Contacts of the helix formed by residues 9 - 19 (chain A) in PDB entry 2OZ6
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 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A MET* 1.3 80.6 + - - +
10A LEU* 1.3 58.1 + - - +
11A LYS* 3.0 19.1 - - + +
12A HIS* 2.7 55.6 + - + +
13A LEU* 3.2 9.2 + - - +
116A GLU* 3.2 26.2 + - - +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LYS* 1.3 73.3 - - - +
11A LYS* 1.3 55.8 + - - +
13A LEU* 3.4 27.1 + - + +
14A ASP* 3.0 28.2 + - + +
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Residues in contact with LYS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LYS* 3.0 19.4 + - + +
10A LEU* 1.3 79.2 - - - +
12A HIS* 1.3 92.6 + - + +
14A ASP* 3.5 9.1 - - - +
15A LYS* 3.2 32.6 + - - +
114A ASP* 5.1 3.6 - - - +
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Residues in contact with HIS 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A MET* 3.5 16.0 - - + -
9A LYS* 2.7 53.9 + - + +
11A LYS* 1.3 98.6 - - + +
13A LEU* 1.3 64.9 + - - +
15A LYS* 3.3 7.2 + - + +
16A LEU* 3.1 29.4 + - - +
114A ASP* 3.6 40.9 + - + +
116A GLU* 3.5 20.6 - - + +
117A ILE* 3.6 20.4 - - + +
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A MET* 4.3 7.8 - - - -
9A LYS 3.2 7.3 + - - +
10A LEU* 3.5 29.4 - - + +
12A HIS* 1.3 78.3 - - - +
14A ASP* 1.3 65.8 + - - +
16A LEU* 3.1 12.0 + - + +
17A LEU* 2.9 49.3 + - + +
43A PHE* 3.3 42.0 - - + -
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Residues in contact with ASP 14 (chain A).
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* 3.0 11.4 + - + +
11A LYS* 3.5 14.8 - - - +
13A LEU* 1.3 80.8 - - - +
15A LYS* 1.3 65.5 + - - +
17A LEU* 3.5 8.3 + - - +
18A ALA* 3.1 23.1 + - - +
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS* 3.2 21.5 - - - +
12A HIS* 3.3 11.1 + - - +
13A LEU 3.2 0.4 - - - -
14A ASP* 1.3 77.9 - - - +
16A LEU* 1.3 60.8 + - + +
18A ALA* 2.8 17.3 + - - -
19A HIS* 2.8 29.8 + - + +
110A LEU* 4.1 22.9 - - + -
113A GLN* 3.8 18.0 + - - +
114A ASP* 2.9 31.3 + - - +
117A ILE* 5.4 3.6 - - + -
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A MET* 3.3 36.6 - - + -
12A HIS 3.1 16.0 + - - +
13A LEU* 3.5 9.6 - - + +
15A LYS* 1.3 79.1 - - - +
17A LEU* 1.3 67.9 + - + +
19A HIS 3.1 20.6 + - - +
20A CYS* 3.6 8.5 - - - +
43A PHE* 4.9 7.4 - - + -
71A PHE* 3.8 13.7 - - + -
102A ILE* 4.0 24.0 - - + +
107A PHE* 4.3 20.9 - - + -
110A LEU* 3.8 25.8 - - + -
117A ILE* 4.3 11.7 - - + -
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 2.9 47.7 + - + +
14A ASP* 3.8 7.9 - - - +
16A LEU* 1.3 76.8 - - + +
18A ALA* 1.3 59.7 + - - +
19A HIS 3.3 0.4 - - - -
20A CYS* 3.7 17.3 + - - +
22A ARG* 5.8 1.8 - - - +
43A PHE* 4.5 4.9 - - + -
45A ILE* 4.0 36.6 - - + -
100A ALA* 4.1 12.6 - - + -
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASP* 3.1 14.1 + - - +
15A LYS* 2.8 13.8 + - - +
17A LEU* 1.3 77.1 - - - +
19A HIS* 1.3 77.3 + - + +
20A CYS 3.8 1.1 - - - -
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Residues in contact with HIS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LYS* 2.8 30.9 + - + +
16A LEU 3.1 6.7 + - - +
18A ALA* 1.3 93.6 + - + +
20A CYS* 1.3 58.9 + - - +
102A ILE* 4.0 16.3 - - - +
106A LYS* 4.3 26.3 - - + +
110A LEU* 4.0 30.9 - - + +
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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