Contacts of the helix formed by residues 2 - 25 (chain K) in PDB entry 6C4Z
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 2 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16I LYS* 5.2 2.5 - - + +
20I LEU* 3.9 27.8 - - + -
1K SER* 1.3 78.3 + - - +
3K LEU* 1.3 55.8 + - + +
5K GLU* 2.9 16.0 + - - +
6K LEU* 2.7 35.1 + - - +
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Residues in contact with LEU 3 (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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20I LEU* 4.0 15.7 - - + -
24I TRP* 4.0 23.8 - - + -
1K SER 3.8 17.5 - - - +
2K LYS* 1.3 81.5 - - + +
4K LEU* 1.3 51.4 + - - +
6K LEU* 3.0 13.6 + - - +
7K LEU* 2.5 39.2 + - - +
3L LEU* 3.9 26.0 - - + -
4L LEU* 3.6 31.0 - - + -
7L LEU* 4.3 13.6 - - + +
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Residues in contact with LEU 4 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1K SER* 3.2 24.1 + - - +
3K LEU* 1.3 73.2 - - - +
5K GLU* 1.3 66.0 + - - +
7K LEU* 3.5 19.5 - - + +
8K ARG* 3.1 18.4 + - - +
3L LEU* 3.7 25.1 - - + -
21M LEU* 4.7 4.7 - - + +
22M GLU* 3.6 32.0 - - + +
25M GLY* 3.5 37.5 - - - +
26M NH2 3.7 3.8 - - - +
24N TRP* 4.2 15.5 - - + -
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Residues in contact with GLU 5 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I LYS* 3.6 29.8 + - + -
1K SER* 3.0 12.3 + - - +
2K LYS* 2.9 16.3 + - - +
4K LEU* 1.3 76.7 - - - +
6K LEU* 1.3 63.7 + - - +
8K ARG* 3.5 4.2 + - - +
9K LYS* 3.4 27.6 + - - +
22M GLU* 4.7 5.4 - - - -
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Residues in contact with LEU 6 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I ALA* 4.2 25.8 - - + +
16I LYS* 4.3 16.7 - - + +
17I ALA* 4.5 15.0 - - + +
20I LEU* 4.6 10.1 - - + -
14J LEU* 5.0 2.2 - - + -
18J ILE* 5.1 5.4 - - + -
21J LEU* 4.1 26.0 - - + -
2K LYS 2.7 16.5 + - - +
3K LEU* 3.2 8.5 - - - +
5K GLU* 1.3 69.6 - - - +
7K LEU* 1.3 67.0 + - - +
9K LYS* 3.0 14.5 + - - +
10K LEU* 3.2 29.2 + - + -
7L LEU* 4.0 22.0 - - + -
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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
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3K LEU 2.5 19.5 + - - +
4K LEU* 3.5 17.5 - - + +
6K LEU* 1.3 72.6 - - - +
8K ARG* 1.3 63.9 + - - +
10K LEU* 3.1 6.0 + - - +
11K GLY* 3.0 19.8 + - - -
3L LEU* 4.0 16.6 - - + -
6L LEU* 4.2 4.3 - - + -
7L LEU* 3.7 17.9 - - + -
10L LEU* 3.3 31.0 - - + -
18M ILE* 3.7 30.5 - - + +
21M LEU* 3.9 29.2 - - + -
22M GLU* 5.7 2.7 - - + +
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Residues in contact with ARG 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 LEU 3.1 7.4 + - - +
5K GLU* 3.8 5.4 - - - +
6K LEU 3.3 0.2 - - - -
7K LEU* 1.3 81.6 - - - +
9K LYS* 1.3 58.2 + - + +
11K GLY* 3.9 0.6 - - - +
12K GLU* 2.9 38.3 + - + +
18M ILE* 4.5 10.3 - - + -
22M GLU* 3.2 33.0 - - - +
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Residues in contact with LYS 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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9I LYS* 4.4 7.8 - - + +
12I GLU* 3.2 35.0 - - + +
13I ALA* 4.1 20.2 - - + +
16I LYS* 3.9 35.9 - - + +
5K GLU* 3.4 17.5 + - - +
6K LEU* 3.0 10.1 + - - +
8K ARG* 1.3 76.3 - - - +
10K LEU* 1.3 55.4 + - - +
12K GLU* 3.2 21.8 + - - +
13K ALA* 2.6 37.6 + - - +
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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
----------------------------------------------------------
13I ALA* 4.3 4.5 - - + -
14J LEU* 3.7 33.7 - - + -
18J ILE* 4.0 26.0 - - + -
6K LEU* 3.2 18.2 + - + +
7K LEU* 3.1 5.9 + - - +
9K LYS* 1.3 74.3 - - - +
11K GLY* 1.3 53.3 - - - +
13K ALA* 3.2 5.7 + - - +
14K LEU* 2.7 39.9 + - - +
7L LEU* 3.5 41.7 - - + +
10L LEU* 4.2 19.1 - - + +
11L GLY* 4.9 5.2 - - - +
14L LEU* 4.2 10.8 - - + +
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Residues in contact with GLY 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 3.0 12.3 + - - -
8K ARG* 3.9 3.4 - - - -
10K LEU* 1.3 75.2 - - - +
12K GLU* 1.3 55.8 + - - +
14K LEU* 3.2 9.3 + - - +
15K HIS* 2.9 31.8 + - - +
10L LEU* 5.0 1.5 - - - +
15M HIS* 5.5 9.4 - - - -
18M ILE* 4.3 23.0 - - - +
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Residues in contact with GLU 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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9I LYS* 3.6 28.5 + - - -
8K ARG* 2.9 25.2 + - + +
9K LYS* 3.3 36.3 + - - +
11K GLY* 1.3 75.2 - - - +
13K ALA* 1.3 63.3 + - - +
15K HIS* 3.3 7.3 + - - +
16K LYS* 3.2 24.4 + - - +
15M HIS* 5.8 5.7 - - + +
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Residues in contact with ALA 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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6I LEU* 4.2 9.3 - - + +
9I LYS* 3.8 28.6 - - + +
10I LEU* 4.7 7.2 - - + +
13I ALA* 5.7 1.8 - - + -
9K LYS 2.6 20.4 + - - +
10K LEU* 3.4 5.4 - - - +
12K GLU* 1.3 72.1 - - - +
14K LEU* 1.3 64.2 + - - +
16K LYS* 3.1 16.1 + - - +
17K ALA* 3.2 12.3 + - - +
14L LEU* 4.1 23.1 - - + -
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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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10K LEU 2.7 19.7 + - - +
11K GLY* 3.5 6.3 - - - +
13K ALA* 1.3 71.0 - - - +
15K HIS* 1.3 65.4 + - - +
17K ALA* 3.3 2.9 + - - +
18K ILE* 3.2 36.6 + - + +
10L LEU* 3.7 35.0 - - + +
13L ALA* 4.2 13.7 - - + +
14L LEU* 4.0 30.9 - - + +
17L ALA* 4.6 8.1 - - + -
11M GLY* 6.4 0.2 - - - -
14M LEU* 4.0 5.2 - - + -
6N LEU* 5.3 2.0 - - + -
10N LEU* 3.7 25.6 - - + -
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Residues in contact with HIS 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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11K GLY 2.9 13.3 + - - +
12K GLU* 3.4 11.8 + - - +
14K LEU* 1.3 76.0 - - - +
16K LYS* 1.3 74.2 + - + +
18K ILE* 3.0 21.5 + - - +
19K GLU* 3.0 27.8 + - + -
11M GLY 6.4 2.0 - - - -
12M GLU* 6.6 0.2 - - - -
15M HIS* 5.3 22.7 - + + -
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Residues in contact with LYS 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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2I LYS* 4.7 3.4 - - + +
5I GLU* 3.4 35.8 + - + +
6I LEU* 4.2 31.0 - - + +
9I LYS* 3.9 26.2 - - + +
12K GLU 3.2 11.4 + - - +
13K ALA* 3.1 12.4 + - - +
15K HIS* 1.3 89.3 + - + +
17K ALA* 1.3 62.4 + - - +
19K GLU* 3.5 6.2 + - - +
20K LEU* 3.2 20.1 + - - +
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Residues in contact with ALA 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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6I LEU* 4.5 11.1 - - + +
13K ALA 3.2 7.7 + - - +
14K LEU 3.5 9.2 - - - +
15K HIS 3.2 0.2 - - - -
16K LYS* 1.3 78.2 - - - +
18K ILE* 1.3 50.3 + - - +
20K LEU* 2.9 10.6 + - - +
21K LEU* 2.7 35.8 + - - +
14L LEU* 4.7 9.9 - - + -
17L ALA* 4.0 24.0 - - + -
18L ILE* 5.4 1.1 - - + -
21L LEU* 4.1 19.8 - - + +
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Residues in contact with ILE 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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14K LEU* 3.2 34.7 + - + +
15K HIS* 3.0 10.5 + - - +
17K ALA* 1.3 76.7 - - + +
19K GLU* 1.3 55.2 + - - +
21K LEU* 2.9 14.4 + - + +
22K GLU* 2.7 36.4 + - + +
17L ALA* 5.5 1.6 - - + -
7M LEU* 3.8 42.4 - - + -
8M ARG* 4.3 17.7 - - + -
11M GLY* 4.1 24.0 - - - -
6N LEU* 5.7 0.9 - - + -
10N LEU* 4.2 6.7 - - + -
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Residues in contact with GLU 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 HIS* 3.0 28.7 + - + +
16K LYS* 3.6 10.8 - - - +
18K ILE* 1.3 76.4 - - - +
20K LEU* 1.3 60.8 + - - +
22K GLU* 3.6 7.9 + - - +
23K LYS* 3.2 22.2 + - - +
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Residues in contact with LEU 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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2I LYS* 4.0 25.1 - - + -
3I LEU* 3.9 32.8 - - + +
6I LEU* 4.9 6.1 - - + -
16K LYS 3.2 9.6 + - - +
17K ALA* 2.9 13.6 + - - +
19K GLU* 1.3 75.5 - - - +
21K LEU* 1.3 62.9 + - - +
23K LYS* 3.0 15.4 + - + +
24K TRP* 2.9 56.1 + - + +
21L LEU* 3.6 30.1 - - + -
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Residues in contact with LEU 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 ALA 2.7 14.9 + - - +
18K ILE* 2.9 20.3 + - + +
20K LEU* 1.3 70.5 - - - +
22K GLU* 1.3 53.5 + - - +
24K TRP* 4.7 2.0 - - - +
25K GLY* 2.8 32.7 + - - -
17L ALA* 4.0 22.0 - - + +
20L LEU* 3.7 26.5 - - + -
21L LEU* 3.7 25.1 - - + +
24L TRP* 3.6 27.5 - - + -
4M LEU* 3.7 4.4 - - + +
7M LEU* 4.4 13.0 - - + -
6N LEU* 3.9 28.0 - - + -
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Residues in contact with GLU 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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18K ILE* 2.7 21.9 + - + +
19K GLU* 3.6 9.6 - - - +
21K LEU* 1.3 73.4 - - - +
23K LYS* 1.3 62.9 + - - +
25K GLY 3.8 0.3 - - - -
26K NH2 3.0 19.9 + - - -
4M LEU* 4.4 21.4 - - + +
7M LEU* 5.6 0.9 - - + +
8M ARG* 5.4 13.5 - - + +
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Residues in contact with LYS 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 GLU 3.2 10.4 + - - +
20K LEU* 3.0 16.6 + - + +
22K GLU* 1.3 80.3 - - - +
24K TRP* 1.3 84.1 + - + +
26K NH2 3.7 4.7 + - - -
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Residues in contact with TRP 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I LEU* 4.0 38.1 - - + -
4J LEU* 4.4 6.7 - - + -
20K LEU* 2.9 37.5 + - + +
21K LEU* 4.2 2.5 - - - +
23K LYS* 1.3 97.8 - - + +
25K GLY* 1.3 64.7 + - - +
26K NH2 3.4 0.7 + - - -
21L LEU* 3.4 41.3 - - + -
24L TRP* 4.6 17.0 - - + -
25L GLY* 3.4 26.7 - - - -
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Residues in contact with GLY 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K LEU 2.8 23.3 + - - -
24K TRP* 1.3 73.1 - - - +
26K NH2 1.3 45.9 + - - -
24L TRP* 3.5 22.1 - - - -
1M SER* 5.4 4.5 - - - -
4M LEU* 3.4 20.0 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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