Contacts of the helix formed by residues 3 - 34 (chain K) in PDB entry 2X17
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 SER 3 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K MET 4.3 0.4 + - - -
2K LEU* 1.3 77.6 - - - +
4K GLU* 1.3 59.8 + - - +
5K ARG* 3.8 1.9 + - - -
6K MET* 3.2 14.2 + - - +
7K LEU* 2.9 26.6 + - - +
111K GLU* 2.6 34.8 + - - -
113K ASP* 5.5 1.4 + - - -
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Residues in contact with GLU 4 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K LEU 3.6 2.9 + - - -
3K SER* 1.3 72.6 - - - +
5K ARG* 1.3 61.8 + - - +
7K LEU* 3.6 10.9 + - + +
8K LYS* 3.3 23.4 + - + +
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Residues in contact with ARG 5 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K SER* 3.2 1.9 - - - +
4K GLU* 1.3 79.2 - - - +
6K MET* 1.3 61.4 + - - +
8K LYS* 3.8 6.1 + - - +
9K ALA* 3.2 21.5 + - - +
107K LEU* 4.4 19.9 - - + +
111K GLU* 3.6 21.8 - - - +
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Residues in contact with MET 6 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K LEU* 4.0 13.7 - - + -
3K SER* 3.0 25.5 + - - +
5K ARG* 1.3 75.8 - - - +
7K LEU* 1.3 56.6 + - - +
8K LYS 3.1 1.8 - - - -
9K ALA* 2.8 7.4 + - - +
10K LEU* 2.7 48.1 + - + +
104K LEU* 4.4 13.9 - - - +
107K LEU* 3.9 18.4 - - + +
108K ALA* 3.7 32.3 - - + +
111K GLU* 3.4 17.9 + - - +
113K ASP* 4.1 16.6 - - + +
116K THR* 3.8 17.3 - - + +
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Residues in contact with LEU 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K LEU* 4.3 18.1 - - + +
3K SER 2.9 14.9 + - - +
4K GLU* 3.9 10.1 - - + +
6K MET* 1.3 74.8 - - - +
8K LYS* 1.3 56.1 + - - +
10K LEU* 3.4 7.4 + - - +
11K ASN* 2.6 55.5 + - - +
61K ILE* 3.8 26.5 - - + -
66K GLY* 4.2 7.4 - - - -
67K ARG* 3.8 25.6 - - + +
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Residues in contact with LYS 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K GLU* 3.3 14.7 + - + +
5K ARG* 3.9 6.3 - - - +
6K MET 3.1 0.6 - - - -
7K LEU* 1.3 79.3 - - - +
9K ALA* 1.3 56.5 + - - +
11K ASN* 3.4 6.0 + - + +
12K ASP* 3.0 56.5 + - - +
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Residues in contact with ALA 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K ARG 3.2 13.0 + - - +
6K MET 2.8 9.0 + - - +
8K LYS* 1.3 78.7 - - - +
10K LEU* 1.3 60.4 + - - +
12K ASP* 3.7 8.8 + - - +
13K GLN* 3.4 18.4 + - - +
16K ARG* 4.6 2.1 + - - -
104K LEU* 3.8 27.6 - - + +
107K LEU* 3.9 16.4 - - + -
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Residues in contact with LEU 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K LEU* 4.0 27.8 - - + -
6K MET* 2.7 35.9 + - + +
7K LEU* 3.7 5.2 - - - +
9K ALA* 1.3 71.5 - - - +
11K ASN* 1.3 60.4 + - - +
12K ASP 3.2 0.2 - - - -
13K GLN* 3.3 4.9 + - - +
14K LEU* 3.0 27.0 + - - +
57K PHE* 4.0 31.0 - - + -
60K TYR* 4.1 13.7 - - + -
61K ILE* 3.9 24.0 - - + +
104K LEU* 4.3 9.9 - - + -
116K THR* 4.0 18.8 - - + -
119K PHE* 4.3 9.0 - - + -
120K LEU* 5.3 1.1 - - + -
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Residues in contact with ASN 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K LEU* 2.6 50.9 + - - +
8K LYS* 3.8 7.9 - - + +
10K LEU* 1.3 74.4 - - - +
12K ASP* 1.3 61.5 + - - +
14K LEU* 3.5 9.7 - - - +
15K ASN* 3.1 27.0 + - - +
61K ILE* 3.8 12.5 - - - +
67K ARG 3.9 4.2 + - - -
68K VAL* 3.4 9.2 - - - +
69K GLU* 2.8 47.2 + - + +
71K ASP* 4.6 5.2 - - - +
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Residues in contact with ASP 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K LYS* 3.0 48.5 + - - +
9K ALA* 3.7 8.1 - - - +
10K LEU 3.2 0.2 - - - -
11K ASN* 1.3 80.1 - - - +
13K GLN* 1.3 57.2 + - - +
15K ASN* 3.3 8.3 + - - +
16K ARG* 2.9 53.5 + - - +
71K ASP* 4.1 12.3 - - - +
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Residues in contact with GLN 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K ALA 3.4 2.8 + - - +
10K LEU 3.3 7.9 + - - +
12K ASP* 1.3 75.5 - - - +
14K LEU* 1.3 61.0 + - - +
15K ASN 3.2 0.2 - - - -
16K ARG* 3.4 22.5 + - - +
17K GLU* 2.8 56.8 + - - +
57K PHE* 3.4 29.2 - - + -
97K ILE* 3.7 10.5 - - - +
100K SER* 2.9 38.0 + - - +
101K ILE* 3.7 14.3 - - + +
104K LEU* 3.7 21.0 - - + +
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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
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252 PHE* 4.5 6.3 - - + -
10K LEU 3.0 12.5 + - - +
11K ASN* 3.5 11.7 - - - +
12K ASP 3.4 0.2 - - - -
13K GLN* 1.3 74.6 - - - +
15K ASN* 1.3 63.3 + - + +
17K GLU* 3.5 4.9 + - - +
18K LEU* 3.2 42.2 + - + +
54K ALA* 3.6 15.9 - - + +
57K PHE* 4.0 15.3 - - + -
58K TYR* 3.6 35.7 - - + +
61K ILE* 4.2 5.4 - - + -
68K VAL* 4.0 22.4 - - + -
69K GLU 5.8 1.3 - - - +
70K LEU* 3.8 20.0 - - + -
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Residues in contact with ASN 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222 TYR* 3.6 9.7 + - - -
11K ASN 3.1 14.3 + - - +
12K ASP* 3.5 11.0 - - - +
14K LEU* 1.3 77.2 - - + +
16K ARG* 1.3 60.0 + - - +
18K LEU* 3.5 7.7 + - - +
19K TYR* 3.1 25.6 + - - +
70K LEU* 5.9 0.2 - - - +
71K ASP* 3.1 51.2 + - - +
72K GLU 3.5 14.2 + - - +
73K ILE* 4.5 5.5 - - - +
74K PRO* 4.8 6.9 - - - +
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Residues in contact with ARG 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K ALA 4.6 2.6 + - - -
12K ASP* 2.9 32.1 + - - +
13K GLN* 3.1 57.1 + - - +
15K ASN* 1.3 77.3 - - - +
17K GLU* 1.3 58.2 + - - +
19K TYR* 3.4 8.9 + - - +
20K SER* 3.0 30.6 + - - -
96K PHE* 4.2 27.1 - - + -
97K ILE* 4.0 8.0 - - + +
100K SER* 3.8 22.7 + - - -
103K GLU* 5.9 0.8 + - - -
104K LEU* 5.6 1.0 - - - +
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Residues in contact with GLU 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K GLN* 2.8 39.4 + - - +
14K LEU 3.8 4.9 - - - +
16K ARG* 1.3 75.2 - - - +
18K LEU* 1.3 58.7 + - - +
20K SER* 3.4 8.1 + - - -
21K ALA* 3.1 21.5 + - - +
50K GLU* 2.8 49.6 - - - +
53K HIS* 3.7 18.8 + - + +
54K ALA* 3.9 7.9 - - + -
57K PHE* 4.1 17.6 - - + -
97K ILE* 3.7 15.3 - - - +
101K ILE* 4.5 1.6 - - - +
123K PHE* 4.3 11.8 - - - -
127K GLN* 4.3 5.9 + - - -
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Residues in contact with LEU 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222 TYR* 3.6 36.3 - - + +
252 PHE* 4.2 12.1 - - + -
14K LEU* 3.2 39.5 + - + +
15K ASN* 3.8 7.4 - - - +
16K ARG 3.3 0.2 - - - -
17K GLU* 1.3 76.4 - - - +
19K TYR* 1.3 58.8 + - - +
21K ALA* 3.4 7.7 - - + +
22K TYR* 3.1 23.7 + - - +
51K ILE* 4.8 21.3 - - + -
54K ALA* 3.8 16.6 - - + -
70K LEU* 4.2 2.5 - - + -
73K ILE* 4.4 17.6 - - + +
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Residues in contact with TYR 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K ASN* 3.1 15.4 + - - +
16K ARG* 3.7 9.0 - - - +
17K GLU 3.3 0.2 - - - -
18K LEU* 1.3 73.9 - - - +
20K SER* 1.3 55.8 + - - +
22K TYR* 3.0 3.7 + - + -
23K LEU* 2.6 48.0 + - + +
73K ILE* 4.1 13.2 - - + +
74K PRO* 3.6 50.7 - - + -
75K LYS 4.6 2.1 + - - -
76K PRO* 3.9 14.2 - - + +
77K PRO* 3.8 23.0 - - - +
93K HIS* 3.7 30.5 - + - -
96K PHE* 6.0 1.3 - + - -
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Residues in contact with SER 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ARG 3.0 14.4 + - - -
17K GLU* 3.4 11.8 + - - -
18K LEU 3.3 0.4 - - - -
19K TYR* 1.3 76.3 - - - +
21K ALA* 1.3 61.5 + - - +
23K LEU* 3.8 2.5 - - - +
24K TYR* 3.0 39.2 + - - -
50K GLU* 3.8 22.7 - - - -
93K HIS* 3.0 28.9 + - - -
94K GLU* 5.8 0.4 - - - -
97K ILE* 3.4 14.7 - - - +
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Residues in contact with ALA 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K GLU 3.1 8.0 + - - +
18K LEU* 3.4 13.5 - - + +
20K SER* 1.3 77.1 - - - +
22K TYR* 1.3 56.0 + - - +
25K PHE* 3.2 23.4 + - - +
47K ALA* 3.3 37.1 - - + +
50K GLU* 3.6 13.1 - - + +
51K ILE* 3.7 20.9 - - + +
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Residues in contact with TYR 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152 ASN* 3.6 9.9 + - - -
182 LEU* 3.6 27.8 - - + +
702 LEU* 3.4 29.9 - - + +
712 ASP 2.7 30.0 + - - -
732 ILE* 3.7 20.9 - - + +
18K LEU 3.1 12.1 + - - +
19K TYR* 3.0 9.5 + + + +
21K ALA* 1.3 75.4 - - - +
23K LEU* 1.3 59.0 + - - +
24K TYR 3.4 0.2 - - - -
25K PHE* 3.4 12.1 + + + +
26K ALA* 2.9 27.9 + - - +
73K ILE* 3.7 25.1 - - + -
74K PRO 4.0 4.3 - - - -
76K PRO* 3.6 30.4 - - + +
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Residues in contact with LEU 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K TYR* 2.6 32.4 + - + +
20K SER* 3.8 4.9 - - - +
22K TYR* 1.3 74.0 - - - +
24K TYR* 1.3 63.5 + - + +
26K ALA* 3.3 6.3 + - - +
27K MET* 2.9 54.3 + - + +
76K PRO* 4.3 4.7 - - + +
77K PRO* 3.8 30.1 - - + -
80K TRP* 4.2 8.1 - - + -
89K ALA 5.2 0.9 - - - +
93K HIS* 3.5 47.1 - - + +
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Residues in contact with TYR 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K SER* 3.0 27.0 + - - +
23K LEU* 1.3 79.7 - - + +
25K PHE* 1.3 60.0 + - - +
27K MET* 3.7 13.2 - - + +
28K ALA* 2.9 22.9 + - - +
42K TRP* 6.1 0.4 - + - -
43K MET* 3.3 50.3 - - + +
46K GLN* 3.7 22.4 - - + -
47K ALA* 4.2 5.6 - - + +
50K GLU* 3.4 31.4 - - + -
90K ALA* 4.1 25.8 + - + -
93K HIS* 4.2 11.2 - + - -
94K GLU* 2.5 35.0 + - - +
134K VAL* 5.0 4.9 - - + +
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Residues in contact with PHE 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142 LEU* 4.5 5.8 - - + -
182 LEU* 4.2 18.8 - - + -
542 ALA* 5.1 4.0 - - + -
552 LEU* 3.8 27.8 - - + -
582 TYR* 3.7 37.5 - + + -
682 VAL* 5.8 0.4 - - + -
702 LEU* 3.6 36.6 - - + +
21K ALA 3.2 19.6 + - - +
22K TYR* 3.6 15.7 - + + +
23K LEU 3.3 0.2 - - - -
24K TYR* 1.3 77.1 - - - +
26K ALA* 1.3 60.4 + - - +
28K ALA* 3.4 8.9 + - + -
29K ALA* 3.2 21.1 + - - +
44K LYS* 4.9 8.1 - - + -
47K ALA* 4.2 9.8 - - + +
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Residues in contact with ALA 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672 ARG* 5.2 0.2 + - - -
702 LEU* 3.6 13.0 - - + +
22K TYR 2.9 14.7 + - - +
23K LEU* 3.3 9.4 + - - +
25K PHE* 1.3 75.8 - - - +
27K MET* 1.3 63.3 + - - +
29K ALA* 3.5 6.8 + - - +
30K TYR* 3.2 19.4 + - - +
76K PRO* 3.7 27.8 - - + -
77K PRO 3.8 13.2 - - - +
78K LYS 4.6 3.3 - - - +
80K TRP* 4.0 7.0 - - + -
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Residues in contact with MET 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K LEU* 2.9 35.6 + - + +
24K TYR* 3.7 13.0 - - + +
25K PHE 3.3 0.2 - - - -
26K ALA* 1.3 73.8 - - - +
28K ALA* 1.3 61.3 + - - +
30K TYR* 3.0 3.6 + - - +
31K PHE* 2.9 40.2 + - + -
43K MET* 3.7 31.4 - - + -
80K TRP* 3.6 37.9 - - + -
86K ALA* 3.4 31.2 - - + +
89K ALA* 4.3 4.9 - - + -
90K ALA* 3.8 22.7 - - + +
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Residues in contact with ALA 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582 TYR* 3.0 14.9 + - - +
24K TYR 2.9 18.5 + - - +
25K PHE* 3.4 12.1 - - + +
27K MET* 1.3 77.0 - - - +
29K ALA* 1.3 56.0 + - - +
31K PHE 3.5 0.2 + - - -
32K GLU* 3.0 23.0 + - - +
40K ALA* 3.5 29.7 - - - +
43K MET* 3.8 8.9 - - + +
44K LYS* 3.8 17.9 - - + +
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Residues in contact with ALA 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582 TYR* 3.4 20.1 + - + -
622 TYR* 2.6 30.8 + - - +
672 ARG* 3.8 10.7 + - - +
682 VAL* 4.0 15.7 - - + +
702 LEU* 5.5 1.6 - - + -
25K PHE 3.2 10.6 + - - +
26K ALA* 3.6 12.6 - - - +
27K MET 3.2 0.2 - - - -
28K ALA* 1.3 77.6 - - - +
30K TYR* 1.3 61.0 + - - +
32K GLU 3.5 0.2 + - - -
33K ASP* 3.3 14.7 + - - +
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Residues in contact with TYR 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672 ARG* 3.8 22.9 - - - +
26K ALA 3.2 11.3 + - - +
27K MET 3.0 10.6 + - - +
29K ALA* 1.3 79.0 - - - +
31K PHE* 1.3 77.4 + + - +
33K ASP* 3.4 16.3 + - + +
34K LEU* 3.6 38.2 + - + +
79K GLU* 4.3 3.1 - - + -
80K TRP* 3.1 60.9 + + + -
81K GLU 3.9 1.6 + - - -
82K SER* 3.2 24.8 - - - -
83K PRO* 3.5 1.6 - - + -
86K ALA* 3.9 23.6 - - + -
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Residues in contact with PHE 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K MET* 2.9 31.3 + - + +
28K ALA 4.0 1.3 - - - +
30K TYR* 1.3 84.3 - + - +
32K GLU* 1.3 63.2 + - - +
34K LEU* 3.2 9.8 + - + -
36K LEU* 3.0 52.1 + - + +
39K PHE* 3.5 32.8 - + + -
40K ALA 3.8 5.6 - - - +
43K MET* 4.1 22.4 - - + -
83K PRO* 3.7 25.8 - - + -
86K ALA* 3.9 17.7 - - + -
87K PHE* 3.7 34.8 - + - -
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Residues in contact with GLU 32 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582 TYR* 3.0 16.3 + - - +
592 ASN* 6.0 0.2 - - - -
622 TYR* 3.7 34.8 - - + -
28K ALA 3.0 16.3 + - - +
29K ALA 3.6 5.2 - - - +
30K TYR 3.3 0.2 - - - -
31K PHE* 1.3 76.2 - - - +
33K ASP* 1.3 60.7 - - - +
35K GLY* 3.3 12.5 + - - +
36K LEU 4.7 2.5 - - - +
37K GLU* 3.4 30.3 - - - +
40K ALA* 3.4 13.4 - - - +
44K LYS* 2.9 30.6 + - - -
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Residues in contact with ASP 33 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622 TYR* 3.7 7.8 - - + -
662 GLY 4.3 9.7 - - - +
672 ARG* 3.6 40.4 + - - +
29K ALA 3.3 5.3 + - - +
30K TYR* 3.5 10.9 - - + +
31K PHE 3.2 0.4 - - - -
32K GLU* 1.3 76.7 - - - +
34K LEU* 1.3 63.0 + - - +
35K GLY* 3.1 8.8 + - - -
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Residues in contact with LEU 34 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1433 PHE* 5.7 6.1 - - - -
30K TYR* 3.6 49.4 - - + +
31K PHE* 3.2 10.5 + - + +
33K ASP* 1.3 82.0 - - + +
35K GLY* 1.3 60.4 + - - +
36K LEU* 3.6 26.9 + - + +
83K PRO* 4.2 11.4 - - + -
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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