Contacts of the helix formed by residues 723 - 736 (chain B) in PDB entry 2WAC
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 SER 723 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720B SER* 3.2 22.7 + - - -
721B VAL 3.2 1.2 - - - -
722B GLU* 1.3 76.8 - - - +
724B GLY* 1.3 63.1 - - - +
725B SER 3.3 3.1 - - - -
726B LYS* 3.1 19.4 + - - +
727B LEU* 3.1 22.7 + - - +
810B TYR* 4.0 25.1 - - - -
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Residues in contact with GLY 724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719B GLN* 5.8 3.6 - - - -
720B SER 3.5 5.7 + - - -
721B VAL* 2.9 17.1 + - - -
722B GLU 3.2 0.6 - - - -
723B SER* 1.3 77.4 - - - +
725B SER* 1.3 55.5 + - - +
727B LEU* 3.6 7.3 + - - +
728B GLU* 3.0 40.6 + - - +
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Residues in contact with SER 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721B VAL 4.8 0.2 + - - -
722B GLU 4.1 10.7 + - - -
724B GLY* 1.3 72.0 - - - +
726B LYS* 1.3 61.7 + - - +
728B GLU* 3.5 14.7 + - - +
729B SER* 2.8 36.0 + - - -
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Residues in contact with LYS 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722B GLU 5.3 1.3 - - - +
723B SER* 3.1 24.2 + - - +
725B SER* 1.3 83.1 + - - +
727B LEU* 1.3 57.0 + - - +
729B SER* 3.8 5.1 - - - -
730B LEU* 2.9 29.5 + - - +
807B GLU* 4.9 0.5 - - - +
810B TYR* 3.5 28.3 + - + +
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Residues in contact with LEU 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719B GLN* 3.5 35.4 - - - +
723B SER 3.1 11.8 + - - +
724B GLY* 3.8 9.6 - - - +
726B LYS* 1.3 74.0 - - - +
728B GLU* 1.3 60.1 + - + +
730B LEU* 3.6 6.0 - - + +
731B MET* 2.8 50.0 + - + +
785B ASP* 3.7 34.1 - - + +
786B TYR* 3.9 20.2 - - + +
810B TYR* 3.8 25.0 - - + -
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Residues in contact with GLU 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724B GLY* 3.0 29.2 + - - +
725B SER* 3.5 11.3 - - - +
727B LEU* 1.3 76.5 - - + +
729B SER* 1.3 55.8 + - - +
731B MET* 3.9 4.0 - - - +
732B SER* 3.0 30.6 + - - -
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Residues in contact with SER 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725B SER 2.8 21.3 + - - -
726B LYS* 3.9 5.6 - - - -
728B GLU* 1.3 70.8 - - - +
730B LEU* 1.3 65.3 + - - +
732B SER* 3.8 5.4 - - - -
733B LYS* 3.0 38.2 + - - +
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Residues in contact with LEU 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726B LYS 2.9 18.5 + - - +
727B LEU* 3.3 6.9 + - + +
729B SER* 1.3 76.6 - - - +
731B MET* 1.3 76.8 + - + +
733B LYS* 3.4 10.2 + - - +
734B LEU* 3.0 41.8 + - + +
768B ARG* 3.8 39.9 - - + +
785B ASP* 4.6 4.3 - - - +
804B PHE* 4.0 16.4 - - + +
807B GLU* 2.6 35.2 - - - +
810B TYR* 3.9 9.9 - - + -
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Residues in contact with MET 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727B LEU* 2.8 33.5 + - + +
728B GLU* 4.0 4.5 - - - +
730B LEU* 1.3 85.2 - - + +
732B SER* 1.3 62.5 + - - +
734B LEU* 4.1 4.2 - - - +
735B HIS* 3.2 23.2 + - - +
765B GLN* 5.1 5.8 - - + -
766B TRP 3.4 27.7 - - - +
767B TYR* 3.8 41.7 - - + +
768B ARG 5.2 1.6 - - - -
785B ASP* 5.3 1.6 - - - +
786B TYR* 3.9 21.8 - - - +
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Residues in contact with SER 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728B GLU 3.0 20.6 + - - -
729B SER* 3.8 7.6 - - - -
731B MET* 1.3 76.5 - - - +
733B LYS* 1.3 59.0 + - - +
734B LEU 3.2 0.7 + - - -
735B HIS* 3.3 13.0 + - - +
736B ALA* 3.2 24.1 + - - +
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Residues in contact with LYS 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729B SER* 3.0 32.2 + - - +
730B LEU* 4.8 2.5 - - - +
732B SER* 1.3 78.5 - - - +
734B LEU* 1.3 56.7 + - - +
736B ALA* 3.9 10.2 - - - +
737B ASP* 3.3 23.0 + - - +
803B ALA* 4.9 11.1 + - + +
804B PHE* 3.6 28.7 - - + -
807B GLU* 5.3 6.4 + - - -
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Residues in contact with LEU 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730B LEU* 3.0 32.2 + - + +
731B MET* 4.1 4.9 - - - +
733B LYS* 1.3 76.2 - - - +
735B HIS* 1.3 60.7 + - - +
736B ALA 3.2 1.1 - - - -
737B ASP* 3.8 2.2 - - - -
738B PHE* 3.1 48.7 + - + +
757B ALA* 5.6 1.6 - - + -
766B TRP* 3.7 34.8 - - + +
767B TYR* 4.7 7.9 - - - +
768B ARG* 4.9 0.9 - - + +
800B LEU* 3.8 20.4 - - + -
804B PHE* 3.2 44.6 - - + -
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Residues in contact with HIS 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731B MET 3.2 14.3 + - - +
732B SER* 3.4 14.1 - - - +
734B LEU* 1.3 78.9 - - - +
736B ALA* 1.3 62.9 + - + +
738B PHE* 3.5 5.0 + - - +
739B GLN* 3.1 61.4 + - + +
765B GLN* 4.0 25.0 + - - +
766B TRP* 5.6 10.8 + - - +
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Residues in contact with ALA 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732B SER 3.2 12.3 + - - +
733B LYS* 3.9 8.0 - - - +
735B HIS* 1.3 84.7 - - + +
737B ASP* 1.3 62.4 + - - +
738B PHE 3.2 1.3 - - - -
739B GLN* 3.8 7.4 - - - +
740B SER* 2.9 31.5 + - - +
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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