Contacts of the helix formed by residues 7 - 20 (chain D) 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 THR 7 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D ALA* 1.3 74.8 - - - +
8D GLU* 1.3 64.9 + - - +
9D THR* 3.1 3.8 + - - -
10D ALA* 3.3 21.9 + - - +
11D THR* 3.7 10.6 + - - +
58D GLY* 3.5 27.8 + - - +
61D ALA* 4.5 13.9 - - + -
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Residues in contact with GLU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ALA 3.1 16.1 + - - +
7D THR* 1.3 79.5 - - - +
9D THR* 1.3 61.9 + - - +
11D THR* 3.4 8.5 + - - -
12D ARG* 3.0 47.7 + - - +
51D GLU* 4.5 7.4 - - - +
54D ALA* 3.1 30.4 - - - +
55D LYS* 3.9 35.0 + - - +
58D GLY* 4.2 8.4 - - - -
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Residues in contact with THR 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLN* 5.0 5.6 - - - +
6D ALA 4.2 9.7 + - - -
7D THR* 3.1 1.0 - - - +
8D GLU* 1.3 77.1 - - - +
10D ALA* 1.3 62.4 + - - +
12D ARG* 2.9 40.9 + - + +
13D ASP* 3.1 21.6 + - - +
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Residues in contact with ALA 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C THR* 5.9 7.0 - - + +
10C ALA* 5.0 19.9 - - + +
13C ASP* 5.2 1.0 - - - +
7D THR* 3.3 21.7 + - - +
9D THR* 1.3 76.4 - - - +
11D THR* 1.3 69.2 + - - +
13D ASP* 3.5 8.3 + - - +
14D GLN* 3.4 17.5 + - - +
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Residues in contact with THR 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D THR* 3.7 8.9 + - - +
8D GLU* 3.4 11.1 + - - -
9D THR 3.3 0.2 - - - -
10D ALA* 1.3 77.0 - - - +
12D ARG* 1.3 70.3 + - - +
14D GLN* 3.0 15.1 + - - +
15D LEU* 3.1 32.6 + - + +
53D GLN* 4.8 1.8 - - + +
54D ALA* 3.7 26.9 + - - +
57D ALA* 5.4 8.9 - - + +
58D GLY* 4.7 6.8 + - - -
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Residues in contact with ARG 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LYS* 5.5 7.2 - - + -
8D GLU* 3.0 50.2 + - - +
9D THR* 2.9 29.1 + - + +
11D THR* 1.3 80.0 - - - +
13D ASP* 1.3 58.1 + - - +
14D GLN 2.6 14.0 + - - -
15D LEU* 3.1 9.0 + - - +
16D THR* 3.1 23.6 + - - +
50D ILE* 4.8 12.1 - - - -
51D GLU* 3.0 30.3 + - - -
54D ALA* 3.4 18.8 - - - +
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Residues in contact with ASP 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ALA* 4.2 8.9 - - - +
13C ASP* 3.5 31.8 - - + +
14C GLN* 2.8 50.2 - - - +
17C LYS* 3.5 25.1 + - - +
9D THR* 3.1 24.1 + - - +
10D ALA* 3.5 9.4 + - - +
12D ARG* 1.3 80.4 - - - +
14D GLN* 1.3 59.0 + - - +
16D THR* 4.3 1.1 - - - -
17D LYS* 3.5 15.6 + - - +
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Residues in contact with GLN 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C THR* 5.6 5.7 - - + +
13C ASP* 3.3 23.1 + - - +
10D ALA 3.4 7.7 + - - +
11D THR* 3.0 10.6 + - - +
12D ARG 2.6 6.7 + - - -
13D ASP* 1.3 72.2 - - - +
15D LEU* 1.3 62.2 + - - +
16D THR 3.0 4.7 - - - -
17D LYS* 2.9 29.7 + - - +
18D GLU* 3.1 32.2 + - - +
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Residues in contact with LEU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D THR* 3.1 34.0 + - + +
14D GLN* 1.3 84.3 - - + +
16D THR* 1.3 60.9 + - - +
18D GLU* 3.5 25.1 + - + +
19D ALA* 3.2 21.8 + - - +
50D ILE* 3.7 35.8 - - + +
53D GLN* 3.3 36.6 - - + +
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Residues in contact with THR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LYS* 3.4 33.9 - - + +
21C GLN* 6.1 0.4 - - - +
12D ARG* 3.1 24.5 + - - +
13D ASP 4.1 0.4 - - - -
14D GLN 3.0 0.6 - - - -
15D LEU* 1.3 74.8 - - - +
17D LYS* 1.3 62.7 + - - +
18D GLU 3.0 4.8 + - - -
19D ALA* 3.2 6.7 + - - +
20D PHE* 3.0 40.9 + - + +
42D LEU* 4.4 14.3 - - + +
50D ILE* 4.2 13.9 - - - +
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Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ARG* 5.0 9.2 - - + +
13C ASP* 3.8 32.9 + - - +
16C THR* 3.6 38.1 - - + +
17C LYS* 5.2 2.7 - - - +
20C PHE* 4.8 6.9 - - + -
13D ASP 3.5 11.9 + - - +
14D GLN* 2.9 19.5 + - - +
16D THR* 1.3 79.9 - - - +
18D GLU* 1.3 64.8 + - - +
20D PHE* 3.9 10.1 - - - +
21D GLN* 3.5 19.2 + - - +
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Residues in contact with GLU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLN* 3.1 41.6 + - - +
15D LEU* 3.6 27.9 + - + +
16D THR 3.0 0.8 - - - -
17D LYS* 1.3 82.4 + - - +
19D ALA* 1.3 65.6 + - - +
20D PHE 3.2 0.9 - - - -
21D GLN* 2.9 23.4 + - - +
22D ASN* 3.8 4.3 + - - +
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Residues in contact with ALA 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU 3.2 11.6 + - - +
16D THR* 3.2 7.4 + - - +
18D GLU* 1.3 76.9 - - - +
20D PHE* 1.3 54.2 + - - +
22D ASN 2.8 27.9 + - - +
25D ASN* 3.1 38.1 + - + +
42D LEU* 4.3 17.0 - - + -
46D VAL* 4.7 10.8 - - + -
50D ILE* 5.4 6.3 - - + -
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Residues in contact with PHE 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LYS* 3.8 16.2 - - - -
20C PHE* 3.2 65.9 - + + -
21C GLN* 3.9 10.1 - - - -
40C GLY* 3.6 8.7 - - - -
16D THR* 3.0 31.1 + - + +
17D LYS* 3.9 8.1 - - - +
19D ALA* 1.3 74.5 - - - +
21D GLN* 1.3 56.2 + - - +
22D ASN 3.0 13.6 + - - +
26D GLN* 3.8 27.3 - - + +
40D GLY 3.2 28.0 - - - -
42D LEU* 3.2 33.4 - - + -
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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