Contacts of the helix formed by residues 84 - 113 (chain A) in PDB entry 2OQH
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 MSE 84 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS 5.2 0.4 + - - -
82A GLN 3.1 1.0 + - - -
83A HIS* 1.3 111.5 + - + +
85A VAL* 1.3 64.8 + - - +
86A PRO 3.3 1.3 - - - -
87A PHE* 3.0 61.4 + - + +
88A PHE* 3.3 27.9 - - + -
199C ASN* 5.9 2.5 - - + +
247C MSE 4.2 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.9 19.5 - - + -
63A MSE 4.3 8.1 - - + -
82A GLN* 3.3 41.5 - - + +
84A MSE 1.3 76.9 - - - +
86A PRO* 1.3 62.0 - - + +
88A PHE* 3.3 3.3 + - - -
89A TYR* 2.9 51.4 + - + +
93A GLY* 4.0 12.8 - - - +
97A ILE* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLN 3.3 12.8 - - - +
83A HIS* 3.3 14.6 - - - +
85A VAL* 1.3 89.4 - - + +
87A PHE* 1.3 60.7 + - - +
90A GLY* 2.8 36.7 + - - +
93A GLY* 4.5 1.8 - - - -
94A TYR* 3.4 53.8 - - + +
97A ILE* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A HIS 4.5 1.9 + - - +
84A MSE 3.0 48.6 + - + +
86A PRO* 1.3 82.4 - - - +
88A PHE* 1.3 80.1 + + - +
251A ARG* 5.8 6.7 - - - +
91C TYR* 3.5 29.0 + + - +
246C ASN* 5.4 0.7 - - - -
247C MSE 4.2 44.0 - - + -
250C VAL* 5.3 4.9 - - + -
273C LYS* 3.8 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A MSE 3.3 39.5 + - + -
85A VAL* 3.3 5.4 + - - +
87A PHE* 1.3 102.5 - + - +
89A TYR* 1.3 65.1 + + + +
90A GLY 3.4 0.7 - - - -
51C MSE 5.4 4.0 - - + -
52C TRP* 3.4 52.5 - + + -
91C TYR* 3.4 35.1 + + + +
92C LEU* 3.1 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.4 33.7 - - + -
62A ARG* 3.2 35.6 + - - -
85A VAL* 2.9 46.3 + - + +
88A PHE* 1.3 75.3 - + + +
90A GLY* 1.3 64.5 + - - +
91A TYR 3.5 0.3 + - - -
92A LEU* 3.4 10.0 + - + +
93A GLY* 3.3 21.6 + - - +
52C TRP* 3.9 24.0 - + - -
55C PRO* 4.3 10.6 - - + +
88C PHE 3.6 3.1 - - - +
89C TYR* 3.4 15.5 - - - +
92C LEU* 3.5 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 2.8 21.0 + - - +
87A PHE 4.6 0.2 - - - -
88A PHE 3.4 2.8 + - - -
89A TYR* 1.3 76.7 - - - +
91A TYR* 1.3 55.7 + - - -
93A GLY* 2.7 24.3 + - - -
94A TYR* 3.2 19.3 + - - -
89C TYR 4.0 0.4 + - - -
90C GLY* 3.9 17.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A MSE 3.5 29.7 - - + +
90A GLY* 1.3 69.8 - - - -
92A LEU* 1.3 64.2 + - + +
94A TYR* 3.1 10.4 + - - +
95A ALA* 2.9 19.9 + - - +
270A ASP* 3.9 10.0 + - - -
272A TYR* 3.9 4.4 - - - +
273A LYS* 3.5 64.4 - - + -
297A HIS* 4.5 7.4 - - - -
299A GLY* 5.2 5.0 - - - -
87C PHE* 3.5 25.9 + + - +
88C PHE* 3.3 50.5 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A MSE 4.6 11.7 - - + -
52A TRP* 3.8 28.3 - - + -
55A PRO* 3.6 26.2 - - + -
56A VAL* 3.9 18.6 - - + +
59A ILE* 3.7 15.4 - - + +
89A TYR* 3.8 7.0 - - + +
90A GLY 3.2 0.4 - - - -
91A TYR* 1.3 78.0 - - + +
93A GLY* 1.3 56.9 + - - +
95A ALA* 3.7 5.3 - - - +
96A ALA* 2.9 29.8 + - - +
88C PHE* 3.1 21.8 + - + +
89C TYR* 3.5 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 4.0 3.6 - - - -
85A VAL* 4.0 12.7 - - - +
86A PRO* 4.5 3.8 - - - -
89A TYR* 3.3 22.7 + - - +
90A GLY 2.7 11.2 + - - -
92A LEU* 1.3 75.8 - - - +
94A TYR* 1.3 64.7 + - - -
96A ALA* 3.2 3.0 + - - +
97A ILE* 3.0 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 3.4 34.8 - - + +
90A GLY* 3.2 20.3 + - - -
91A TYR* 3.1 9.7 + - - +
93A GLY* 1.3 74.3 - - - +
95A ALA* 1.3 53.6 + - - +
97A ILE* 3.3 4.6 + - + +
98A ALA* 2.8 35.3 + - - +
250A VAL* 4.9 4.5 - - + -
251A ARG* 3.7 39.1 + - + +
253A GLU* 4.3 8.3 + - - -
272A TYR 3.7 1.8 - - - -
273A LYS 3.2 27.4 - - - +
274A TRP* 3.9 22.0 - - - -
275A GLY* 3.4 9.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
50A THR* 2.8 33.7 + - - +
51A MSE 3.8 25.6 - - + -
56A VAL* 4.7 4.5 - - + -
91A TYR 2.9 16.2 + - - +
92A LEU* 3.7 7.0 - - - +
94A TYR* 1.3 75.4 - - - +
96A ALA* 1.3 64.0 + - - +
98A ALA* 3.4 1.4 + - - +
99A ALA 3.2 13.5 + - - -
272A TYR 3.2 17.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
56A VAL* 3.8 13.8 - - + +
59A ILE* 3.6 35.0 - - + -
60A VAL* 3.8 16.3 - - + +
63A MSE 3.9 5.1 - - + +
92A LEU 2.9 18.0 + - - +
93A GLY 3.2 2.7 + - - +
95A ALA* 1.3 72.5 - - - +
97A ILE* 1.3 67.8 + - - +
99A ALA* 3.2 14.6 + - - +
100A VAL* 3.4 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A MSE 3.8 25.8 - - - -
78A PHE* 4.0 10.4 - - + -
79A HIS* 3.4 25.1 - - + +
82A GLN* 3.7 32.3 - - + +
85A VAL* 4.1 3.6 - - + -
86A PRO* 3.8 20.6 - - + -
93A GLY 3.0 14.8 + - - +
94A TYR* 3.6 9.6 - - + +
96A ALA* 1.3 76.7 - - - +
98A ALA* 1.3 56.9 + - - +
100A VAL* 3.1 5.9 + - - +
101A ASP* 2.8 24.8 + - - +
275A GLY* 3.3 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR 2.8 20.5 + - - +
95A ALA 3.7 5.4 - - - +
96A ALA 3.3 0.2 - - - -
97A ILE* 1.3 74.0 - - - +
99A ALA* 1.3 56.8 + - - +
101A ASP* 3.1 3.0 + - - +
102A VAL* 2.8 36.9 + - - +
271A VAL* 3.3 28.5 - - + +
272A TYR* 3.7 20.2 - - + -
275A GLY 3.4 13.4 + - - -
276A GLY* 4.0 0.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
36A VAL* 3.9 24.4 - - + +
48A GLY* 3.7 9.8 - - - -
49A GLU 4.6 8.1 - - - +
50A THR* 3.7 35.1 - - + +
60A VAL* 5.0 0.7 - - + -
95A ALA 3.2 4.0 + - - -
96A ALA* 3.2 11.2 + - - +
98A ALA* 1.3 77.6 - - - +
100A VAL* 1.3 62.3 + - - +
102A VAL* 3.5 3.8 + - - -
103A ALA* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 5.3 0.9 - - + -
36A VAL* 4.7 8.3 - - + -
38A VAL* 4.9 6.3 - - + -
60A VAL* 3.9 24.9 - - + -
63A MSE 4.1 11.9 - - + -
67A LEU* 3.6 36.1 - - + -
78A PHE* 3.7 17.9 - - + -
96A ALA 3.4 12.5 + - - +
97A ILE 3.1 7.2 + - - +
99A ALA* 1.3 74.1 - - + +
101A ASP* 1.3 66.5 + - - +
103A ALA* 3.3 6.7 + - - +
104A CYS* 3.0 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.8 21.3 - - - +
78A PHE* 4.6 2.0 - - + -
79A HIS* 2.7 27.6 + - + +
97A ILE 2.8 13.6 + - - +
98A ALA* 3.3 9.2 - - - +
100A VAL* 1.3 77.7 - - - +
102A VAL* 1.3 63.4 + - - +
104A CYS* 3.2 4.5 + - - +
105A TRP* 3.1 40.5 + - - -
275A GLY 3.7 9.4 - - - +
276A GLY* 3.3 11.3 - - - -
277A ILE* 2.9 24.5 + - - +
278A ALA* 5.1 2.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
47A TRP 3.8 5.6 - - - +
48A GLY* 4.1 7.6 - - - -
49A GLU 5.0 0.7 - - - +
98A ALA 2.8 22.7 + - - +
99A ALA* 3.8 5.2 - - - +
101A ASP* 1.3 71.5 - - - +
103A ALA* 1.3 65.4 + - - +
105A TRP* 3.1 8.5 + - - +
106A ASP* 2.9 21.7 + - - +
271A VAL* 4.0 13.7 - - + -
272A TYR* 4.0 28.9 - - + +
277A ILE* 4.7 6.5 - - + -
304A ILE* 4.9 2.2 - - + -
308A ALA* 3.9 18.6 - - + -
353A LEU* 3.8 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 4.3 6.3 - - + +
38A VAL* 3.5 26.5 - - + -
46A GLY* 3.3 23.8 - - - +
47A TRP 3.5 19.7 + - - -
48A GLY 3.9 1.8 - - - +
99A ALA 3.1 17.4 + - - +
100A VAL* 3.3 4.5 + - - +
102A VAL* 1.3 76.8 - - - +
104A CYS* 1.3 57.1 + - - +
106A ASP 3.3 0.5 + - - -
107A ALA* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.5 13.9 - - - -
38A VAL* 4.7 6.5 - - - -
67A LEU* 5.1 3.8 - - - -
72A PRO* 3.5 35.5 - - - +
75A LEU* 3.8 11.9 - - + -
78A PHE* 5.9 1.1 - - - -
100A VAL* 3.0 30.4 + - - +
101A ASP 3.5 7.6 - - - +
102A VAL 3.2 0.2 - - - -
103A ALA* 1.3 74.8 - - - +
105A TRP* 1.3 59.7 + - - +
107A ALA* 3.2 7.4 + - - +
108A MSE 2.8 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.1 27.5 - - + +
101A ASP* 3.1 42.8 + - - -
102A VAL* 3.1 8.8 + - + +
104A CYS* 1.3 73.2 - - - +
106A ASP* 1.3 67.1 + - - +
108A MSE 3.2 17.1 + - + +
109A GLY 2.9 19.8 + - - -
116A VAL* 3.7 27.8 - - + +
119A LEU* 3.9 32.9 - - + +
120A LEU* 3.4 26.9 - - + -
277A ILE* 3.6 34.3 - - + +
278A ALA* 4.4 15.6 - - + +
353A LEU* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY* 3.4 0.7 - - - -
47A TRP* 2.9 31.3 + - - +
102A VAL 2.9 12.2 + - - +
103A ALA 3.5 8.7 - - - +
105A TRP* 1.3 78.1 - - - +
107A ALA* 1.3 61.5 + - - +
109A GLY 3.3 0.5 + - - -
110A LYS* 3.1 55.9 + - - +
116A VAL* 4.3 2.4 - - - +
352A GLY* 3.5 6.4 - - - -
353A LEU* 2.8 45.6 + - + +
354A GLY 4.6 0.5 + - - -
355A VAL* 5.4 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 5.5 0.2 - - - +
38A VAL* 5.0 3.8 - - + +
40A THR* 4.7 7.9 - - + -
44A VAL* 3.5 23.8 - - + +
45A GLU 4.4 0.4 - - - -
46A GLY* 3.9 13.6 - - - +
72A PRO* 4.3 19.3 - - + -
103A ALA 3.0 17.4 + - - +
104A CYS* 3.5 6.7 - - - +
106A ASP* 1.3 78.3 - - - +
108A MSE 1.3 50.7 + - - +
110A LYS 3.3 0.5 + - - -
111A ALA* 2.8 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PRO* 2.9 32.5 - - + +
73A PHE* 3.6 50.5 - - + +
75A LEU* 3.2 33.7 - - + -
104A CYS 2.8 34.3 + - - +
105A TRP* 3.2 24.2 + - - +
107A ALA* 1.3 75.1 - - - +
109A GLY* 1.3 61.3 + - - +
111A ALA* 3.3 1.1 + - - -
112A THR* 2.9 35.4 + - - +
119A LEU* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TRP 2.9 11.3 + - - -
106A ASP 3.3 1.5 + - - -
108A MSE 1.3 76.2 - - - +
110A LYS* 1.3 52.3 + - - +
112A THR* 3.2 4.7 + - - -
113A GLY* 2.7 30.8 + - - -
114A GLN 2.8 30.4 + - - +
115A SER 5.1 0.4 - - - -
116A VAL 5.1 0.2 - - - -
119A LEU* 3.7 9.6 - - - +
351A PRO* 4.0 0.3 - - - +
352A GLY* 3.6 12.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 3.8 19.1 - - + +
45A GLU* 3.0 32.5 + - - +
47A TRP* 4.1 12.9 - - - +
106A ASP* 3.1 39.4 + - - +
107A ALA 3.6 4.3 - - - +
108A MSE 3.2 0.2 - - - -
109A GLY* 1.3 77.3 - - - +
111A ALA* 1.3 60.7 + - - +
113A GLY* 3.2 10.9 + - - -
351A PRO* 4.3 17.4 - - + +
352A GLY* 4.5 5.6 - - - +
354A GLY 6.2 0.2 - - - +
355A VAL 4.6 13.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
3A LEU* 3.7 29.6 - - + -
44A VAL* 4.3 14.6 - - + +
73A PHE* 4.3 9.2 - - + -
107A ALA 2.8 20.9 + - - +
108A MSE 3.8 4.7 - - - +
110A LYS* 1.3 73.4 - - - +
112A THR* 1.3 59.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 3.9 22.9 - - + -
108A MSE 2.9 23.4 + - - +
109A GLY* 3.2 8.7 + - - -
111A ALA* 1.3 78.2 - - - +
113A GLY* 1.3 61.6 + - - +
114A GLN* 3.3 30.5 + - - +
119A LEU* 3.8 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLY 2.7 11.1 + - - -
110A LYS 3.2 10.4 + - - -
112A THR* 1.3 75.4 - - - +
114A GLN* 1.3 65.6 + - - +
351A PRO* 4.3 19.9 - - - +
----------------------------------------------------------
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