Contacts of the helix formed by residues 6 - 22 (chain N) in PDB entry 2ZQK
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 ALA 6 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7N THR* 1.3 68.7 + - + +
8N GLU* 3.2 16.4 - - + +
9N THR* 3.1 33.4 + - - +
10N ALA* 4.1 2.4 + - - +
58N GLY* 5.4 3.6 - - - -
62N LYS* 6.4 2.5 - - + -
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Residues in contact with THR 7 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N ALA* 1.3 78.3 - - + +
8N GLU* 1.3 58.8 + - - +
9N THR 3.0 6.3 - - - -
10N ALA* 3.3 11.7 + - - +
11N THR* 2.9 30.9 + - - -
57N ALA* 3.7 23.3 - - + +
58N GLY* 3.8 10.3 - - - +
61N ALA* 3.7 20.1 - - + +
62N LYS* 5.1 0.9 - - + +
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Residues in contact with GLU 8 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N ALA* 4.1 12.8 - - + +
7N THR* 1.3 81.2 - - - +
9N THR* 1.3 67.0 + - - +
11N THR* 3.8 3.1 - - - -
12N ARG* 2.9 62.2 + - - +
54N ALA* 3.1 31.2 - - - +
55N LYS* 3.8 26.3 + - - +
58N GLY* 4.0 11.3 - - - +
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Residues in contact with THR 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N ALA 3.1 30.2 + - - -
8N GLU* 1.3 79.9 - - - +
10N ALA* 1.3 67.0 + - - +
12N ARG* 3.2 19.1 + - - +
13N ASP* 3.0 35.1 + - - +
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Residues in contact with ALA 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M ALA* 4.7 21.3 - - + +
13M ASP* 4.3 4.4 - - - +
6N ALA 4.1 1.9 + - - +
7N THR* 3.3 18.0 + - - +
9N THR* 1.3 80.4 - - - +
11N THR* 1.3 62.9 + - - +
13N ASP* 3.3 12.4 + - - +
14N GLN* 3.0 22.9 + - - +
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Residues in contact with THR 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N THR* 2.9 23.0 + - - -
8N GLU* 3.9 5.6 - - - -
9N THR 3.2 0.2 - - - -
10N ALA* 1.3 72.7 - - - +
12N ARG* 1.3 66.7 + - - +
14N GLN* 3.1 12.3 + - - +
15N LEU* 2.9 44.0 + - + +
53N GLN* 3.9 6.1 - - + +
54N ALA* 3.5 25.6 - - - -
57N ALA* 3.7 17.0 - - + +
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Residues in contact with ARG 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M LYS* 5.4 9.0 - - + +
8N GLU* 2.9 52.2 + - - +
9N THR* 3.4 20.5 + - - +
11N THR* 1.3 77.3 - - - +
13N ASP* 1.3 71.1 + - - +
15N LEU* 3.2 1.6 + - - +
16N THR* 2.9 31.1 + - - +
50N ILE* 3.9 10.9 - - + +
51N GLU* 2.6 45.3 + - - +
54N ALA* 3.7 13.0 - - + +
55N LYS* 4.9 1.0 - - - +
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Residues in contact with ASP 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M ALA* 4.3 4.0 - - - +
13M ASP* 3.5 19.7 - - + -
14M GLN* 3.6 30.9 + - - +
17M LYS* 3.3 35.6 + - - +
9N THR* 3.0 26.7 + - - +
10N ALA* 3.4 11.1 - - - +
12N ARG* 1.3 80.8 - - - +
14N GLN* 1.3 59.3 + - - +
16N THR* 3.0 5.0 + - - -
17N LYS* 2.8 27.9 + - - +
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Residues in contact with GLN 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M ASP* 3.8 22.4 - - - +
10N ALA 3.0 10.9 + - - +
11N THR* 3.7 12.1 + - - +
13N ASP* 1.3 79.5 - - - +
15N LEU* 1.3 67.9 + - - +
17N LYS* 3.1 12.1 + - - +
18N GLU* 2.9 59.3 + - - +
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Residues in contact with LEU 15 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N THR* 2.9 36.6 + - + +
14N GLN* 1.3 83.9 - - - +
16N THR* 1.3 57.3 + - - +
18N GLU* 3.6 19.6 - - - +
19N ALA* 3.1 24.4 + - - +
50N ILE* 3.4 31.5 - - + +
53N GLN* 3.5 47.3 - - + +
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Residues in contact with THR 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M LYS* 3.4 29.8 - - + +
21M GLN* 5.7 1.6 - - - +
12N ARG* 2.9 22.4 + - - +
13N ASP 3.0 8.8 + - - -
15N LEU* 1.3 77.7 - - - +
17N LYS* 1.3 61.0 + - - +
18N GLU 3.2 0.2 - - - -
19N ALA* 3.0 5.3 + - - +
20N PHE* 2.8 38.9 + - + +
42N LEU* 3.6 20.6 - - + -
50N ILE* 3.6 15.3 - - - +
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Residues in contact with LYS 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M ARG* 5.8 3.8 - - - -
13M ASP* 2.9 38.6 + - - +
16M THR* 3.9 29.6 - - + -
17M LYS* 4.8 6.9 - - - +
20M PHE* 5.1 2.2 - - + -
13N ASP 2.8 12.4 + - - +
14N GLN* 3.1 14.4 + - - +
16N THR* 1.3 78.5 - - - +
18N GLU* 1.3 81.2 + - - +
20N PHE* 3.4 7.0 + - - +
21N GLN* 3.0 45.7 + - - +
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Residues in contact with GLU 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N GLN* 2.9 53.5 + - - +
15N LEU* 3.6 20.0 - - + +
17N LYS* 1.3 89.3 + - + +
19N ALA* 1.3 67.5 + - - +
21N GLN* 2.9 36.3 + - - +
22N ASN* 3.6 4.7 + - - +
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Residues in contact with ALA 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N LEU 3.1 17.7 + - - +
16N THR* 3.0 10.7 + - - +
18N GLU* 1.3 76.4 - - - +
20N PHE* 1.3 63.2 + - - +
22N ASN 2.9 17.2 + - - +
25N ASN* 3.0 22.9 + - - +
42N LEU* 3.5 25.1 - - + -
46N VAL* 4.1 16.6 - - + -
50N ILE* 4.5 3.4 - - + -
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Residues in contact with PHE 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M LYS* 4.0 13.9 - - - -
20M PHE* 3.3 57.8 - + + -
21M GLN* 4.2 7.6 - - + -
40M GLY* 3.6 8.0 - - - -
16N THR* 2.8 37.0 + - + +
17N LYS* 3.7 5.6 - - - +
18N GLU 3.2 0.2 - - - -
19N ALA* 1.3 76.8 - - - +
21N GLN* 1.3 60.6 + - - +
22N ASN 3.0 7.3 + - - +
23N PRO* 4.4 0.5 - - - +
26N GLN* 3.8 37.3 - - + +
40N GLY* 3.3 28.0 - - - -
42N LEU* 3.3 33.4 - - + -
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Residues in contact with GLN 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M PHE* 5.1 4.0 - - + -
39M SER 4.3 1.6 - - - +
40M GLY* 3.7 23.6 - - - +
17N LYS* 3.0 46.2 + - + +
18N GLU* 2.9 26.3 + - - +
20N PHE* 1.3 75.9 - - - +
22N ASN* 1.3 56.5 + - - +
23N PRO* 3.2 12.1 - - - +
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Residues in contact with ASN 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N GLU 3.6 3.1 + - - +
19N ALA 2.9 9.7 + - - +
20N PHE 4.0 3.1 - - - +
21N GLN* 1.3 77.9 - - - +
23N PRO* 1.3 58.1 - - - +
24N ASP* 2.6 44.7 + - - +
25N ASN* 2.9 38.9 + - - +
26N GLN* 3.9 2.6 + - - +
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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