Contacts of the helix formed by residues 86 - 115 (chain A) in PDB entry 6R90
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 86 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 1.3 74.6 - - - +
87A SER* 1.3 65.5 + - - +
88A SER* 4.0 14.1 + - - +
89A ALA* 3.1 16.0 + - - +
90A VAL* 3.3 13.3 + - - +
81B THR* 4.3 10.8 - - + +
82B VAL 3.0 18.6 + - - +
83B THR* 3.2 38.5 - - + +
84B ALA* 3.3 7.1 + - - +
48I T 4.9 5.1 + - - -
49I C 3.5 22.0 + - - +
101J A 5.2 9.9 + - - -
102J G 5.3 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 5.2 4.7 - - - -
85A PHE 3.8 2.0 + - - -
86A GLN* 1.3 72.4 - - - +
88A SER* 1.3 66.8 + - - +
90A VAL* 3.0 10.8 + - - +
91A MET* 3.0 31.9 + - - +
49I C 4.0 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN* 4.0 12.3 + - - +
87A SER* 1.3 82.8 + - - +
89A ALA* 1.3 59.5 + - - +
91A MET* 3.4 9.0 + - - +
92A ALA* 2.9 30.3 + - - +
84B ALA* 3.4 19.9 - - - +
101B PHE* 4.0 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 4.7 9.6 - - + -
86A GLN 3.1 13.0 + - - +
88A SER* 1.3 82.0 + - - +
90A VAL* 1.3 56.3 + - - +
92A ALA* 3.3 4.3 + - - +
93A LEU* 2.9 35.1 + - + +
82B VAL 4.2 8.1 - - - +
83B THR 3.8 9.4 - - - +
84B ALA* 3.7 28.5 - - - +
87B VAL* 4.0 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS 5.1 1.3 - - - +
68A PHE* 3.7 20.8 - - + -
69A GLN* 3.6 42.6 - - + +
72A VAL* 5.4 7.2 - - + -
85A PHE* 4.3 21.8 - - + -
86A GLN 3.5 15.0 - - - +
87A SER* 3.0 6.9 + - - +
89A ALA* 1.3 74.3 - - - +
91A MET* 1.3 78.5 + - + +
93A LEU* 3.3 8.9 + - - +
94A GLN* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.2 23.6 - - + +
65A LYS* 3.3 44.6 - - + +
87A SER* 3.0 21.9 + - - +
88A SER* 3.8 8.3 - - - +
90A VAL* 1.3 93.1 - - + +
92A ALA* 1.3 57.1 + - - +
94A GLN* 3.3 9.8 + - - +
95A GLU* 3.0 33.5 + - + +
101B PHE* 4.2 15.3 - - + -
----------------------------------------------------------
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 SER 2.9 19.1 + - - +
89A ALA* 3.5 7.6 - - - +
91A MET* 1.3 76.8 - - - +
93A LEU* 1.3 62.2 + - - +
95A GLU* 3.3 2.8 + - - +
96A ALA* 3.0 24.1 + - - +
84B ALA* 5.2 3.4 - - + +
87B VAL* 4.6 9.9 - - + -
88B VAL* 5.5 0.9 - - + -
98B LEU* 3.7 23.9 - - + +
101B PHE* 3.7 27.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 3.9 12.6 - - + -
72A VAL* 4.4 24.7 - - + -
85A PHE* 4.8 7.9 - - + -
89A ALA 2.9 23.2 + - - +
90A VAL* 3.7 7.9 - - - +
92A ALA* 1.3 76.2 - - - +
94A GLN* 1.3 59.5 + - - +
96A ALA* 3.4 4.9 + - + +
97A CYS* 2.9 37.7 + - - -
62B PHE* 6.1 0.7 - - + -
63B LEU* 5.0 6.7 - - + -
66B VAL* 3.5 34.3 - - + -
67B ILE* 4.6 15.7 - - + -
87B VAL* 3.7 23.6 - - + -
91B LEU* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.1 19.3 - - + +
63A ILE* 2.8 29.1 - - + +
65A LYS* 4.0 18.6 + - - +
68A PHE* 3.4 49.5 - - + +
90A VAL* 2.9 11.4 + - - +
91A MET* 3.8 19.0 - - - +
92A ALA 3.2 0.4 - - - -
93A LEU* 1.3 75.4 - - - +
95A GLU* 1.3 64.6 + - - +
97A CYS* 3.7 0.4 - - - +
98A GLU* 2.9 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR 5.0 0.9 - - - +
61A LEU* 3.0 23.9 - - + +
91A MET* 3.0 21.7 + - + +
92A ALA* 3.3 5.8 + - - +
94A GLN* 1.3 76.3 - - - +
96A ALA* 1.3 63.5 + - - +
98A GLU* 4.0 2.1 - - - +
99A ALA* 3.0 25.9 + - - +
98B LEU* 5.0 2.7 - - + -
101B PHE* 4.5 7.4 - - + -
102G THR* 5.3 2.5 - - + -
103G ILE 4.9 0.5 - - - +
104G ALA* 3.9 21.2 - - + -
105G GLN* 2.3 61.8 + - + +
106G GLY 4.6 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ALA 3.0 15.9 + - - +
93A LEU* 3.8 4.7 - - + +
95A GLU* 1.3 76.7 - - - +
97A CYS* 1.3 63.7 + - - +
99A ALA* 3.4 5.1 + - - +
100A TYR* 2.9 25.4 + - - +
62B PHE* 4.7 7.3 - - + -
91B LEU* 4.2 29.6 - - + -
96B ARG* 4.8 6.7 + - + +
98B LEU* 4.7 9.3 - - + +
102G THR* 4.9 9.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 6.4 0.7 - - + -
68A PHE* 4.0 22.7 - - + -
93A LEU* 2.9 27.3 + - - +
94A GLN* 3.7 6.3 - - - +
96A ALA* 1.3 77.0 - - - +
98A GLU* 1.3 59.1 + - + +
100A TYR* 3.2 5.3 + - - +
101A LEU* 2.9 35.5 + - + +
59B LEU* 4.6 15.0 - - + -
62B PHE* 3.5 34.1 - - - -
63B LEU* 4.4 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.2 11.0 - - + +
62A LEU* 3.3 23.0 + - - +
63A ILE* 3.0 41.1 + - + +
94A GLN* 2.9 37.5 + - + +
95A GLU* 4.1 2.9 - - - +
97A CYS* 1.3 77.3 - - + +
99A ALA* 1.3 58.2 + - - +
101A LEU* 3.3 5.7 + - + +
102A VAL* 2.9 36.5 + - + +
38B LEU* 3.4 30.3 - - + +
41B ARG* 5.0 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU 3.0 17.2 + - - +
96A ALA 3.9 1.8 - - - +
98A GLU* 1.3 76.6 - - - +
100A TYR* 1.3 62.6 + - - +
102A VAL* 3.3 7.6 + - - +
103A GLY* 3.0 20.6 + - - -
96B ARG* 5.0 0.4 - - - +
102G THR* 3.7 29.6 - - + +
107G GLY 5.9 2.9 - - - +
108G VAL* 5.9 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA 2.9 18.4 + - - +
97A CYS* 3.4 6.7 - - - +
99A ALA* 1.3 77.4 - - - +
101A LEU* 1.3 76.3 + - + +
103A GLY* 3.3 2.3 + - - -
104A LEU* 2.9 37.4 + - + +
129A ARG* 4.0 9.4 + - - +
132A ARG* 4.1 17.5 + - - -
134A GLU* 2.8 41.0 + - - -
58B VAL* 4.3 11.5 - - + +
59B LEU* 6.2 0.7 - - + -
62B PHE* 3.8 41.8 - + + +
96B ARG* 3.3 42.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 5.1 6.5 - - + -
97A CYS* 2.9 23.9 + - + +
98A GLU* 3.8 5.4 - - - +
100A TYR* 1.3 90.3 - - + +
102A VAL* 1.3 60.5 + - - +
104A LEU* 3.2 10.4 + - + +
105A PHE* 2.9 43.4 + - + -
30B ILE* 6.5 0.2 - - + -
35B ILE* 6.3 0.7 - - + -
38B LEU* 4.3 25.8 - - + -
55B THR* 4.7 22.0 - - + -
58B VAL* 4.9 9.6 - - + -
59B LEU* 4.2 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 2.9 23.0 + - + +
99A ALA* 3.6 6.7 - - - +
101A LEU* 1.3 76.6 - - - +
103A GLY* 1.3 62.8 + - - +
105A PHE* 3.3 5.6 + - - +
106A GLU* 3.0 44.9 + - - +
38B LEU* 3.9 33.0 - - + +
41B ARG* 4.1 20.6 - - + +
42B GLY* 4.2 12.9 - - - +
108G VAL* 3.4 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ALA 3.0 14.8 + - - -
100A TYR 3.3 3.3 + - - -
102A VAL* 1.3 77.2 - - - +
104A LEU* 1.3 61.2 + - - +
106A GLU* 3.2 14.3 + - - +
107A ASP* 3.0 32.2 + - - +
132A ARG* 4.7 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 2.9 28.6 + - + +
101A LEU* 3.2 14.6 + - + +
103A GLY* 1.3 77.5 - - - +
105A PHE* 1.3 56.9 + - + +
107A ASP* 3.3 3.1 + - + -
108A THR* 2.5 41.2 + - - +
125A ILE* 4.5 15.3 - - + +
128A ALA* 3.9 19.5 - - + -
129A ARG* 3.9 26.2 - - + +
132A ARG* 4.8 18.1 - - - +
55B THR* 6.4 1.8 - - + -
58B VAL* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 2.9 35.2 + - + +
102A VAL* 3.9 4.7 - - - +
104A LEU* 1.3 80.6 - - + +
106A GLU* 1.3 57.7 + - - +
108A THR* 3.6 6.2 - - - -
109A ASN* 2.8 30.5 + - - +
120A ILE* 3.9 22.6 - - + +
125A ILE* 4.1 13.2 - - + -
35B ILE* 4.1 17.7 - - + -
38B LEU* 4.8 6.5 - - + -
39B ALA* 4.1 32.5 - - + -
42B GLY* 4.9 2.9 - - - -
44B VAL* 4.3 9.3 - - + +
47B ILE* 6.1 0.4 - - + -
51B ILE* 3.8 23.1 - - + -
55B THR* 3.6 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN* 5.3 1.2 + - - +
102A VAL* 3.0 39.4 + - - +
103A GLY* 3.5 13.2 - - - +
104A LEU 3.2 0.2 - - - -
105A PHE* 1.3 76.1 - - - +
107A ASP* 1.3 67.8 + - - +
109A ASN* 3.1 6.2 + - - +
110A LEU* 3.0 28.8 + - + +
41B ARG 4.4 0.5 - - - +
42B GLY* 3.5 26.5 - - - +
108G VAL* 3.7 17.2 - - - +
111G ASN* 6.2 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY* 3.0 18.3 + - - +
104A LEU* 3.9 4.5 - - + +
106A GLU* 1.3 81.9 - - - +
108A THR* 1.3 56.9 + - - +
110A LEU* 3.2 14.9 + - - +
111A CYS* 2.9 35.0 + - - -
128A ALA* 4.6 12.3 - - + -
132A ARG* 3.7 23.3 + - - +
131E ILE* 3.7 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 2.5 26.1 + - - +
105A PHE* 3.6 11.3 - - + -
107A ASP* 1.3 77.4 - - - +
109A ASN* 1.3 56.0 + - - +
111A CYS* 3.2 7.5 + - - +
112A ALA* 2.9 27.4 + - - +
120A ILE* 4.4 15.5 - - + -
124A ASP* 3.5 26.0 - - + +
125A ILE* 3.6 31.4 - - + +
128A ALA* 3.9 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE 2.8 17.2 + - - +
106A GLU* 3.6 6.5 - - - +
108A THR* 1.3 76.4 - - - +
110A LEU* 1.3 59.3 + - + +
112A ALA* 3.2 6.4 + - - +
113A ILE* 2.9 53.1 + - - +
118A VAL* 4.3 12.3 - - - +
120A ILE* 3.9 15.3 - - - +
42B GLY 5.0 2.7 + - - +
43B GLY 3.8 20.8 + - - -
44B VAL* 4.1 19.6 - - + +
45B LYS 5.6 0.2 + - - -
113G GLN* 4.0 12.3 - - + +
116G LEU* 4.3 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 3.0 19.6 + - + +
107A ASP* 3.2 17.5 + - - +
109A ASN* 1.3 77.9 - - + +
111A CYS* 1.3 57.1 + - - +
113A ILE* 3.2 9.4 + - + +
114A HIS* 2.9 28.2 + - - +
127E LEU* 4.1 20.4 - - + +
130E ARG* 4.4 38.1 - - + +
131E ILE* 5.7 2.5 - - + -
113G GLN* 3.2 41.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASP 2.9 20.5 + - - -
108A THR* 3.2 11.6 + - - +
110A LEU* 1.3 75.4 - - - +
112A ALA* 1.3 63.2 + - - +
114A HIS* 3.3 20.5 - - - +
115A ALA 3.4 3.5 + - - -
124A ASP* 4.0 9.9 - - - +
127A LEU* 3.9 33.2 - - + -
128A ALA* 4.8 7.2 - - - -
131A ILE* 4.7 1.6 - - - -
114E HIS* 3.6 12.0 - - + -
127E LEU* 4.3 9.4 - - - -
131E ILE* 3.6 27.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A THR 2.9 11.6 + - - +
109A ASN* 3.4 14.8 - - - +
110A LEU 3.2 0.2 - - - -
111A CYS* 1.3 74.5 - - - +
113A ILE* 1.3 59.9 + - - +
115A ALA* 2.9 21.4 + - - +
117A ARG* 3.2 26.7 + - - +
118A VAL 5.2 0.2 - - - -
119A THR 4.3 16.6 - - - +
120A ILE* 4.4 8.1 - - + -
124A ASP* 3.1 23.5 + - - +
114E HIS* 4.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASN* 2.9 35.1 + - - +
110A LEU* 3.6 8.3 - - + +
112A ALA* 1.3 76.3 - - - +
114A HIS* 1.3 58.7 + - - +
116A LYS* 2.9 21.7 + - - +
117A ARG 3.4 14.1 - - - +
118A VAL* 5.3 3.4 - - + -
113G GLN* 3.5 44.9 - - + +
115G VAL* 4.1 25.1 - - + -
116G LEU* 5.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU 2.9 13.0 + - - +
111A CYS 3.3 12.6 - - - +
112A ALA 3.1 0.4 - - - -
113A ILE* 1.3 78.4 - - - +
115A ALA* 1.3 56.4 + - - +
116A LYS* 3.2 8.2 + - - +
111E CYS 3.6 21.2 + - - -
114E HIS* 5.9 0.7 - + + -
115E ALA* 3.6 13.2 - - + +
117E ARG* 3.2 15.8 + - - -
123E LYS* 3.7 26.3 + - + +
124E ASP* 2.5 59.4 + - - +
127E LEU* 3.6 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A CYS 3.4 0.4 + - - -
112A ALA 2.9 10.9 + - - +
114A HIS* 1.3 77.9 - - - +
116A LYS* 1.3 69.8 + - - +
117A ARG* 3.1 28.7 + - - +
114E HIS* 3.7 32.5 - - + +
115E ALA* 3.7 18.4 - - + +
116E LYS* 5.8 5.0 - - + +
----------------------------------------------------------
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