Contacts of the helix formed by residues 1 - 31 (chain C) in PDB entry 1IJ2
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 ARG 1 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A MET* 3.8 39.2 - - - +
3A LYS* 4.0 12.9 - - - +
6A GLU* 2.7 45.9 + - + +
0C ACE 1.3 68.3 - - - +
2C MET* 1.3 66.9 + - - +
4C GLN* 3.2 8.4 + - + +
5C LEU* 3.1 24.6 + - + +
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Residues in contact with MET 2 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A MET* 3.5 37.8 - - + +
5A LEU* 3.9 9.4 - - + -
1B ARG* 3.4 41.3 - - + +
2B MET* 4.2 25.6 - - - -
5B LEU* 4.2 16.4 - - + -
0C ACE 3.4 0.2 - - - -
1C ARG* 1.3 79.9 - - - +
3C LYS* 1.3 57.6 + - - +
5C LEU* 3.4 21.7 + - + +
6C GLU* 3.0 28.8 + - - +
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Residues in contact with LYS 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ARG* 4.1 16.9 - - - +
0C ACE 3.3 16.3 + - + +
1C ARG 3.2 0.4 - - - -
2C MET* 1.3 77.5 - - - +
4C GLN* 1.3 59.6 + - - +
6C GLU* 3.3 26.2 + - - +
7C ASP* 2.9 67.4 + - - +
10C GLU* 5.9 0.6 + - - -
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Residues in contact with GLN 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C ACE 2.9 20.5 + - - +
1C ARG* 3.2 9.2 + - - +
3C LYS* 1.3 78.1 - - - +
5C LEU* 1.3 61.9 + - - +
7C ASP* 3.0 32.1 + - - +
8C LYS* 3.0 32.6 + - + +
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Residues in contact with LEU 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A MET* 3.5 33.2 - - + -
5A LEU* 4.1 10.1 - - + +
6A GLU* 3.8 38.8 - - + +
9A VAL* 3.5 34.3 - - + -
5B LEU* 4.7 4.5 - - + -
1C ARG* 3.1 15.2 + - + +
2C MET* 3.6 21.3 - - + +
4C GLN* 1.3 76.7 - - + +
6C GLU* 1.3 56.6 + - - +
8C LYS* 3.3 6.0 + - - +
9C VAL* 2.9 36.2 + - + +
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Residues in contact with GLU 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ARG* 3.3 33.5 + - - -
5B LEU* 4.2 26.0 - - + +
2C MET* 3.0 15.7 + - - +
3C LYS* 3.4 27.4 + - - +
5C LEU* 1.3 78.5 - - - +
7C ASP* 1.3 62.6 + - - +
9C VAL* 3.2 4.8 + - - +
10C GLU* 2.9 45.1 + - + +
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Residues in contact with ASP 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LYS* 2.9 46.3 + - - +
4C GLN* 3.0 34.4 + - - +
6C GLU* 1.3 77.8 - - - +
8C LYS* 1.3 63.0 + - + +
10C GLU* 3.2 18.4 + - - +
11C GLU* 3.1 22.2 + - - +
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Residues in contact with LYS 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.9 26.0 - - + -
13A LEU* 3.3 44.0 - - - +
4C GLN* 3.0 21.8 + - - +
5C LEU* 3.6 9.2 - - + +
7C ASP* 1.3 74.2 - - + +
9C VAL* 1.3 61.9 + - - +
11C GLU* 3.2 30.5 + - - +
12C LEU* 2.9 37.4 + - - +
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Residues in contact with VAL 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.0 14.1 - - + -
12A LEU* 6.1 0.2 - - + -
5B LEU* 3.2 28.3 - - + -
8B LYS* 3.3 35.2 - - + -
9B VAL* 3.7 17.5 - - + -
12B LEU* 3.8 10.3 - - + +
5C LEU 2.9 22.3 + - - +
6C GLU* 3.2 3.8 + - - +
8C LYS* 1.3 75.7 - - - +
10C GLU* 1.3 58.5 + - + +
12C LEU* 3.3 8.3 + - + +
13C LEU* 2.9 28.8 + - + +
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Residues in contact with GLU 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LYS* 5.9 0.3 + - - -
6C GLU* 2.9 38.5 + - + +
7C ASP* 3.4 18.3 - - - +
9C VAL* 1.3 76.7 - - + +
11C GLU* 1.3 62.9 + - - +
13C LEU* 3.3 9.5 + - - +
14C SER* 3.3 24.4 + - - -
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Residues in contact with GLU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.6 6.2 - - - +
7C ASP 3.1 12.4 + - - +
8C LYS* 3.2 41.6 + - - +
10C GLU* 1.3 76.0 - - - +
12C LEU* 1.3 63.7 + - - +
14C SER* 3.3 6.5 + - - -
15C LYS* 3.0 41.9 + - + +
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Residues in contact with LEU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.0 24.5 - - + +
12A LEU* 3.8 33.0 - - + +
13A LEU* 3.6 25.6 - - + +
16A THR* 4.0 8.7 - - + +
12B LEU* 4.3 8.5 - - + -
8C LYS* 2.9 26.2 + - - +
9C VAL* 3.8 9.0 - - + +
11C GLU* 1.3 77.7 - - - +
13C LEU* 1.3 60.1 + - - +
15C LYS* 3.4 27.9 - - - +
16C THR* 2.8 40.8 + - + +
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LYS* 4.7 20.9 - - + +
12B LEU* 3.9 25.7 - - + +
15B LYS* 3.9 17.7 - - - +
9C VAL* 2.9 18.3 + - + +
10C GLU* 3.5 9.0 - - - +
12C LEU* 1.3 76.0 - - - +
14C SER* 1.3 68.8 + - - +
16C THR* 3.0 18.7 + - - +
17C TYR* 3.1 14.9 + - + +
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Residues in contact with SER 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU 3.3 11.0 + - - -
11C GLU* 3.7 8.3 - - - -
12C LEU 3.2 0.6 - - - -
13C LEU* 1.3 84.3 - - - +
15C LYS* 1.3 65.8 + - - +
17C TYR* 3.2 6.7 + - - +
18C HIS* 3.0 23.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.1 24.6 + - - +
16A THR* 2.8 34.7 + - - -
17A TYR* 4.7 3.8 - - - +
20A GLU* 3.5 24.8 + - - +
11C GLU* 3.0 33.7 + - + +
12C LEU* 3.4 21.1 - - - +
14C SER* 1.3 78.8 - - - +
16C THR* 1.3 56.6 + - - +
18C HIS* 3.2 9.9 + - - +
19C LEU* 2.9 34.0 + - + +
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Residues in contact with THR 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.9 0.2 - - + -
16A THR* 4.2 13.0 - - + -
12B LEU* 3.4 28.0 - - + +
15B LYS* 4.5 11.7 + - - +
16B THR* 4.0 26.7 - - + -
19B LEU* 4.0 9.6 - - + +
12C LEU* 2.8 26.6 + - + +
13C LEU* 3.0 17.2 + - - +
15C LYS* 1.3 74.3 - - - +
17C TYR* 1.3 64.3 + - - +
19C LEU* 3.2 10.5 + - + +
20C GLU* 2.9 23.6 + - - +
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Residues in contact with TYR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.1 18.1 + - + +
14C SER* 3.2 6.5 + - - +
16C THR* 1.3 82.1 + - - +
18C HIS* 1.3 63.2 + - - +
20C GLU* 3.3 28.2 + - - +
21C ASN* 3.0 54.3 + - - -
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Residues in contact with HIS 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 5.4 7.6 - - + -
27A LYS* 5.9 0.4 + - - -
14C SER 3.0 13.5 + - - +
15C LYS* 3.3 13.7 - - - +
17C TYR* 1.3 76.5 - - - +
19C LEU* 1.3 75.0 + - + +
21C ASN* 3.1 10.1 + - - +
22C GLU* 3.0 54.2 + - + +
203C CD 2.4 34.9 - - - -
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 4.0 21.8 - - + +
19A LEU* 4.0 31.4 - - + +
20A GLU* 3.6 35.0 - - + +
23A VAL* 4.4 15.3 - - + -
16B THR* 6.4 0.2 - - + -
19B LEU* 3.9 11.9 - - + -
15C LYS 2.9 23.7 + - - +
16C THR* 3.7 10.1 - - + +
18C HIS* 1.3 84.7 - - + +
20C GLU* 1.3 59.8 + - - +
22C GLU* 3.2 4.9 + - + +
23C VAL* 2.8 38.1 + - + +
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Residues in contact with GLU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 6.1 1.1 - - - +
19B LEU* 3.8 23.7 - - + +
16C THR 2.9 14.0 + - - +
17C TYR* 3.4 35.3 - - - +
19C LEU* 1.3 76.4 - - - +
21C ASN* 1.3 60.2 + - - +
23C VAL* 3.9 1.4 - - - +
24C ALA* 3.0 32.1 + - + +
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Residues in contact with ASN 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 3.0 59.4 + - - -
18C HIS* 3.1 12.0 + - - +
20C GLU* 1.3 80.3 - - - +
22C GLU* 1.3 64.0 + - - +
24C ALA* 3.5 5.8 + - - +
25C ARG* 3.1 36.6 + - + +
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Residues in contact with GLU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 3.9 22.7 - - + -
27A LYS* 2.8 31.9 + - + +
18C HIS* 3.0 51.9 + - + +
19C LEU* 3.7 8.3 - - + +
21C ASN* 1.3 75.4 - - - +
23C VAL* 1.3 66.4 + - - +
25C ARG* 2.8 35.4 + - - +
26C LEU* 3.0 27.8 + - - +
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Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 4.0 13.0 - - + -
19B LEU* 4.2 19.1 - - + -
22B GLU* 3.8 27.8 - - + -
23B VAL* 3.9 24.7 - - + -
26B LEU* 4.2 11.9 - - + -
19C LEU* 2.8 26.1 + - + +
20C GLU 3.9 3.4 - - - +
22C GLU* 1.3 72.1 - - - +
24C ALA* 1.3 58.4 + - - +
26C LEU* 3.2 9.4 + - + +
27C LYS* 2.8 36.0 + - + +
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLU* 3.0 20.3 + - + +
21C ASN* 3.7 7.0 - - - +
23C VAL* 1.3 76.4 - - - +
25C ARG* 1.3 63.8 + - + +
27C LYS* 3.3 4.1 + - - -
28C LYS* 2.6 48.6 + - - +
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Residues in contact with ARG 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 4.1 11.7 - - - +
21C ASN* 3.1 24.4 + - + +
22C GLU* 2.8 45.8 + - - +
23C VAL 3.2 0.2 - - - -
24C ALA* 1.3 78.3 - - + +
26C LEU* 1.3 62.9 + - + +
28C LYS* 3.2 5.7 + - - +
29C LEU* 2.8 43.4 + - + +
----------------------------------------------------------
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Residues in contact with LEU 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 4.2 22.0 - - + -
26A LEU* 3.9 33.4 - - + -
27A LYS* 4.1 27.6 - - + +
30A VAL* 4.4 16.8 - - + +
26B LEU* 3.9 15.3 - - + -
22C GLU 3.0 17.2 + - - +
23C VAL* 3.6 9.9 - - + +
25C ARG* 1.3 73.2 - - + +
27C LYS* 1.3 67.3 + - - +
29C LEU* 3.1 11.4 + - + +
30C VAL* 2.9 37.3 + - + +
----------------------------------------------------------
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Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU* 2.7 43.2 + - - +
25B ARG* 4.0 21.8 - - - +
26B LEU* 4.1 26.5 - - + -
201B CD 4.0 4.6 - - - -
23C VAL* 2.8 25.5 + - + +
24C ALA* 4.7 2.2 - - - -
25C ARG 3.3 0.2 - - - -
26C LEU* 1.3 75.6 - - - +
28C LYS* 1.3 84.5 + - + +
31C GLY* 2.8 30.5 + - - -
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Residues in contact with LYS 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ALA* 2.6 45.4 + - - +
25C ARG* 3.7 8.3 - - - +
27C LYS* 1.3 104.9 - - + +
29C LEU* 1.3 65.9 + - + +
30C VAL 3.5 0.2 - - - -
31C GLY* 4.4 3.9 + - - -
----------------------------------------------------------
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 5.1 19.1 - - + +
25C ARG* 2.8 45.1 + - + +
26C LEU* 3.1 12.3 + - + +
28C LYS* 1.3 85.6 - - + +
30C VAL* 1.3 64.0 + - + +
----------------------------------------------------------
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.4 17.3 - - + -
26B LEU* 4.2 13.9 - - + -
29B LEU* 4.2 33.9 - - + -
30B VAL* 4.2 22.2 - - + -
26C LEU* 2.9 24.4 + - + +
29C LEU* 1.3 83.1 - - + +
31C GLY* 1.3 63.8 + - - +
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Residues in contact with GLY 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 6.2 2.0 - - - -
26B LEU* 5.6 0.4 - - - +
29B LEU* 5.0 11.0 - - - -
27C LYS* 2.8 24.8 + - - +
28C LYS 4.4 3.3 - - - -
29C LEU 3.8 0.6 - - - -
30C VAL* 1.3 82.9 - - - +
----------------------------------------------------------
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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