Contacts of the helix formed by residues 727 - 733 (chain A) in PDB entry 2WSF
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 ILE 727 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580A PRO* 3.5 31.9 - - + -
697A ARG* 4.0 12.7 - - + +
725A LEU 2.6 14.0 + - - -
726A SER* 1.3 64.5 - - - +
728A VAL* 1.3 62.1 + - + +
729A GLN 3.5 0.2 - - - -
730A GLY* 3.5 5.7 + - - -
731A ARG* 3.5 36.0 + - - +
842A PQN 4.3 6.4 - - - -
856A SF4 3.9 13.9 - - - -
562B PRO* 5.5 3.4 - - + -
565B GLY 5.1 0.4 - - - +
566B GLY* 3.7 20.0 - - - -
567B THR 3.7 19.5 - - - +
568B CYS* 3.6 29.6 - - - -
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Residues in contact with VAL 728 (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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578A ARG* 4.9 16.8 - - + +
579A PHE 5.0 0.9 - - - -
580A PRO* 4.0 31.6 - - + -
595A TRP* 3.2 41.3 - - + +
726A SER* 2.2 23.0 + - - +
727A ILE* 1.3 66.5 - - + +
729A GLN* 1.3 54.2 + - - +
730A GLY 3.1 1.1 - - - -
731A ARG* 3.3 22.7 + - - +
732A ALA* 2.7 27.7 + - - +
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Residues in contact with GLN 729 (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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52A THR* 5.3 0.2 - - - +
55A TRP* 2.9 53.8 - - + +
725A LEU* 3.5 20.2 - - + +
726A SER* 2.6 49.1 + - - +
728A VAL* 1.3 73.6 - - - +
730A GLY* 1.3 50.0 + - - +
732A ALA* 2.7 15.2 + - + +
733A VAL* 2.7 40.1 + - + +
838A CLA 3.0 29.2 - - + +
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Residues in contact with GLY 730 (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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692A PHE* 3.5 17.9 - - - +
725A LEU* 4.3 5.4 - - - +
726A SER 4.2 0.2 + - - -
727A ILE 3.5 5.7 + - - -
728A VAL 3.1 0.6 - - - -
729A GLN* 1.3 78.6 - - - +
731A ARG* 1.3 55.5 + - - +
733A VAL* 3.2 12.1 + - - +
734A GLY 2.9 21.5 + - - -
842A PQN 3.7 32.8 - - - -
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Residues in contact with ARG 731 (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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579A PHE 5.6 0.2 - - - -
580A PRO* 2.8 34.9 + - - +
581A CYS* 4.6 4.0 - - - +
590A CYS 5.3 0.2 - - - -
591A GLN* 3.9 20.5 - - - +
595A TRP* 3.6 5.7 - - + -
596A ASP* 2.6 36.9 + - - -
599A PHE* 3.0 39.0 - - + -
692A PHE 5.1 2.0 - - - +
693A LEU* 5.5 2.2 - - - +
727A ILE* 3.5 27.5 + - - +
728A VAL* 3.3 24.3 + - - +
729A GLN 3.2 0.4 - - - -
730A GLY* 1.3 75.4 - - - +
732A ALA* 1.3 60.4 + - - +
734A GLY* 2.8 17.8 + - - +
735A VAL* 2.9 18.5 - - - +
842A PQN 6.1 0.7 - - + -
856A SF4 5.2 2.4 - - - -
667B TRP* 5.5 8.7 - - - +
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Residues in contact with ALA 732 (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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595A TRP* 3.4 19.9 - - + -
728A VAL 2.7 18.4 + - - +
729A GLN* 2.7 21.7 + - + +
731A ARG* 1.3 70.7 - - - +
733A VAL* 1.3 56.8 + - + +
734A GLY 3.4 7.1 - - - +
735A VAL* 4.7 1.5 - - - +
736A THR* 3.5 12.5 + - - -
838A CLA 3.4 32.8 - - + +
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Residues in contact with VAL 733 (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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689A SER* 4.8 0.3 - - - +
692A PHE* 3.2 28.6 - - + +
725A LEU* 3.7 14.4 - - + -
729A GLN* 2.7 26.7 + - + +
730A GLY 3.2 6.9 + - - +
732A ALA* 1.3 69.7 - - - +
734A GLY* 1.3 64.2 + - - +
737A HIS* 3.3 27.7 + - + +
838A CLA 3.0 72.5 - - + +
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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