Contacts of the helix formed by residues 3 - 31 (chain B) in PDB entry 1CE9
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 VAL 3 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.2 6.7 - - + +
2A SER* 6.0 0.2 - - - -
3A VAL* 5.0 18.6 - - + +
6A LEU* 3.8 15.9 - - + -
1B MET 4.0 0.4 + - - +
2B SER* 1.3 74.1 - - - +
4B LYS* 1.3 58.7 + - - +
6B LEU* 3.2 10.8 + - - +
7B GLU* 2.9 51.0 + - - +
22D ASN* 4.2 9.2 - - - +
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Residues in contact with LYS 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 3.9 9.6 - - - +
3B VAL* 1.3 77.7 - - - +
5B GLU* 1.3 65.4 + - - +
7B GLU* 3.4 14.4 + - - +
8B ASP* 2.8 58.9 + - - +
22D ASN* 6.0 3.6 - - - +
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Residues in contact with GLU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.9 25.9 + - + +
2B SER* 3.2 25.4 + - - +
4B LYS* 1.3 81.1 - - - +
6B LEU* 1.3 62.8 + - - +
8B ASP* 3.5 6.9 + - - +
9B LYS* 3.2 24.3 + - + +
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Residues in contact with LEU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 3.5 44.6 - - + +
6A LEU* 3.9 21.1 - - + -
7A GLU* 3.9 23.1 - - + +
10A VAL* 4.1 11.2 - - + +
1B MET* 3.7 24.7 - - + -
2B SER 3.4 13.0 + - - +
3B VAL* 3.2 9.8 + - - +
4B LYS 3.2 0.2 - - - -
5B GLU* 1.3 76.3 - - + +
7B GLU* 1.3 66.1 + - - +
9B LYS* 3.1 7.8 + - + +
10B VAL* 3.0 26.9 + - - +
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.2 3.3 - - - +
6A LEU* 3.9 18.1 - - + +
3B VAL* 2.9 31.3 + - - +
4B LYS* 3.4 15.1 + - - +
6B LEU* 1.3 75.0 - - - +
8B ASP* 1.3 66.3 + - - +
10B VAL* 3.3 4.0 + - - +
11B GLU* 3.1 29.9 + - - +
18D TYR* 3.7 49.0 - - + +
21D GLU* 5.2 1.7 - - - +
22D ASN* 3.1 33.8 + - - +
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Residues in contact with ASP 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LYS* 2.8 58.9 + - - +
5B GLU* 3.8 7.0 - - - +
6B LEU 3.2 0.2 - - - -
7B GLU* 1.3 78.9 - - - +
9B LYS* 1.3 58.3 + - - +
11B GLU* 3.5 18.3 + - - +
12B GLU* 3.0 27.9 + - - +
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Residues in contact with LYS 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.7 30.3 - - + -
5B GLU* 3.2 15.2 + - + +
6B LEU* 3.1 12.7 + - + +
8B ASP* 1.3 75.1 - - - +
10B VAL* 1.3 61.2 + - - +
12B GLU* 2.6 32.1 + - - +
13B LEU* 3.0 43.2 + - + +
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Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.1 10.1 - - + +
9A LYS* 3.8 20.9 - - + -
10A VAL* 3.6 19.3 - - + +
13A LEU* 4.0 19.3 - - + +
6B LEU 3.0 17.1 + - - +
7B GLU 3.5 7.4 - - - +
9B LYS* 1.3 75.1 - - - +
11B GLU* 1.3 60.3 + - - +
13B LEU* 3.1 3.4 + - - +
14B LEU* 2.8 29.0 + - + +
14D LEU* 4.0 14.1 - - + -
18D TYR* 3.3 31.9 - - + +
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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 GLU* 3.1 19.2 + - - +
8B ASP* 3.8 15.5 - - - +
10B VAL* 1.3 80.5 - - - +
12B GLU* 1.3 61.5 + - - +
14B LEU* 3.5 6.7 + - - +
15B SER* 3.2 24.4 + - - -
11D GLU* 5.5 4.2 - - - +
14D LEU* 4.7 11.2 - - + -
15D SER* 4.0 26.0 + - - +
18D TYR* 3.7 26.0 - - + +
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASP 3.0 17.1 + - - +
9B LYS* 2.6 41.8 + - - +
10B VAL 3.2 0.2 - - - -
11B GLU* 1.3 77.6 - - - +
13B LEU* 1.3 67.7 - - + +
15B SER* 3.6 5.0 + - - -
16B LYS* 3.2 21.9 + - + +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.7 42.2 - - + +
13A LEU* 4.1 16.6 - - + +
14A LEU* 4.2 27.4 - - + +
17A ASN* 3.2 23.9 + - - +
9B LYS* 3.0 30.9 + - + +
10B VAL 3.8 2.9 - - - +
12B GLU* 1.3 84.3 - - - +
14B LEU* 1.3 60.8 + - - +
16B LYS* 3.4 6.7 + - + -
17B ASN* 2.8 25.1 + - - +
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.2 22.8 - - + +
10B VAL 2.8 17.5 + - - +
11B GLU* 3.9 6.3 - - - +
13B LEU* 1.3 73.8 - - - +
15B SER* 1.3 64.9 + - - +
17B ASN* 3.2 9.7 + - - +
18B TYR* 3.1 51.5 + - + +
10D VAL* 4.3 11.4 - - + -
11D GLU* 3.9 24.2 - - + -
14D LEU* 3.7 27.6 - - + -
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Residues in contact with SER 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU 3.2 15.3 + - - -
12B GLU* 3.9 5.6 - - - -
14B LEU* 1.3 78.8 - - - +
16B LYS* 1.3 62.3 + - - +
18B TYR* 3.4 2.9 + - - +
19B HIS* 3.1 44.9 + - - -
11D GLU* 3.6 26.1 + - - -
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASN* 3.4 19.5 - - + +
21A GLU* 4.3 18.7 + - - -
12B GLU* 3.2 14.2 + - + +
13B LEU* 3.5 13.0 - - + +
15B SER* 1.3 80.0 - - - +
17B ASN* 1.3 61.2 + - - +
19B HIS* 3.4 12.4 + - - +
20B LEU* 3.2 36.8 + - + +
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Residues in contact with ASN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.6 11.2 - - + +
16A LYS* 4.1 16.1 - - - +
17A ASN* 2.8 28.5 + - - +
20A LEU* 3.4 15.9 - - - +
13B LEU 2.8 12.1 + - - +
14B LEU* 3.3 19.2 + - - +
16B LYS* 1.3 77.1 - - - +
18B TYR* 1.3 76.7 + - - +
20B LEU* 3.1 5.8 + - - +
21B GLU* 2.9 40.7 + - - +
1C MET* 4.9 3.0 - - - +
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Residues in contact with TYR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.1 33.6 + - + +
15B SER 3.8 4.9 - - - +
16B LYS 3.4 0.2 - - - -
17B ASN* 1.3 87.2 - - - +
19B HIS* 1.3 65.6 + - + +
21B GLU* 3.2 3.6 + - + +
22B ASN* 3.0 32.5 + - - +
1C MET* 3.8 30.7 - - + +
6C LEU* 4.0 14.9 - - + +
9C LYS* 4.5 8.7 - - - +
7D GLU* 3.9 39.3 - - + +
10D VAL* 3.2 38.1 - - + +
11D GLU* 3.2 23.6 - - + +
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Residues in contact with HIS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER* 3.1 41.0 + - - +
16B LYS* 3.7 13.2 - - - +
17B ASN 3.3 0.2 - - - -
18B TYR* 1.3 76.7 - - + +
20B LEU* 1.3 62.8 + - + +
22B ASN* 3.6 13.4 + - - +
23B GLU* 3.3 21.9 + - - +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASN* 3.7 39.7 - - + +
20A LEU* 3.6 18.6 - - + +
21A GLU* 3.9 30.5 - - + +
24A VAL* 4.7 7.8 - - + +
16B LYS* 3.2 30.9 + - + +
17B ASN 3.1 7.1 + - - +
19B HIS* 1.3 77.6 - - + +
21B GLU* 1.3 63.7 + - - +
22B ASN 3.2 0.4 - - - -
23B GLU* 3.2 21.2 + - - +
24B VAL* 3.0 28.9 + - - +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.9 27.1 - - + +
17B ASN* 2.9 27.5 + - - +
18B TYR* 3.2 12.5 + - + +
20B LEU* 1.3 76.0 - - - +
22B ASN* 1.3 64.2 + - - +
24B VAL* 4.1 5.7 - - - +
25B ALA* 3.1 24.9 + - - +
1C MET* 3.4 56.0 + - + +
7D GLU* 4.8 0.2 - - - +
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Residues in contact with ASN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 3.0 15.2 + - - +
19B HIS* 3.7 14.7 + - - +
21B GLU* 1.3 77.2 - - - +
23B GLU* 1.3 63.6 + - - +
25B ALA* 3.5 6.9 + - - +
26B ARG* 3.2 37.8 + - - +
1C MET* 5.5 1.0 + - - +
3D VAL* 3.8 10.6 - - - +
4D LYS* 5.7 2.8 - - - +
7D GLU* 2.8 38.8 + - - +
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 3.7 29.4 - - + +
28A LYS* 3.9 15.8 + - - -
19B HIS 3.3 10.4 + - - +
20B LEU* 3.2 28.3 + - - +
22B ASN* 1.3 80.2 - - - +
24B VAL* 1.3 57.5 + - - +
26B ARG* 3.3 25.0 + - - +
27B LEU* 3.0 35.7 + - + +
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.8 22.9 - - + +
23A GLU* 4.1 16.8 - - + +
24A VAL* 3.5 25.1 - - + +
27A LEU* 3.7 21.1 - - + +
20B LEU 3.0 21.3 + - - +
21B GLU* 4.1 7.4 - - - +
23B GLU* 1.3 73.2 - - - +
25B ALA* 1.3 66.3 + - - +
27B LEU* 4.5 1.1 - - - -
28B LYS* 3.0 39.5 + - + +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLU 3.1 19.0 + - - +
22B ASN* 3.8 7.6 - - - +
24B VAL* 1.3 77.7 - - - +
26B ARG* 1.3 61.6 + - - +
28B LYS* 3.7 9.3 + - - +
29B LYS* 3.4 33.8 + - - +
1C MET 5.0 8.3 - - - +
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASN* 3.2 37.8 + - - +
23B GLU* 3.5 28.4 - - - +
24B VAL 3.1 0.2 - - - -
25B ALA* 1.3 74.6 - - - +
27B LEU* 1.3 63.8 - - + +
28B LYS 3.1 2.0 - - - -
29B LYS* 3.2 24.6 + - + +
30B LEU* 3.3 12.3 + - - +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 3.9 25.4 - - + +
27A LEU* 3.9 24.2 - - + -
28A LYS* 3.9 33.9 - - + -
31A VAL* 4.9 8.3 - - + -
34A ARG* 4.4 20.0 - - - +
23B GLU* 3.0 26.1 + - + +
24B VAL 3.4 0.2 + - - -
26B ARG* 1.3 77.8 - - + +
28B LYS* 1.3 57.0 + - - +
30B LEU* 3.3 19.4 + - + +
31B VAL* 3.0 35.4 + - + +
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 4.7 5.5 + - - -
26A ARG* 4.4 7.7 - - - +
27A LEU* 3.9 8.5 - - + -
24B VAL* 3.0 36.8 + - + +
25B ALA* 3.7 9.2 - - - +
26B ARG 3.1 0.2 - - - -
27B LEU* 1.3 76.1 - - - +
29B LYS* 1.3 60.1 + - + +
31B VAL* 3.3 6.7 - - - +
32B GLY 3.0 8.7 + - - -
33B GLU* 2.9 70.0 + - + +
34B ARG 4.2 16.3 + - - +
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 3.4 22.9 + - - +
26B ARG* 3.2 14.4 + - + +
28B LYS* 1.3 77.7 - - + +
30B LEU* 1.3 61.8 + - - +
31B VAL 3.7 0.2 + - - -
32B GLY* 3.7 7.9 + - - -
33B GLU 4.5 3.8 - - - +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 3.6 34.5 - - + -
34A ARG* 5.1 5.4 - - - +
26B ARG 3.3 9.2 + - - +
27B LEU* 3.4 24.7 - - + +
28B LYS 3.1 0.2 - - - -
29B LYS* 1.3 82.5 - - - +
31B VAL* 1.3 59.9 + - - +
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.7 32.5 - - + +
30A LEU* 4.3 19.7 - - + -
31A VAL* 3.4 25.6 - - + -
27B LEU 3.0 15.7 + - - +
28B LYS 3.3 11.2 - - - +
30B LEU* 1.3 76.8 - - - +
32B GLY* 1.3 60.9 + - - +
33B GLU* 3.5 24.5 - - + +
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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