Contacts of the helix formed by residues 721 - 724 (chain F) in PDB entry 2W3S
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 721 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534F ASP* 4.2 11.9 - - - +
538F MET* 4.5 2.2 - - - -
602F TYR* 5.9 1.3 - - - -
620F LEU* 4.0 17.0 - - + -
621F TYR* 3.7 20.4 - - + -
717F ASN* 3.5 25.1 - - - +
719F GLU* 3.0 4.2 + - + -
720F GLU* 1.3 80.4 - - - +
722F ILE* 1.3 68.5 + - - +
723F PHE 3.0 1.4 + - - -
724F ARG* 2.7 25.3 + - - -
725F SER* 2.4 28.2 + - - +
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Residues in contact with ILE 722 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499F VAL* 4.1 12.8 - - + -
533F ALA 4.0 11.7 - - - +
534F ASP* 3.8 20.3 + - - +
537F GLY* 3.6 26.9 - - - +
538F MET* 3.7 30.7 - - + +
541F LYS* 3.7 28.5 - - + +
655F LEU* 4.0 11.8 - - + +
721F THR* 1.3 68.0 - - - +
723F PHE* 1.3 78.3 - - + +
724F ARG 2.9 5.2 + - - -
725F SER* 2.8 39.4 + - - +
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Residues in contact with PHE 723 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F VAL* 3.4 49.4 - - + -
499F VAL* 4.2 20.0 - - + -
502F ALA* 4.6 6.7 - - + -
503F VAL* 4.2 16.8 - - + -
541F LYS* 5.4 9.8 - - - +
653F ALA* 3.5 14.4 - - - +
655F LEU* 4.1 5.8 - - + -
721F THR 3.0 2.2 + - - -
722F ILE* 1.3 87.8 - - + +
724F ARG* 1.3 71.6 + - - +
725F SER 3.1 1.2 + - - -
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Residues in contact with ARG 724 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ALA* 3.5 40.4 + - + +
135B ALA* 4.5 5.9 - - - +
653F ALA* 2.7 30.2 + - + -
716F PRO* 3.9 15.3 - - + -
717F ASN* 2.9 41.7 + - - +
718F ARG* 3.1 21.8 + - - +
719F GLU 3.3 13.9 + - - -
720F GLU* 4.1 23.0 + - - +
721F THR* 2.7 27.5 + - - -
723F PHE* 1.3 73.5 - - - +
725F SER* 1.3 55.3 + - - +
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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