Contacts of the helix formed by residues 2 - 25 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B SER* 1.3 76.4 - - - +
3B LEU* 1.3 65.8 + - - +
5B GLU* 3.5 16.4 + - - +
6B LEU* 3.1 20.6 + - - +
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Residues in contact with LEU 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.4 20.9 - - + +
4A LEU* 3.8 28.3 - - + -
7A LEU* 4.8 15.0 - - + -
1B SER 3.9 6.4 - - - +
2B LYS* 1.3 77.3 - - - +
4B LEU* 1.3 55.2 + - + +
6B LEU* 2.8 14.7 + - + +
7B LEU* 2.7 62.6 + - + +
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Residues in contact with LEU 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.5 32.1 - - + -
1B SER* 3.9 25.5 + - - +
3B LEU* 1.3 78.6 - - + +
5B GLU* 1.3 56.1 + - - +
7B LEU* 3.1 13.5 + - + +
8B ARG* 2.8 32.0 + - - +
24C TRP* 4.2 13.9 - - + -
18D ILE* 4.9 2.9 - - + +
21D LEU* 4.5 12.1 - - + +
22D GLU* 4.0 27.9 - - + +
25D GLY* 4.2 29.6 - - - -
26D NH2 4.3 3.1 - - - +
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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 SER 3.5 11.1 + - - +
2B LYS* 3.5 20.0 + - - +
3B LEU 3.2 0.2 - - - -
4B LEU* 1.3 78.6 - - - +
6B LEU* 1.3 61.4 + - - +
8B ARG* 3.4 31.7 + - - +
9B LYS* 3.0 33.0 + - + +
22D GLU* 4.9 2.3 - - - +
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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
----------------------------------------------------------
7A LEU* 4.1 27.6 - - + -
2B LYS 3.1 9.3 + - - +
3B LEU* 2.8 17.7 + - + +
5B GLU* 1.3 78.3 - - - +
7B LEU* 1.3 67.3 + - - +
9B LYS* 3.1 17.6 + - + +
10B LEU* 3.2 29.6 + - + +
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Residues in contact with LEU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.0 26.0 - - + +
6A LEU* 3.7 28.9 - - + -
7A LEU* 3.8 22.2 - - + +
10A LEU* 3.5 33.4 - - + +
3B LEU* 2.7 35.9 + - + +
4B LEU* 3.3 17.9 - - + +
6B LEU* 1.3 75.5 - - - +
8B ARG* 1.3 63.6 + - - +
10B LEU* 3.2 6.9 + - - +
11B GLY* 3.2 17.0 + - - -
18D ILE* 4.0 10.4 - - + +
21D LEU* 4.9 3.1 - - + -
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Residues in contact with ARG 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU 2.8 17.3 + - - +
5B GLU* 3.6 34.6 + - - +
7B LEU* 1.3 72.3 - - - +
9B LYS* 1.3 84.7 + - - +
11B GLY* 3.2 3.8 + - - -
12B GLU* 3.1 41.8 + - + +
15D HIS* 5.0 2.3 - - + -
18D ILE* 3.6 20.8 - - + +
19D GLU* 4.6 23.8 - - + +
22D GLU* 2.6 41.0 + - + +
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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
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5B GLU* 3.0 26.2 + - + +
6B LEU* 3.1 15.0 + - + +
8B ARG* 1.3 92.4 - - - +
10B LEU* 1.3 62.7 + - + +
12B GLU* 3.4 27.3 + - - +
13B ALA* 3.2 20.3 + - - +
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.3 35.7 - - + +
10A LEU* 4.4 23.8 - - + +
11A GLY* 4.8 6.7 - - - +
14A LEU* 4.0 25.6 - - + +
6B LEU* 3.2 22.5 + - + +
7B LEU 3.2 6.3 + - - +
9B LYS* 1.3 77.0 - - + +
11B GLY* 1.3 52.8 + - - +
13B ALA* 2.7 27.9 + - + +
14B LEU* 2.7 20.8 + - - +
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Residues in contact with GLY 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.6 7.4 - - - +
7B LEU 3.2 7.0 + - - -
8B ARG 3.2 7.7 + - - -
10B LEU* 1.3 77.7 - - - +
12B GLU* 1.3 54.6 + - - +
14B LEU* 3.5 7.3 + - - +
15B HIS* 3.0 30.5 + - - +
11D GLY 5.2 0.3 - - - +
14D LEU* 5.7 1.1 - - - -
15D HIS* 4.2 15.4 - - - +
18D ILE* 4.4 17.5 - - - -
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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
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8B ARG* 3.1 43.9 + - + +
9B LYS* 3.5 31.3 + - - +
11B GLY* 1.3 75.2 - - - +
13B ALA* 1.3 62.7 + - - +
15B HIS* 3.5 8.3 + - - +
16B LYS* 3.1 31.4 + - + +
15D HIS* 3.5 26.5 + - + +
19D GLU* 4.6 2.8 - - - +
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Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 4.2 17.4 - - + +
9B LYS 3.2 9.6 + - - +
10B LEU* 2.7 18.2 + - + +
12B GLU* 1.3 72.9 - - - +
14B LEU* 1.3 59.4 + - - +
16B LYS* 3.3 8.2 + - - +
17B ALA* 2.9 29.6 + - - +
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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
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10A LEU* 3.8 30.3 - - + +
13A ALA* 3.9 19.3 - - + +
14A LEU* 3.8 37.8 - - + +
17A ALA* 4.4 7.0 - - + -
10B LEU 2.7 18.0 + - - +
11B GLY* 3.8 5.6 - - - +
13B ALA* 1.3 70.3 - - - +
15B HIS* 1.3 66.3 + - - +
17B ALA* 3.3 1.9 + - - +
18B ILE* 3.0 49.4 + - + +
6C LEU* 5.0 1.6 - - + -
10C LEU* 3.6 22.4 - - + -
11D GLY* 5.9 1.1 - - - -
14D LEU* 4.1 5.2 - - + -
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Residues in contact with HIS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLY 3.0 18.4 + - - +
12B GLU* 3.5 7.2 - - - +
14B LEU* 1.3 77.6 - - - +
16B LYS* 1.3 74.9 + - - +
18B ILE* 3.4 8.9 + - - +
19B GLU* 2.7 55.6 + - + +
8D ARG* 4.8 3.7 + - + +
11D GLY* 4.2 6.1 + - - +
12D GLU* 3.4 44.6 + - + +
15D HIS* 4.1 29.9 + + + -
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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
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12B GLU* 3.1 18.8 + - + +
13B ALA* 3.3 8.0 + - - +
15B HIS* 1.3 83.8 - - - +
17B ALA* 1.3 65.9 + - - +
19B GLU* 3.3 30.0 + - - +
20B LEU* 3.0 24.9 + - - +
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 4.3 9.0 - - + -
17A ALA* 4.1 17.9 - - + -
18A ILE* 5.4 2.0 - - + -
21A LEU* 4.0 22.1 - - + +
13B ALA 2.9 16.8 + - - +
14B LEU* 3.3 8.7 + - - +
16B LYS* 1.3 76.7 - - - +
18B ILE* 1.3 57.0 + - - +
20B LEU* 3.4 5.9 + - - +
21B LEU* 3.0 33.5 + - - +
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA* 5.1 1.8 - - + -
14B LEU* 3.0 34.6 + - + +
15B HIS* 3.8 4.5 - - - +
17B ALA* 1.3 72.9 - - - +
19B GLU* 1.3 64.4 + - - +
21B LEU* 3.2 17.9 + - + +
22B GLU* 2.9 22.0 + - - +
6C LEU* 5.1 7.4 - - + -
10C LEU* 3.8 38.1 - - + -
4D LEU* 4.7 4.3 - - + +
7D LEU* 3.8 13.0 - - + +
8D ARG* 3.6 35.4 - - + +
11D GLY* 4.2 16.2 - - - -
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B HIS* 2.7 54.0 + - + +
16B LYS* 3.5 26.0 + - - +
18B ILE* 1.3 75.5 - - - +
20B LEU* 1.3 62.1 + - - +
22B GLU* 3.2 11.3 + - - +
23B LYS* 3.1 22.1 + - - +
8D ARG* 4.2 21.1 - - + -
12D GLU* 5.6 0.9 - - - -
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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
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21A LEU* 3.6 28.5 - - + -
16B LYS 3.0 13.2 + - - +
17B ALA* 3.5 9.4 - - - +
19B GLU* 1.3 72.7 - - - +
21B LEU* 1.3 65.4 + - - +
23B LYS* 3.0 13.3 + - + +
24B TRP* 2.9 65.4 + - + +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA* 4.0 26.9 - - + +
20A LEU* 3.5 30.3 - - + -
21A LEU* 3.7 24.3 - - + +
24A TRP* 3.3 32.6 - - + -
17B ALA 3.0 18.7 + - - +
18B ILE* 3.4 16.2 - - + +
20B LEU* 1.3 73.4 - - - +
22B GLU* 1.3 54.0 + - - +
24B TRP* 4.8 0.9 - - - +
25B GLY* 2.8 33.8 + - - -
3C LEU* 6.3 0.2 - - + -
6C LEU* 4.1 17.5 - - + -
4D LEU* 4.3 9.9 - - + +
7D LEU* 5.7 1.3 - - + -
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE 2.9 12.2 + - - +
19B GLU* 3.3 11.5 - - - +
21B LEU* 1.3 76.7 - - - +
23B LYS* 1.3 63.4 + - - +
25B GLY 3.7 0.7 - - - -
26B NH2 3.0 21.0 + - - -
1D SER 5.5 1.1 - - - +
4D LEU* 3.9 37.9 - - + +
5D GLU* 4.6 7.7 - - - +
8D ARG* 2.8 43.3 + - + -
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU 3.1 8.7 + - - +
20B LEU* 3.0 16.2 + - + +
22B GLU* 1.3 80.4 - - - +
24B TRP* 1.3 74.2 + - + +
26B NH2 3.8 4.5 + - - -
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Residues in contact with TRP 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.5 30.5 - - + -
24A TRP* 4.4 16.9 - - + +
25A GLY* 3.5 36.8 - - - -
20B LEU* 2.9 51.4 + - + +
21B LEU 4.2 1.3 - - - +
23B LYS* 1.3 86.2 - - + +
25B GLY* 1.3 63.7 + - - +
26B NH2 3.4 0.9 + - - -
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Residues in contact with GLY 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TRP* 3.9 20.6 - - - -
21B LEU 2.8 23.7 + - - -
22B GLU 3.7 1.3 - - - -
24B TRP* 1.3 73.4 - - - +
26B NH2 1.3 44.7 + - - -
4D LEU* 4.2 14.8 - - - +
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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