Contacts of the helix formed by residues 8 - 34 (chain Y) in PDB entry 2BKC
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 8 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Y VAL* 1.3 74.9 - - - +
9Y THR* 1.3 64.5 + - - +
10Y LYS* 3.6 19.5 + - - +
11Y GLU* 3.2 28.5 + - - +
12Y PHE* 3.2 17.0 + - - +
119Y LEU* 3.6 10.4 - - - +
123Y GLU* 3.1 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 9 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Y ASP* 1.3 72.2 - - - +
10Y LYS* 1.3 66.6 + - - +
12Y PHE* 3.3 7.6 + - + +
13Y LEU* 3.1 24.0 + - + +
67Y ILE* 4.0 13.7 - - + -
119Y LEU* 4.5 3.3 - - - +
120Y THR* 3.9 23.3 + - - -
123Y GLU* 2.8 35.1 + - - +
125Y ASP* 3.6 25.4 + - - +
128Y THR* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 10 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155N LEU* 5.9 0.8 - - - +
8Y ASP* 3.3 18.5 + - - +
9Y THR* 1.3 80.6 - - - +
11Y GLU* 1.3 58.7 + - + +
14Y ASN* 3.1 23.2 + - - +
64Y LEU* 3.2 23.1 - - + +
67Y ILE* 3.3 38.0 + - + +
68Y GLY* 4.4 7.6 - - - -
69Y GLY* 3.6 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Y VAL* 3.9 29.2 + - + +
8Y ASP* 3.2 20.6 + - - +
10Y LYS* 1.3 76.6 - - + +
12Y PHE* 1.3 64.2 + - - +
14Y ASN* 3.8 8.7 - - + +
15Y HIS* 3.1 23.7 + - - +
72Y PHE* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 12 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Y VAL* 4.4 8.5 - - + +
8Y ASP 3.2 16.6 + - - +
9Y THR* 3.7 5.4 - - + +
10Y LYS 3.3 0.2 - - - -
11Y GLU* 1.3 77.7 - - - +
13Y LEU* 1.3 75.5 + - + +
15Y HIS* 3.1 17.1 + - + +
16Y GLN* 3.1 49.9 + - + +
112Y GLU* 3.1 28.9 - - + -
113Y TYR* 3.9 11.4 - + - -
115Y GLN* 5.0 2.7 - - + -
116Y GLY* 3.5 29.4 - - - -
119Y LEU* 3.8 14.6 - - + -
132Y LEU* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Y THR* 3.1 21.8 + - + +
10Y LYS 3.7 4.7 - - - +
12Y PHE* 1.3 98.9 - - + +
14Y ASN* 1.3 61.9 + - - +
16Y GLN* 3.1 2.8 + - - -
17Y VAL* 3.1 20.2 + - - +
60Y VAL* 3.2 31.0 - - + +
63Y ARG* 4.2 8.5 - - + -
64Y LEU* 4.0 33.9 - - + +
67Y ILE* 4.3 5.6 - - + -
128Y THR* 3.6 35.2 - - + +
131Y MET* 4.6 3.6 - - + -
132Y LEU* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 14 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Y LYS 3.1 18.2 + - - +
11Y GLU* 4.0 10.7 - - + +
12Y PHE 3.3 0.2 - - - -
13Y LEU* 1.3 77.8 - - - +
15Y HIS* 1.3 63.0 + - - +
17Y VAL* 3.4 6.3 + - - +
18Y ALA 3.2 16.5 + - - -
64Y LEU* 3.2 12.6 - - + +
70Y SER 3.5 12.7 + - - -
71Y PRO* 3.2 10.6 - - - +
72Y PHE* 3.0 74.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 15 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Y GLU 3.1 13.3 + - - +
12Y PHE* 3.1 14.4 + - + +
14Y ASN* 1.3 77.5 - - - +
16Y GLN* 1.3 61.7 + - - +
18Y ALA* 3.3 8.1 + - - +
19Y ASN* 2.8 33.6 + - - +
72Y PHE* 4.5 4.4 - - - -
81Y ASN* 2.9 32.6 + - + -
82Y ALA 4.1 0.2 - - - -
83Y SER* 3.0 38.1 + - - -
112Y GLU* 3.3 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 16 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Y PHE* 3.1 52.1 + - + +
13Y LEU* 3.1 7.4 + - + +
15Y HIS* 1.3 81.5 + - - +
17Y VAL* 1.3 54.3 + - - +
18Y ALA 3.1 1.8 - - - -
19Y ASN* 2.5 29.2 + - - +
20Y LEU* 2.7 46.4 + - + +
60Y VAL* 4.3 11.9 - - + -
109Y LEU* 3.7 9.7 - - - +
112Y GLU* 3.0 25.4 + - - +
113Y TYR* 3.7 21.7 - - + -
132Y LEU* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32V TRP* 4.5 12.1 - - + -
13Y LEU 3.1 16.5 + - - +
14Y ASN* 3.4 18.8 + - - +
16Y GLN* 1.3 74.3 - - - +
18Y ALA* 1.3 62.2 + - - +
20Y LEU* 3.6 0.6 + - - -
21Y ASN* 3.0 38.4 + - - +
57Y MET* 4.0 11.0 - - - +
60Y VAL* 3.9 15.9 - - + +
61Y ALA* 4.2 20.4 - - + +
64Y LEU* 4.8 2.0 - - + -
71Y PRO* 4.8 3.6 - - + -
72Y PHE* 3.8 13.7 - - + +
78Y PHE* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Y ASN 3.2 9.4 + - - +
15Y HIS 3.4 9.2 - - - +
16Y GLN 3.1 0.2 - - - -
17Y VAL* 1.3 78.4 - - - +
19Y ASN* 1.3 68.5 + - - +
21Y ASN* 3.4 2.8 + - - +
22Y VAL* 3.3 23.2 + - - +
72Y PHE* 4.2 2.9 - - + -
78Y PHE* 3.7 39.7 - - + +
81Y ASN* 4.2 11.0 - - + -
82Y ALA* 4.0 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 19 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Y HIS* 2.8 18.6 + - - +
16Y GLN* 2.5 33.6 + - - +
18Y ALA* 1.3 72.0 - - - +
20Y LEU* 1.3 63.9 + - - +
22Y VAL* 3.0 7.8 + - - +
23Y PHE* 2.9 22.5 + - - +
82Y ALA* 3.6 4.7 - - - -
83Y SER* 2.9 35.4 + - - -
84Y VAL* 3.3 18.3 + - + +
108Y LEU* 4.5 0.8 - - - +
109Y LEU* 3.8 17.0 - - + +
112Y GLU* 3.0 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Y GLN* 2.7 28.4 + - + +
19Y ASN* 1.3 73.5 - - - +
21Y ASN* 1.3 57.3 + - - +
23Y PHE* 3.4 6.2 + - + +
24Y THR* 3.0 33.8 + - - -
53Y PHE* 3.9 27.5 - - + +
56Y GLN* 3.8 12.1 - - - +
57Y MET* 3.6 42.6 - - + +
60Y VAL* 3.9 17.7 - - + -
109Y LEU* 4.5 17.3 - - + -
113Y TYR* 3.5 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 21 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25V VAL* 4.1 13.2 - - - +
28V HIS* 5.3 1.9 - - - -
32V TRP* 4.9 0.4 - - - -
50V TYR* 5.5 1.2 + - - -
75V LEU* 3.8 4.6 - - + +
17Y VAL* 3.0 24.4 + - - +
18Y ALA 3.9 2.5 - - - +
19Y ASN 3.0 0.8 + - - -
20Y LEU* 1.3 78.0 - - - +
22Y VAL* 1.3 63.4 + - - +
24Y THR* 3.6 10.9 - - - +
25Y VAL* 3.4 26.5 + - - +
57Y MET* 3.0 40.6 - - - +
78Y PHE* 3.7 42.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 22 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75V LEU* 3.7 25.4 - - + -
18Y ALA 3.3 12.8 + - - +
19Y ASN 3.0 6.5 + - - +
21Y ASN* 1.3 75.9 - - - +
23Y PHE* 1.3 66.1 + - - +
25Y VAL* 3.3 5.4 + - - +
26Y LYS* 3.1 19.9 + - + +
78Y PHE 4.4 4.3 - - - +
79Y LEU* 5.1 6.3 - - + -
82Y ALA* 3.8 17.7 - - + -
84Y VAL* 3.7 30.5 - - + +
85Y GLU 4.4 0.2 - - - +
86Y GLU* 3.8 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Y ASN 2.9 13.5 + - - +
20Y LEU* 3.6 11.0 - - + +
22Y VAL* 1.3 76.4 - - - +
24Y THR* 1.3 63.2 + - - +
26Y LYS* 2.9 17.4 + - + +
27Y ILE* 2.8 44.9 + - + +
49Y LEU* 4.9 0.9 - - + -
53Y PHE* 3.8 44.9 - + + -
84Y VAL* 4.3 6.3 - - + +
102Y LEU* 3.5 35.0 - - + -
105Y THR* 3.6 30.3 - - + -
106Y LEU* 4.0 15.7 - - + -
109Y LEU* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50V TYR* 5.8 2.9 - - - +
20Y LEU 3.0 20.6 + - - -
21Y ASN* 3.6 19.5 - - - +
23Y PHE* 1.3 73.0 - - - +
25Y VAL* 1.3 69.8 + - + +
27Y ILE* 3.2 8.8 + - - +
28Y HIS 3.2 16.6 + - - -
50Y TYR* 3.4 45.6 + - + +
53Y PHE* 4.3 4.9 + - - +
54Y GLY* 4.1 22.3 + - - -
57Y MET* 5.5 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21V ASN* 4.2 9.6 - - - +
73V SER* 3.3 23.7 - - - +
74V THR* 3.8 7.0 - - - -
75V LEU* 3.6 17.7 - - + -
78V PHE* 3.7 31.4 - - + -
21Y ASN 3.4 14.8 - - - +
22Y VAL 3.3 8.6 + - - +
23Y PHE 3.2 0.6 - - - -
24Y THR* 1.3 78.3 - - + +
26Y LYS* 1.3 61.1 + - - +
28Y HIS* 3.3 12.8 + - + +
29Y GLN* 3.0 24.3 + - - +
50Y TYR* 5.3 0.2 - - - -
86Y GLU* 4.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73V SER 4.9 1.6 - - - -
22Y VAL* 3.1 12.0 + - + +
23Y PHE* 2.9 20.9 + - + +
25Y VAL* 1.3 76.3 - - - +
27Y ILE* 1.3 57.1 + - - +
29Y GLN* 2.8 41.5 + - - +
30Y ILE* 2.9 29.3 + - + +
84Y VAL* 4.4 7.4 - - - -
85Y GLU 3.0 28.7 + - - -
86Y GLU* 3.9 14.6 - - + +
87Y ALA 4.8 1.0 - - - +
101Y ASP* 3.0 33.5 + - - +
102Y LEU* 5.4 0.2 - - - -
105Y THR* 3.7 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 27 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Y PHE* 2.8 58.2 + - + +
24Y THR* 3.2 11.0 + - - +
26Y LYS* 1.3 75.2 - - - +
28Y HIS* 1.3 63.4 - - - +
30Y ILE* 3.5 8.8 + - + +
31Y HIS* 3.0 22.1 + - + +
46Y MET* 3.5 42.1 - - + +
49Y LEU* 4.1 28.5 - - + +
50Y TYR* 4.2 10.8 - - + +
53Y PHE* 4.7 2.2 - - + -
102Y LEU* 4.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 28 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21V ASN* 5.3 2.0 - - - -
57V MET* 3.4 27.1 - - + +
58V ASP* 3.3 30.9 + - - -
24Y THR 3.2 8.4 + - - +
25Y VAL* 3.3 14.6 - - + +
27Y ILE* 1.3 79.9 - - - +
29Y GLN* 1.3 56.5 + - - +
31Y HIS* 3.3 9.9 + + - +
32Y TRP* 2.8 62.5 + + + -
50Y TYR* 3.6 46.9 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73V SER* 3.1 48.4 + - - +
74V THR* 4.0 1.8 - - - +
25Y VAL 3.0 10.0 + - - +
26Y LYS* 2.8 41.3 + - - +
28Y HIS* 1.3 70.5 - - - +
30Y ILE* 1.3 66.8 + - + +
32Y TRP* 3.2 5.0 + - - -
33Y TYR* 3.0 38.8 + - + +
86Y GLU* 6.1 0.4 - - - +
87Y ALA 3.1 25.0 + - - +
89Y TYR* 4.0 19.3 + - + -
98Y LEU* 5.6 5.5 - - + +
101Y ASP* 5.0 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Y LYS* 2.9 35.2 + - + +
27Y ILE* 3.6 11.2 - - + +
28Y HIS 3.3 0.2 - - - -
29Y GLN* 1.3 78.3 - - + +
31Y HIS* 1.3 65.4 + - - +
33Y TYR 3.8 0.2 - - - -
34Y MET* 2.9 39.7 + - + +
46Y MET* 4.0 8.3 - - + -
98Y LEU* 3.8 46.6 - - + +
99Y MET* 3.7 24.9 - - + -
101Y ASP* 5.3 1.8 - - + -
102Y LEU* 4.1 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 31 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144O TRP* 4.9 12.4 - + - -
58V ASP* 6.0 1.3 - - - -
62V GLU* 4.8 12.2 + - - -
27Y ILE 3.0 12.6 + - - +
28Y HIS* 3.4 14.8 - + - +
30Y ILE* 1.3 81.1 - - - +
32Y TRP* 1.3 75.6 + + + +
34Y MET* 3.6 22.8 - - - +
39Y PHE* 4.4 11.4 - + - -
43Y GLY* 2.9 41.8 + - - -
46Y MET* 3.5 12.8 - - + +
47Y ASP* 3.2 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 32 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144O TRP* 4.6 6.9 + + - -
17V VAL* 4.3 5.2 - - + -
21V ASN* 5.0 1.8 - - - -
57V MET* 3.8 23.3 - - + -
58V ASP* 5.0 11.2 + - - +
61V ALA* 3.5 26.6 - - + +
62V GLU* 5.1 7.5 + - + +
65V LEU* 3.5 46.2 - - + +
71V PRO* 3.8 18.8 - - + -
72V PHE 3.3 24.5 - - - -
73V SER* 4.2 15.3 - - - -
78V PHE* 5.0 3.8 - + - -
25Y VAL* 6.3 0.2 - - + -
28Y HIS* 2.8 62.7 + + + +
29Y GLN 3.7 2.7 - - - +
30Y ILE 3.1 0.2 + - - -
31Y HIS* 1.3 92.8 - + - +
33Y TYR* 1.3 67.4 + - + +
34Y MET 4.8 1.6 - - - +
39Y PHE* 5.7 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 33 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65V LEU* 5.0 3.4 - - + -
70V SER* 3.2 25.2 - - - -
71V PRO* 2.6 55.2 + - + -
73V SER* 3.7 16.8 + - - -
29Y GLN* 3.0 27.1 + - + +
30Y ILE* 3.8 1.1 - - - +
32Y TRP* 1.3 81.8 - - + +
34Y MET* 1.3 67.8 + - - +
35Y ARG* 3.4 15.3 + - - +
89Y TYR* 3.2 70.2 + + + +
93Y LYS 5.5 0.9 - - - +
98Y LEU* 4.7 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 34 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144O TRP* 5.8 0.5 + - - -
148O ALA* 4.4 0.9 - - - +
30Y ILE* 2.9 34.9 + - + +
31Y HIS* 3.6 17.0 - - - +
32Y TRP 3.6 1.8 - - - +
33Y TYR* 1.3 78.6 - - - +
35Y ARG* 1.3 65.0 + - - +
39Y PHE* 3.4 35.6 - - + +
42Y LEU* 3.9 20.0 - - + -
43Y GLY* 3.6 25.1 - - - -
46Y MET* 3.9 14.6 - - + -
95Y MET* 3.7 26.5 - - + -
98Y LEU* 4.0 12.3 - - + -
99Y MET* 4.6 0.9 - - + -
----------------------------------------------------------
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