Contacts of the helix formed by residues 10 - 20 (chain V) in PDB entry 2ZJR
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 GLN 10 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8V ASN 5.7 0.6 + - - -
9V LEU* 1.3 84.1 + - + +
11V ALA* 1.3 67.6 + - - +
12V THR* 3.5 16.2 + - - +
13V ASP* 2.8 34.8 + - - +
14V PHE* 2.9 14.3 + - - -
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Residues in contact with ALA 11 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V LEU 4.0 1.2 + - - -
10V GLN* 1.3 70.2 - - - +
12V THR* 1.3 66.3 + - + +
14V PHE* 2.9 30.5 + - - +
15V ALA* 3.2 5.0 + - - +
57V LYS* 5.3 12.6 - - + +
60V LEU* 6.2 5.8 - - + -
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Residues in contact with THR 12 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V GLN* 3.5 14.9 + - - +
11V ALA* 1.3 81.4 - - + +
13V ASP* 1.3 60.3 + - - +
15V ALA* 3.0 13.1 + - - +
16V LYS* 2.8 25.1 + - - +
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Residues in contact with ASP 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V LEU* 3.8 33.8 - - + +
10V GLN* 2.8 39.9 + - - +
12V THR* 1.3 79.6 + - - +
14V PHE* 1.3 53.3 + - - +
16V LYS* 2.8 35.4 + - - +
17V GLU* 2.4 43.8 + - + +
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Residues in contact with PHE 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6V MET* 2.9 30.7 - - + -
7V ARG* 3.6 27.1 - - + -
9V LEU* 4.7 9.2 - - + -
10V GLN 2.9 14.0 + - - -
11V ALA* 2.9 18.2 - - - +
13V ASP* 1.3 74.5 - - - +
15V ALA* 1.3 53.3 + - - +
17V GLU* 2.7 28.9 + - + +
18V ILE* 2.8 20.0 + - - +
53V LEU* 4.2 17.2 - - + +
56V VAL* 3.6 13.7 - - + -
57V LYS* 3.1 62.4 - - + -
60V LEU* 4.8 9.0 - - + -
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Residues in contact with ALA 15 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11V ALA 3.2 3.4 + - - +
12V THR* 3.0 16.0 + - - +
14V PHE* 1.3 78.7 - - - +
16V LYS* 1.3 52.0 + - - +
18V ILE* 2.6 18.1 + - - +
19V ASP* 2.6 41.2 + - + +
57V LYS* 5.8 1.7 - - - +
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Residues in contact with LYS 16 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V LEU* 6.3 0.2 - - - +
12V THR 2.8 13.2 + - - +
13V ASP* 2.8 35.2 + - - +
15V ALA* 1.3 73.7 - - - +
17V GLU* 1.3 74.7 + - - +
18V ILE 3.1 1.6 + - - -
19V ASP* 3.2 12.8 - - - +
20V ALA* 3.0 33.9 + - + +
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Residues in contact with GLU 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V LEU* 4.2 24.0 - - + +
13V ASP* 2.4 34.4 + - - +
14V PHE* 2.7 13.0 + - + +
16V LYS* 1.3 97.1 - - - +
18V ILE* 1.3 57.7 + - - +
20V ALA* 5.9 0.2 - - - +
21V ARG* 2.5 54.8 + - - +
53V LEU* 2.8 26.7 - - + +
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Residues in contact with ILE 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V PHE* 2.8 25.5 + - + +
15V ALA* 2.6 20.0 + - - +
17V GLU* 1.3 72.4 - - - +
19V ASP* 1.3 56.5 + - + +
20V ALA 2.5 17.3 + - - -
21V ARG* 2.7 16.0 + - - +
22V LYS* 3.3 34.6 + - + +
50V VAL* 4.3 10.8 - - + -
53V LEU* 3.3 31.4 - - + +
54V ASN* 3.0 29.4 - - - +
57V LYS* 5.1 8.1 - - + +
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Residues in contact with ASP 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Q SER* 4.9 19.5 - - - -
4Q TYR* 3.8 17.5 - - - +
15V ALA* 2.6 15.6 + - + +
16V LYS* 3.2 28.2 - - - +
18V ILE* 1.3 74.4 - - + +
20V ALA* 1.3 59.1 + - - +
22V LYS* 4.5 10.2 - - - +
23V LYS* 3.7 13.4 + - - +
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Residues in contact with ALA 20 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16V LYS* 3.0 24.6 + - + +
18V ILE 2.5 7.5 + - - -
19V ASP* 1.3 77.7 - - - +
21V ARG* 1.3 72.3 + - - +
22V LYS 3.4 0.2 - - - -
23V LYS* 3.0 26.4 - - + +
24V GLU* 3.3 6.4 + - - +
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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