Contacts of the helix formed by residues 4 - 35 (chain K) in PDB entry 3E1J
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 4 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K GLY* 1.3 70.9 - - - -
5K THR* 1.3 65.4 + - - +
6K LYS* 3.0 6.1 + - - -
7K VAL* 2.9 45.2 + - + +
8K ILE* 3.2 19.8 + - - +
65K LEU* 5.4 0.6 - - - +
107K TYR* 2.9 27.9 + - - -
111K VAL* 3.8 19.2 - - + +
113K ASP* 5.5 3.4 + - + +
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Residues in contact with THR 5 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K LYS* 4.7 12.5 + - - -
3K GLY 3.5 3.7 + - - -
4K ASP* 1.3 74.0 - - - +
6K LYS* 1.3 58.1 + - - +
8K ILE* 3.1 13.8 + - + +
9K ASN* 2.9 40.0 + - - +
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Residues in contact with LYS 6 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K ASP* 3.0 10.1 + - - +
5K THR* 1.3 76.3 - - - +
7K VAL* 1.3 66.8 + - - +
9K ASN* 3.2 19.4 + - + +
10K TYR* 2.9 50.3 + - + -
107K TYR* 3.4 32.4 - - + +
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Residues in contact with VAL 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K ASP* 2.9 31.3 + - + +
6K LYS* 1.3 76.6 - - - +
8K ILE* 1.3 57.5 + - - +
10K TYR* 3.2 8.6 + - + +
11K LEU* 2.8 46.6 + - + +
65K LEU* 4.2 4.3 - - + -
107K TYR* 3.7 18.4 - - + -
108K ALA* 4.4 7.9 - - + -
111K VAL* 3.7 17.7 - - + -
113K ASP* 3.4 29.6 - - + +
116K SER* 4.1 7.4 - - - +
120K MET* 5.8 1.3 - - + -
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Residues in contact with ILE 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K GLY 4.4 9.4 - - - +
4K ASP 3.2 15.5 + - - +
5K THR* 3.1 12.6 + - + +
7K VAL* 1.3 77.0 - - - +
9K ASN* 1.3 58.3 + - - +
11K LEU* 3.2 7.3 + - - +
12K ASN* 2.9 37.7 + - - +
62K ILE* 4.0 25.1 - - + -
65K LEU* 3.6 43.3 - - + +
66K GLU 4.6 0.9 - - - -
67K GLY* 4.1 19.7 - - - +
68K LEU 4.7 0.9 - - - +
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Residues in contact with ASN 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K THR* 2.9 33.1 + - - +
6K LYS* 3.2 23.6 + - + +
8K ILE* 1.3 76.0 - - - +
10K TYR* 1.3 57.7 + - + +
12K ASN* 3.3 8.5 + - - +
13K LYS* 2.9 28.8 + - - +
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Residues in contact with TYR 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K LYS* 2.9 48.3 + - + -
7K VAL* 3.5 8.5 - - + +
9K ASN* 1.3 76.4 - - + +
11K LEU* 1.3 59.1 + - + +
13K LYS* 3.0 19.9 + - + +
14K LEU* 2.8 37.5 + - + +
100K ASN* 4.8 4.0 - - + -
103K GLU* 4.2 27.0 + - + +
104K ALA* 3.7 40.4 - - + +
107K TYR* 3.7 37.9 - + + +
120K MET* 6.2 0.2 - - + -
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Residues in contact with LEU 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K VAL* 2.8 32.0 + - + +
8K ILE* 3.5 5.8 - - - +
10K TYR* 1.3 74.2 - - + +
12K ASN* 1.3 56.9 + - - +
14K LEU* 3.4 4.8 + - + +
15K LEU* 2.8 29.8 + - - +
58K TYR* 4.1 25.3 - - + +
61K ARG* 3.8 27.8 - - + -
62K ILE* 3.6 25.1 - - + +
65K LEU* 3.9 19.3 - - + -
116K SER* 4.2 5.8 - - - +
119K MET* 5.6 1.6 - - - -
120K MET* 4.0 30.3 - - + -
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Residues in contact with ASN 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K ILE* 2.9 28.5 + - - +
9K ASN* 3.7 7.9 + - - +
11K LEU* 1.3 72.8 - - - +
13K LYS* 1.3 61.0 + - - +
15K LEU* 3.3 7.1 + - - +
16K GLY* 2.8 26.2 + - - -
62K ILE* 3.2 17.6 - - - +
68K LEU 3.0 23.2 + - - +
70K ASN* 2.7 41.5 + - + +
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Residues in contact with LYS 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K ASN 2.9 14.4 + - - +
10K TYR* 3.0 22.2 + - + +
12K ASN* 1.3 77.6 - - - +
14K LEU* 1.3 64.3 + - + +
16K GLY* 3.0 4.0 + - - -
17K ASN* 3.0 23.5 + - - +
100K ASN* 3.5 42.4 + - + +
103K GLU* 5.7 2.5 - - - -
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Residues in contact with LEU 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K TYR* 2.8 25.5 + - + +
11K LEU* 3.7 3.1 - - + +
13K LYS* 1.3 69.5 - - + +
15K LEU* 1.3 66.1 + - - +
17K ASN* 2.9 22.9 + - - +
18K GLU* 3.0 15.6 + - - +
58K TYR* 3.6 34.5 - - + +
97K GLY 4.6 0.2 - - - +
100K ASN* 3.6 33.7 - - + +
101K LEU* 3.8 24.5 - - + +
104K ALA* 3.9 10.5 - - + -
120K MET* 3.6 29.8 - - - -
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Residues in contact with LEU 15 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K LEU 2.8 21.0 + - - +
12K ASN* 3.5 19.5 - - - +
14K LEU* 1.3 70.7 - - - +
16K GLY* 1.3 57.4 + - - +
18K GLU* 3.1 2.6 + - - +
19K LEU* 2.9 47.9 + - + +
55K ALA* 3.6 40.6 - - + +
58K TYR* 3.8 14.5 - - + -
59K ILE* 3.9 21.1 - - + -
62K ILE* 4.3 5.4 - - + -
69K PRO* 4.2 4.0 - - + -
70K ASN 3.8 22.7 - - - +
71K LEU* 4.1 5.2 - - + -
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Residues in contact with GLY 16 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K ASN 2.8 15.1 + - - -
13K LYS* 3.0 6.2 + - - -
15K LEU* 1.3 77.2 - - - +
17K ASN* 1.3 62.4 + - - +
19K LEU* 3.3 14.3 + - - +
20K VAL* 3.2 27.5 + - - +
70K ASN 5.3 2.0 + - - -
73K ASP 5.1 5.8 - - - +
74K LEU* 5.1 0.5 - - - +
75K GLY 5.2 1.5 + - - -
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Residues in contact with ASN 17 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13K LYS* 3.0 17.6 + - - +
14K LEU* 2.9 16.7 + - - +
16K GLY* 1.3 77.6 - - - +
18K GLU* 1.3 64.0 + - + +
20K VAL* 3.3 9.6 + - - +
21K ALA* 3.0 21.8 + - - +
93K LEU* 5.0 9.0 - - + +
96K ASP* 6.2 0.6 - - - +
97K GLY* 3.7 24.0 - - - -
100K ASN* 2.9 36.5 + - - +
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Residues in contact with GLU 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K LEU* 3.0 17.6 + - - +
15K LEU 3.7 5.4 - - - +
17K ASN* 1.3 78.0 - - - +
19K LEU* 1.3 59.5 + - - +
21K ALA* 3.2 4.7 + - - +
22K ILE* 2.8 34.4 + - - +
51K GLU* 2.9 47.9 - - - +
54K HIS* 3.3 18.9 + - + +
55K ALA* 4.3 8.1 - - + +
58K TYR* 3.7 20.2 + - + -
101K LEU* 5.2 2.4 - - - +
123K ILE* 3.7 11.1 - - - +
127K GLU* 2.7 21.6 - - - +
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Residues in contact with LEU 19 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K LEU* 2.9 53.6 + - + +
16K GLY* 3.3 19.3 + - - +
17K ASN 3.2 0.4 - - - -
18K GLU* 1.3 80.0 - - - +
20K VAL* 1.3 61.6 + - - +
22K ILE* 3.6 12.2 + - + +
23K ASN* 3.6 19.0 + - - +
55K ALA* 4.7 4.5 - - + -
70K ASN 4.3 9.9 - - - +
71K LEU* 4.0 30.3 - - + +
73K ASP 4.5 11.4 - - - +
74K LEU* 3.8 17.7 - - + +
23L ASN* 4.8 7.4 - - - +
200L HEM 4.4 15.5 - - + -
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Residues in contact with VAL 20 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K GLY 3.2 18.2 + - - +
17K ASN* 3.9 7.6 - - - +
18K GLU 3.3 0.2 - - - -
19K LEU* 1.3 74.3 - - - +
21K ALA* 1.3 59.1 + - - +
23K ASN* 3.2 4.7 + - - +
24K GLN* 2.9 27.9 + - - +
74K LEU* 3.8 8.9 - - + +
75K GLY* 3.9 28.0 - - - +
76K LYS 3.9 15.3 - - - +
77K LEU* 3.7 25.5 - - + +
93K LEU* 3.7 26.9 - - + -
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Residues in contact with ALA 21 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K ASN 3.0 14.9 + - - +
18K GLU* 3.2 8.7 + - - +
20K VAL* 1.3 76.9 - - - +
22K ILE* 1.3 53.2 + - - +
24K GLN* 4.4 0.7 - - - +
25K TYR* 2.8 48.5 + - + +
51K GLU* 3.9 24.9 - - + +
93K LEU* 3.8 20.6 - - + -
94K GLU* 5.6 1.6 - - - +
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Residues in contact with ILE 22 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K GLU 2.8 24.5 + - - +
19K LEU* 3.8 11.4 - - + +
20K VAL 3.3 0.2 - - - -
21K ALA* 1.3 72.3 - - - +
23K ASN* 1.3 66.7 + - - +
26K PHE* 3.0 16.5 + - - +
48K SER* 2.8 31.9 + - - +
51K GLU* 3.6 12.7 - - + +
52K MET* 3.6 44.6 - - + +
55K ALA* 4.1 13.5 - - + -
200L HEM 3.5 45.1 - - + -
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Residues in contact with ASN 23 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K LEU* 3.6 10.7 + - - +
20K VAL 3.2 7.6 + - - +
22K ILE* 1.3 79.8 - - - +
24K GLN* 1.3 67.7 + - - +
26K PHE* 3.3 2.7 + - - +
27K LEU* 3.0 26.4 + - - +
74K LEU* 3.8 12.4 - - - +
77K LEU* 4.4 10.3 - - + -
19L LEU* 4.7 5.0 - - - +
71L LEU* 3.4 45.6 - - + +
200L HEM 3.3 34.6 - - - +
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Residues in contact with GLN 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K VAL* 2.9 19.1 + - - +
21K ALA 4.0 2.2 - - - +
23K ASN* 1.3 76.8 - - - +
25K TYR* 1.3 59.5 + - + +
27K LEU* 4.0 0.9 - - - +
28K HIS* 3.0 47.0 + - + +
76K LYS 4.8 0.5 - - - +
77K LEU* 3.8 15.6 - - + +
78K ASN* 3.0 35.1 + - - +
79K ILE* 4.5 9.0 - - + -
89K SER* 3.1 24.3 + - - -
90K ASP* 2.9 34.7 + - - +
93K LEU* 4.0 19.2 - - + +
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Residues in contact with TYR 25 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K ALA* 2.8 29.3 + - + +
24K GLN* 1.3 78.4 - - + +
26K PHE* 1.3 56.0 + - - +
28K HIS* 3.4 1.6 + - - +
29K ALA* 2.8 30.3 + - - +
44K GLU* 3.4 38.5 - - - +
47K GLU* 3.6 34.7 + - + -
48K SER* 3.9 9.9 - - - +
51K GLU* 3.9 25.4 - - + -
90K ASP* 3.5 28.7 - - + +
93K LEU* 6.1 1.3 - - + -
94K GLU* 2.4 39.6 + - + +
130K HIS* 4.0 3.9 - - - +
134K LEU* 3.6 12.7 - - + +
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Residues in contact with PHE 26 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K ILE 3.0 18.7 + - - +
23K ASN* 3.3 6.2 + - - +
25K TYR* 1.3 74.1 - - - +
27K LEU* 1.3 64.2 + - - +
29K ALA* 3.3 4.9 + - - +
30K ARG* 3.0 39.4 + - + +
45K TYR* 3.6 29.8 - + - -
48K SER* 3.6 20.1 + - - +
52K MET* 4.6 0.7 - - + -
56L ASP* 3.3 43.5 - - + -
59L ILE* 3.9 14.8 - - + -
71L LEU* 5.2 2.0 - - + -
200L HEM 3.6 50.9 - - + -
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Residues in contact with LEU 27 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K ASN 3.0 16.3 + - - +
24K GLN 4.0 2.2 - - - +
26K PHE* 1.3 76.4 - - - +
28K HIS* 1.3 66.4 + - + +
30K ARG* 3.2 1.7 + - - -
31K MET* 2.9 38.3 + - + +
77K LEU* 5.6 0.9 - - + -
79K ILE* 3.6 42.6 - - + -
59L ILE* 4.4 6.7 - - + -
63L LEU* 4.2 6.3 - - + -
69L PRO* 3.8 44.6 - - + +
71L LEU* 4.0 23.5 - - + +
----------------------------------------------------------
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Residues in contact with HIS 28 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K GLN* 3.0 32.8 + - + +
25K TYR 3.7 0.2 - - - +
27K LEU* 1.3 76.1 - - - +
29K ALA* 1.3 64.2 + - - +
31K MET* 3.1 3.6 + - - +
32K PHE* 2.9 32.0 + - + -
44K GLU* 3.1 16.2 - - - +
78K ASN 4.4 0.9 - - - -
79K ILE* 2.8 42.6 + - + -
86K MET* 3.2 49.5 + - + +
90K ASP* 2.7 37.3 + - - -
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Residues in contact with ALA 29 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K TYR 2.8 18.0 + - - +
26K PHE* 3.4 7.9 - - - +
28K HIS* 1.3 76.9 - - - +
30K ARG* 1.3 60.5 + - + +
32K PHE* 3.3 1.7 + - - +
33K LYS 2.9 21.7 + - - -
41K ASN* 3.0 29.3 - - - +
44K GLU* 3.9 7.8 - - + +
45K TYR* 3.6 33.4 - - + +
----------------------------------------------------------
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Residues in contact with ARG 30 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K PHE* 3.0 34.4 + - + +
27K LEU 4.1 0.7 - - - +
29K ALA* 1.3 73.4 - - - +
31K MET* 1.3 59.8 + - - +
33K LYS* 3.5 14.1 - - + +
34K ASN* 2.9 28.9 + - - +
41K ASN* 3.4 29.5 + - - +
45K TYR* 3.3 34.6 - - - -
56L ASP* 2.7 45.9 + - - +
59L ILE* 4.1 9.4 - - + -
60L GLU* 2.9 33.4 + - + +
63L LEU* 3.7 20.8 - - + +
----------------------------------------------------------
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Residues in contact with MET 31 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K LEU* 2.9 35.2 + - + +
28K HIS* 3.3 7.6 - - - +
30K ARG* 1.3 74.8 - - - +
32K PHE* 1.3 66.3 + - - +
34K ASN* 3.1 6.1 + - - +
35K TRP* 2.9 49.3 + - + -
79K ILE* 3.7 22.0 - - + -
80K GLY 3.8 16.4 - - - +
81K GLU* 4.9 2.2 - - - +
86K MET* 3.7 34.5 - - + -
63L LEU* 4.0 17.5 - - + +
----------------------------------------------------------
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Residues in contact with PHE 32 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K HIS* 2.9 24.3 + - + -
29K ALA 3.5 5.4 - - - +
31K MET* 1.3 74.5 - - - +
33K LYS* 1.3 60.6 + - - +
35K TRP* 3.2 13.3 + + - -
36K GLY 3.0 4.5 + - - -
37K LEU* 2.8 36.2 + - + +
40K LEU* 3.6 39.7 - - + -
41K ASN 3.9 12.3 - - - +
44K GLU* 3.9 27.6 - - + -
83K VAL* 4.0 21.1 - - + -
86K MET* 3.4 39.7 - - + -
87K LEU* 3.9 18.4 - - + -
----------------------------------------------------------
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Residues in contact with LYS 33 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K ALA 2.9 6.4 + - - +
30K ARG* 3.5 19.5 - - + +
32K PHE* 1.3 73.3 - - - +
34K ASN* 1.3 69.0 + - - +
36K GLY* 2.9 15.1 + - - -
37K LEU 4.8 2.5 - - - +
38K LYS* 5.3 3.3 - - + +
41K ASN* 3.5 42.0 - - - +
60L GLU* 3.5 28.5 - - + -
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Residues in contact with ASN 34 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G ASP* 3.9 19.1 + - - +
136G THR* 3.4 20.3 + - - +
30K ARG 2.9 17.6 + - - +
31K MET* 3.5 5.8 - - - +
33K LYS* 1.3 79.0 - - - +
35K TRP* 1.3 71.8 + - + +
36K GLY 3.2 0.9 + - - -
60L GLU 5.2 0.8 + - - -
63L LEU* 4.2 23.5 - - + +
64L PHE* 4.0 25.5 - - - +
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Residues in contact with TRP 35 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G THR* 3.4 12.8 - - - +
139G ASP* 5.6 3.6 - - - -
140G LEU* 3.5 18.7 - - - +
143G LYS* 3.8 32.5 + - + +
31K MET* 2.9 34.7 + - + -
32K PHE* 3.6 22.7 - + - +
34K ASN* 1.3 86.1 + - - +
36K GLY* 1.3 60.1 + - - +
37K LEU* 3.4 17.4 + - + +
81K GLU 3.4 26.5 - - - -
82K ASP* 4.3 1.6 - - - -
83K VAL* 4.4 11.0 - - + -
86K MET* 3.7 32.5 - - + -
----------------------------------------------------------
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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