Contacts of the helix formed by residues 430 - 434 (chain B) in PDB entry 4ZG9
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 PRO 430 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B TYR* 4.4 9.0 - - + -
428B HIS 3.5 1.1 - - - +
429B LEU* 1.3 95.4 - - + +
431B LYS* 1.3 67.4 + - - +
432B ARG* 2.9 26.1 + - + +
433B LEU* 3.0 32.3 + - + +
434B HIS 4.1 1.2 + - - -
447B LEU* 4.7 2.7 - - + -
822B MET* 3.8 28.5 - - + +
823B HIS* 3.4 34.5 - - + +
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Residues in contact with LYS 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B GLN* 4.5 8.2 + - - +
429B LEU 3.3 9.5 + - - +
430B PRO* 1.3 71.4 - - - +
432B ARG* 1.3 62.3 + - - +
433B LEU 3.1 1.0 + - - -
434B HIS* 3.1 27.8 + - + +
436B ALA* 5.5 2.8 - - - +
740B ASP* 3.3 27.2 + - - +
743B TYR* 3.9 23.2 + - - +
745B GLY* 4.9 4.2 - - - +
767B HIS* 3.6 39.1 - - + +
795B ILE* 4.0 37.5 + - + +
823B HIS* 4.6 3.2 + - - +
825B ALA* 5.8 0.2 - - + -
829B ASP* 5.4 2.5 - - + -
833B LEU* 4.3 18.8 - - + -
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Residues in contact with ARG 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B TYR* 5.3 0.3 - - - -
430B PRO* 2.9 15.9 + - + +
431B LYS* 1.3 77.1 - - - +
433B LEU* 1.3 76.7 + - - +
434B HIS* 3.1 16.5 - - - -
478B ASP* 3.0 41.8 + - - -
479B ASN* 3.9 14.0 + - - +
480B LYS* 3.8 18.5 - - - +
505B GLU* 6.2 0.2 - - - +
822B MET* 2.8 45.0 + - - -
824B THR* 3.4 38.5 + - - +
825B ALA* 4.9 2.0 - - - +
826B ARG* 6.1 0.2 - - + -
829B ASP* 4.3 16.4 + - - +
856B LEU* 4.2 21.1 - - + -
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Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 6.0 0.3 - - - +
206B TYR* 3.6 57.0 + - + +
222B TYR* 5.1 1.9 - - - -
223B PRO* 5.9 0.7 - - - +
429B LEU* 4.4 10.5 - - + -
430B PRO* 3.0 37.9 + - + +
432B ARG* 1.3 100.9 - - - +
434B HIS* 1.3 67.8 + - - +
435B TYR* 3.3 11.1 + - + +
447B LEU* 4.2 22.9 - - + -
478B ASP* 4.2 10.5 - - - +
479B ASN* 3.7 12.0 + - - +
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Residues in contact with HIS 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B TYR 5.4 0.3 - - - +
222B TYR* 3.3 55.4 + + + +
223B PRO* 5.3 1.9 - - - +
224B GLU* 3.0 46.2 + - - +
430B PRO 4.1 1.2 + - - -
431B LYS* 3.1 20.6 + - + -
432B ARG 3.1 23.3 - - - -
433B LEU* 1.3 77.7 - - - +
435B TYR* 1.3 59.1 + - - +
745B GLY* 5.2 8.5 - - - -
829B ASP* 3.1 31.4 + - + -
832B HIS* 5.3 4.5 - + + -
833B LEU* 6.5 1.1 - - + -
1D NAG 4.2 13.7 - - + +
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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
------------------------------------------------------------
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