Contacts of the helix formed by residues 1 - 35 (chain B) in PDB entry 1KD9
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 LYS 1 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 4.4 23.3 - - + -
2B VAL* 1.3 72.6 + - - +
3B LYS* 2.7 8.7 + - - +
4B GLN* 2.7 26.3 + - + +
5B LEU* 3.0 30.8 + - + +
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Residues in contact with VAL 2 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GLU* 4.0 28.0 - - + -
2A VAL* 3.6 27.6 - - + +
5A LEU* 3.8 13.5 - - + +
1B LYS* 1.3 78.6 - - + +
3B LYS* 1.3 62.2 + - - +
5B LEU* 3.8 7.1 - - - +
6B LYS* 2.9 29.9 + - + +
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Residues in contact with LYS 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LYS 2.7 9.5 + - - +
2B VAL* 1.3 77.5 - - - +
4B GLN* 1.3 64.4 + - - +
6B LYS* 2.9 9.8 + - - +
7B ALA* 2.8 23.1 + - - +
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Residues in contact with GLN 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LYS* 2.7 24.8 + - + +
3B LYS* 1.3 74.6 - - - +
5B LEU* 1.3 62.7 + - + +
7B ALA* 3.1 10.9 - - - +
8B LYS* 3.1 19.4 + - - +
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Residues in contact with LEU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 3.9 28.5 - - + +
5A LEU* 3.6 31.6 - - + +
6A GLU* 4.2 9.4 - - + +
9A VAL* 4.5 17.3 - - + -
1B LYS* 3.0 32.8 + - + +
2B VAL* 3.8 8.3 - - - +
4B GLN* 1.3 74.7 - - + +
6B LYS* 1.3 70.0 + - - +
7B ALA 2.9 1.3 - - - -
8B LYS* 2.7 19.3 + - + +
9B VAL* 2.8 16.8 + - + +
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Residues in contact with LYS 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.8 19.2 - - + +
2B VAL* 2.9 24.3 + - + +
3B LYS* 2.9 11.2 + - - +
5B LEU* 1.3 74.6 - - - +
7B ALA* 1.3 63.1 + - - +
9B VAL* 3.2 8.2 + - - +
10B GLU* 2.9 29.9 + - + +
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Residues in contact with ALA 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS 2.8 11.7 + - - +
4B GLN* 3.1 15.3 - - - +
5B LEU 2.9 0.4 + - - -
6B LYS* 1.3 77.5 - - - +
8B LYS* 1.3 62.7 + - - +
10B GLU* 3.2 7.2 + - - +
11B GLU* 3.0 22.7 + - - +
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Residues in contact with LYS 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.3 15.4 - - + +
13A GLU* 3.4 23.6 + - - -
4B GLN 3.1 11.8 + - - +
5B LEU* 2.7 18.1 + - + +
7B ALA* 1.3 71.8 - - - +
9B VAL* 1.3 62.8 + - - +
11B GLU* 3.0 25.6 + - - +
12B LEU* 2.8 53.7 + - + +
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.1 11.2 - - + +
8A GLU* 3.5 43.7 - - + +
9A VAL* 3.6 21.7 - - + +
12A LEU* 3.6 13.8 - - + +
5B LEU 2.8 23.7 + - - +
6B LYS* 3.4 12.6 - - - +
8B LYS* 1.3 72.4 - - - +
10B GLU* 1.3 62.0 + - - +
12B LEU* 3.3 2.2 + - - -
13B LYS* 3.0 39.8 + - - +
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS* 2.9 21.3 + - + +
7B ALA* 3.6 6.3 - - - +
9B VAL* 1.3 79.8 - - + +
11B GLU* 1.3 64.9 + - - +
12B LEU 3.2 0.3 + - - -
13B LYS* 3.2 32.8 + - - +
14B SER* 3.2 22.5 + - - -
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ALA 3.0 13.5 + - - +
8B LYS* 3.0 28.7 + - + +
10B GLU* 1.3 75.8 - - - +
12B LEU* 1.3 65.1 + - + +
14B SER* 3.7 5.0 + - - +
15B LYS* 3.2 23.5 + - + +
----------------------------------------------------------
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.7 41.3 - - + +
12A LEU* 3.7 26.5 - - + -
13A GLU* 4.0 10.8 - - + -
16A LEU* 3.4 28.8 - - + +
8B LYS* 2.8 42.6 + - + +
9B VAL 3.6 4.0 - - - +
11B GLU* 1.3 81.2 - - + +
13B LYS* 1.3 58.7 + - - +
15B LYS* 3.2 5.2 + - + +
16B LEU* 3.0 29.0 + - - +
----------------------------------------------------------
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Residues in contact with LYS 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU* 3.7 24.2 + - - -
12A LEU* 4.3 17.6 - - + +
9B VAL* 3.0 22.1 + - - +
10B GLU* 3.2 34.3 + - - +
12B LEU* 1.3 77.4 - - - +
14B SER* 1.3 61.3 + - - +
16B LEU* 3.3 13.9 + - + +
17B TRP* 3.1 22.3 + - - +
----------------------------------------------------------
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Residues in contact with SER 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU 3.2 13.0 + - - -
11B GLU* 4.0 6.1 - - - -
13B LYS* 1.3 75.3 - - - +
15B LYS* 1.3 66.1 + - - +
17B TRP* 3.3 7.1 + - - +
18B HIS* 2.9 38.6 + - - -
----------------------------------------------------------
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.9 18.0 - - + +
20A GLU* 2.8 29.1 + - - -
11B GLU* 3.2 16.9 + - + +
12B LEU* 3.2 6.3 + - + +
14B SER* 1.3 79.1 - - - +
16B LEU* 1.3 63.1 + - - +
18B HIS* 3.5 8.7 + - + +
19B LEU* 3.0 41.0 + - + +
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.6 17.7 - - + +
15A GLU* 3.3 42.2 - - + +
16A LEU* 3.6 18.8 - - + +
19A LEU* 3.5 16.8 - - + +
12B LEU 3.0 13.8 + - - +
13B LYS* 3.4 13.5 - - + +
15B LYS* 1.3 77.3 - - - +
17B TRP* 1.3 57.9 + - - +
19B LEU* 3.2 3.7 + - - +
20B LYS* 2.9 58.0 + - - +
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Residues in contact with TRP 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LYS 3.1 15.9 + - - +
14B SER* 3.3 6.7 + - - +
16B LEU* 1.3 79.3 - - + +
18B HIS* 1.3 75.7 + + - +
20B LYS* 3.4 14.8 + - + +
21B ASN* 2.9 59.4 + - - +
----------------------------------------------------------
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Residues in contact with HIS 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B SER* 2.9 33.4 + - - +
15B LYS* 3.6 13.0 - - + +
17B TRP* 1.3 90.5 - + - +
19B LEU* 1.3 60.6 + - + +
21B ASN* 3.3 8.9 + - - +
22B LYS* 2.9 27.3 + - - +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.7 27.6 - - + -
19A LEU* 4.2 21.3 - - + -
20A GLU* 4.0 20.2 - - + -
23A VAL* 3.8 25.1 - - + -
15B LYS* 3.0 34.6 + - + +
16B LEU 3.2 4.4 + - - +
18B HIS* 1.3 75.9 - - + +
20B LYS* 1.3 60.3 + - - +
22B LYS* 3.3 14.4 + - + +
23B VAL* 2.9 32.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 3.1 27.9 + - - -
19A LEU* 4.1 16.6 - - + -
16B LEU* 2.9 40.5 + - - +
17B TRP* 3.4 14.8 + - + +
19B LEU* 1.3 74.9 - - - +
21B ASN* 1.3 59.7 + - - +
23B VAL* 3.7 7.2 - - - +
24B ALA* 2.9 30.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TRP* 2.9 69.5 + - - +
18B HIS* 3.6 7.5 - - - +
20B LYS* 1.3 80.1 - - - +
22B LYS* 1.3 61.2 + - - +
24B ALA* 3.4 6.7 + - - +
25B ARG* 3.2 21.3 + - - +
----------------------------------------------------------
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 3.8 25.3 - - + +
27A GLU* 3.2 27.9 + - - -
18B HIS 2.9 17.4 + - - +
19B LEU* 3.6 15.1 - - + +
21B ASN* 1.3 77.9 - - - +
23B VAL* 1.3 57.3 + - - +
25B ARG* 3.3 31.7 + - - +
26B LEU* 3.0 39.1 + - + +
----------------------------------------------------------
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.1 17.0 - - + +
22A GLU* 3.6 25.4 - - - +
23A VAL* 3.6 23.3 - - + +
26A LEU* 3.9 19.0 - - + +
19B LEU 2.9 19.7 + - - +
20B LYS* 3.7 7.2 - - - +
22B LYS* 1.3 73.9 - - - +
24B ALA* 1.3 68.5 + - - +
26B LEU* 3.2 2.4 + - - +
27B LYS* 3.0 43.9 + - + +
----------------------------------------------------------
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS 2.9 17.8 + - - +
21B ASN* 3.8 8.3 - - - +
22B LYS 3.4 0.2 - - - -
23B VAL* 1.3 78.6 - - - +
25B ARG* 1.3 60.5 + - - +
27B LYS* 3.7 8.3 + - - +
28B LYS* 3.2 24.1 + - - +
----------------------------------------------------------
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN 3.2 13.0 + - - +
22B LYS* 3.6 41.8 - - - +
23B VAL 3.1 0.8 - - - -
24B ALA* 1.3 74.7 - - - +
26B LEU* 1.3 72.5 + - - +
28B LYS* 3.3 5.7 + - - +
29B LYS* 2.8 59.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 4.2 9.4 - - + +
26A LEU* 3.8 26.2 - - + -
27A GLU* 3.6 36.1 - - + +
30A ASN* 5.0 11.0 - - + -
22B LYS* 3.0 40.0 + - + +
23B VAL* 3.2 4.5 + - - +
25B ARG* 1.3 90.9 - - + +
27B LYS* 1.3 57.4 + - - +
29B LYS* 4.4 11.0 - - + -
30B ASN* 2.7 42.1 + - - +
----------------------------------------------------------
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU* 3.7 25.6 + - - -
26A LEU* 3.9 20.6 - - + +
23B VAL* 3.0 34.6 + - + +
24B ALA* 3.9 7.0 - - - +
26B LEU* 1.3 76.3 - - - +
28B LYS* 1.3 58.8 + - - +
30B ASN* 3.3 5.0 + - - +
31B ALA* 2.8 30.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA 3.2 16.7 + - - +
25B ARG* 3.8 5.6 - - - +
26B LEU 3.2 0.2 - - - -
27B LYS* 1.3 80.4 - - - +
29B LYS* 1.3 52.7 + - + +
31B ALA* 3.3 7.8 + - + +
32B GLU* 2.7 68.0 + - + +
----------------------------------------------------------
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASN* 3.8 20.2 + - - +
34A GLU* 5.0 5.5 + - - +
25B ARG* 2.8 55.3 + - + +
26B LEU* 3.8 10.1 - - + +
28B LYS* 1.3 77.6 - - + +
30B ASN* 1.3 57.1 + - - +
32B GLU* 3.4 16.5 + - - +
33B CYS* 3.0 28.4 + - - +
----------------------------------------------------------
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Residues in contact with ASN 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 2.9 31.7 + - - +
29A GLU* 3.0 40.1 + - + +
30A ASN* 2.5 45.3 + - - +
33A CYS* 4.9 3.4 - - + +
26B LEU* 2.7 25.9 + - - +
27B LYS* 3.8 4.9 - - - +
29B LYS* 1.3 70.1 - - - +
31B ALA* 1.3 66.5 + - - +
33B CYS* 4.2 2.9 - - - +
34B LYS* 3.0 25.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS 2.8 18.4 + - - +
28B LYS* 3.5 13.5 - - + +
30B ASN* 1.3 77.7 - - - +
32B GLU* 1.3 65.9 + - + +
34B LYS* 3.5 5.1 - - - +
35B ALA* 3.1 23.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 2.7 55.5 + - - +
29B LYS* 3.5 17.0 - - - +
31B ALA* 1.3 77.0 - - + +
33B CYS* 1.3 62.9 + - - +
35B ALA* 3.1 19.2 - - - +
----------------------------------------------------------
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Residues in contact with CYS 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASN* 5.2 1.3 - - - +
33A CYS* 2.0 65.0 - - + -
34A GLU* 3.9 20.4 - - + +
29B LYS 3.0 16.1 + - - +
30B ASN* 4.2 2.5 - - - +
32B GLU* 1.3 73.0 - - - +
34B LYS* 1.3 68.5 + - - +
35B ALA* 2.9 9.2 - - - +
----------------------------------------------------------
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A CYS* 3.3 12.7 - - - -
30B ASN 3.0 18.6 + - - +
31B ALA* 3.2 6.9 + - - +
33B CYS* 1.3 78.8 - - - +
35B ALA* 1.3 61.8 + - + +
----------------------------------------------------------
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA 3.1 9.2 + - - +
32B GLU* 3.1 14.9 - - - +
33B CYS 2.9 16.1 - - - +
34B LYS* 1.3 79.1 - - + +
----------------------------------------------------------
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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