
95A ALA* 1.3 78.0 - - - +
97A LEU* 1.3 70.7 + - + +
99A GLY* 3.4 1.4 + - - -
100A LEU* 2.9 30.5 + - + +
125A ARG* 2.8 21.5 + - - +
128A ARG* 4.2 11.6 + - - -
130A GLU* 2.3 40.3 + - - -
57B VAL* 4.0 21.2 - - + +
58B LEU* 5.8 0.7 - - + -
61B PHE* 3.6 51.0 - + + +
95B ARG* 3.7 31.0 - - - +
101G THR* 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 5.5 2.7 - - + -
93A SER 3.0 20.1 + - - +
94A GLU* 3.2 4.9 + - + +
96A TYR* 1.3 91.5 - - + +
98A VAL* 1.3 58.2 + - - +
100A LEU* 3.4 20.4 + - + +
101A PHE* 2.9 37.2 + - + -
29B ILE* 6.0 1.1 - - + -
34B ILE* 6.3 0.4 - - + -
37B LEU* 3.8 30.3 - - + -
54B THR* 4.1 26.2 - - + -
57B VAL* 4.7 5.8 - - + -
58B LEU* 3.7 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU 3.0 15.5 + - - +
95A ALA* 3.3 17.5 - - - +
97A LEU* 1.3 73.7 - - - +
99A GLY* 1.3 60.2 + - - +
101A PHE* 3.2 5.6 + - - +
102A GLU* 2.9 33.3 + - - +
37B LEU* 3.4 39.9 - - + +
40B ARG* 3.7 30.1 - - + -
41B GLY* 4.2 4.6 - - - +
107G VAL* 4.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA 3.0 16.0 + - - -
96A TYR* 3.9 1.6 - - - -
98A VAL* 1.3 78.2 - - - +
100A LEU* 1.3 60.2 + - - +
102A GLU* 3.3 11.8 + - - +
103A ASP* 3.1 30.9 + - - +
128A ARG* 4.5 7.2 - - - -
95B ARG* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 2.9 21.7 + - + +
97A LEU* 3.7 17.3 - - + +
99A GLY* 1.3 75.0 - - - +
101A PHE* 1.3 63.6 + - + +
103A ASP* 3.1 3.9 + - - +
104A THR* 2.9 45.7 + - + +
121A ILE* 4.3 16.6 - - + -
124A ALA* 4.5 7.4 - - + -
125A ARG* 3.8 24.7 - - + -
128A ARG* 3.4 27.6 - - - +
54B THR* 5.6 2.0 - - + -
57B VAL* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 2.9 29.9 + - + +
98A VAL 3.8 3.8 - - - +
99A GLY 3.2 0.2 - - - -
100A LEU* 1.3 78.6 - - + +
102A GLU* 1.3 61.7 + - - +
104A THR* 3.3 14.5 + - + -
105A ASN* 2.9 28.9 + - - +
116A ILE* 3.9 23.3 - - + -
121A ILE* 4.4 11.9 - - + -
34B ILE* 4.0 13.5 - - + -
37B LEU* 3.7 39.5 - - + +
38B ALA* 4.0 11.0 - - + -
41B GLY* 4.3 8.5 - - - -
43B VAL* 3.9 9.7 - - + +
50B ILE* 4.4 4.0 - - + -
54B THR* 3.7 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLN* 5.3 4.3 + - - -
98A VAL 2.9 20.7 + - - +
99A GLY* 3.5 11.6 - - - +
100A LEU 3.3 0.2 - - - -
101A PHE* 1.3 77.8 - - - +
103A ASP* 1.3 66.4 + - - +
105A ASN* 3.2 5.9 + - - +
106A LEU* 3.0 27.9 + - + +
40B ARG 5.1 1.9 - - - +
41B GLY* 3.7 22.5 - - - +
107G VAL* 4.4 19.0 - - + +
108G LEU 5.2 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLY 3.1 13.0 + - - +
100A LEU* 3.1 6.3 + - - +
102A GLU* 1.3 82.6 - - - +
104A THR* 1.3 56.9 + - - +
106A LEU* 3.1 16.6 + - - +
107A CYS* 2.9 31.6 + - - -
124A ALA* 4.0 15.7 - - + -
128A ARG* 3.2 36.7 + - - +
129E ARG 5.4 1.0 - - - +
130E ILE* 4.5 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 2.9 22.8 + - + +
101A PHE* 3.3 22.3 + - + -
103A ASP* 1.3 74.3 - - - +
105A ASN* 1.3 64.3 + - - +
107A CYS* 3.7 8.2 - - - +
108A ALA* 2.9 28.8 + - - +
116A ILE* 3.8 12.6 - - - +
120A ASP* 3.7 18.0 - - - +
121A ILE* 3.7 36.6 - - + -
124A ALA* 4.0 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE 2.9 18.9 + - - +
102A GLU* 3.5 7.4 - - - +
104A THR* 1.3 78.5 + - - +
106A LEU* 1.3 59.8 + - + +
108A ALA* 3.3 1.4 + - - +
109A ILE* 2.9 41.6 + - - +
114A VAL 4.4 8.8 - - - +
116A ILE* 4.3 13.0 - - - +
41B GLY 4.5 2.3 + - - +
42B GLY* 2.5 34.0 + - - -
43B VAL* 4.2 11.1 - - + -
44B LYS 5.1 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLU* 3.0 17.3 + - + +
103A ASP* 3.1 19.3 + - - +
105A ASN* 1.3 77.6 - - + +
107A CYS* 1.3 57.3 + - - +
109A ILE* 3.4 9.8 + - + +
110A HIS* 3.0 28.9 + - - +
126E LEU* 4.1 20.2 - - + +
129E ARG* 3.9 29.6 - - + -
130E ILE* 5.0 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASP 2.9 19.6 + - - -
104A THR 3.7 6.3 - - - +
105A ASN 3.3 0.4 - - - -
106A LEU* 1.3 76.9 - - - +
108A ALA* 1.3 61.7 + - - +
110A HIS* 3.4 8.4 + - - +
111A ALA 3.3 15.4 + - - -
120A ASP* 4.0 15.9 - - + -
123A LEU* 3.7 28.3 - - + -
124A ALA* 3.9 17.7 - - - -
113E HIS* 3.4 14.0 + - - +
126E LEU* 4.9 2.9 - - - -
130E ILE* 3.7 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR 2.9 17.4 + - - +
105A ASN* 3.9 4.9 - - - +
107A CYS* 1.3 74.8 - - - +
109A ILE* 1.3 66.4 + - - +
111A ALA 3.3 5.7 + - - -
113A ARG* 2.8 35.3 + - - +
114A VAL 4.7 0.9 - - - +
115A THR 3.4 25.8 - - - +
116A ILE* 3.7 13.9 - - + -
120A ASP* 3.9 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASN* 2.9 33.7 + - - +
106A LEU* 3.8 11.2 - - + +
108A ALA* 1.3 75.2 - - - +
110A HIS* 1.3 58.3 + - - +
112A LYS* 3.0 25.6 + - - +
113A ARG 3.7 15.5 - - - +
114A VAL* 4.7 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU 3.0 18.6 + - - +
107A CYS* 3.5 6.3 - - - +
108A ALA 3.2 0.2 - - - -
109A ILE* 1.3 78.6 - - - +
111A ALA* 1.3 57.1 + - - +
112A LYS* 3.3 10.0 + - - +
110E CYS 3.4 21.9 + - - -
113E HIS* 4.9 4.5 - + - -
114E ALA* 3.7 15.9 - - + +
116E ARG* 3.5 12.5 + - - -
122E LYS* 3.9 32.9 + - + +
123E ASP* 3.0 30.7 + - - -
126E LEU* 3.6 30.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A CYS 3.3 5.4 + - - +
108A ALA 3.3 1.7 + - - +
109A ILE 3.2 0.8 - - - -
110A HIS* 1.3 76.9 - - - +
112A LYS* 1.3 69.0 + - - +
113A ARG* 3.4 34.0 + - - +
113E HIS* 3.8 31.6 - - + +
114E ALA* 4.4 11.8 - - - +
----------------------------------------------------------
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