Contacts of the helix formed by residues 726 - 735 (chain B) in PDB entry 5XA0
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 ASP 726 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697B TRP* 5.4 13.0 - - + -
722B GLY* 4.0 14.7 + - - +
724B LYS* 3.4 3.7 - - - +
725B GLU* 1.3 80.6 - - - +
727B ARG* 1.3 70.3 + - - +
728B ASP 2.9 2.4 - - - +
729B ILE* 2.7 20.0 + - - +
730B LEU* 3.1 12.3 + - - +
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Residues in contact with ARG 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 ALA* 3.0 46.4 - - + +
722B GLY* 4.5 13.1 + - - +
726B ASP* 1.3 76.3 - - - +
728B ASP* 1.3 62.6 + - - +
730B LEU* 3.1 7.5 + - - +
731B SER* 3.0 26.6 + - - -
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Residues in contact with ASP 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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726B ASP 2.8 1.9 + - - +
727B ARG* 1.3 80.0 - - - +
729B ILE* 1.3 65.0 + - - +
731B SER* 4.1 2.9 - - - -
732B TYR* 3.0 23.2 + - - +
862B LEU* 4.1 2.5 - - - +
865B GLU* 3.0 11.0 - - + -
866B VAL* 2.7 52.5 - - + +
869B LEU* 4.1 2.5 - - + +
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Residues in contact with ILE 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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701B ARG* 5.1 10.1 - - + -
725B GLU 4.5 4.0 - - - +
726B ASP* 2.7 15.7 + - - +
728B ASP* 1.3 77.7 - - - +
730B LEU* 1.3 63.7 + - - +
732B TYR* 3.1 4.8 + - - +
733B TYR* 3.0 23.5 + - - +
865B GLU* 3.3 16.8 - - + +
869B LEU* 5.7 0.2 - - - -
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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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701B ARG* 4.7 14.6 - - + +
719B ALA* 6.2 0.9 - - + -
726B ASP 3.1 10.1 + - - +
727B ARG* 3.1 10.7 + - - +
729B ILE* 1.3 77.1 - - - +
731B SER* 1.3 63.4 + - - +
733B TYR* 3.3 2.4 + - - +
734B ARG* 3.0 22.9 + - - +
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Residues in contact with SER 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B GLN* 5.8 7.6 - - - -
719B ALA* 5.5 7.6 - - - +
727B ARG 3.0 15.2 + - - -
728B ASP* 4.2 2.7 - - - -
730B LEU* 1.3 76.2 - - - +
732B TYR* 1.3 63.1 + - - +
734B ARG* 3.0 17.2 + - - +
735B TYR* 3.1 17.7 + - - +
832B ARG* 6.3 2.5 - - - -
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Residues in contact with TYR 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 ASP 3.0 12.3 + - - +
729B ILE* 3.6 4.3 - - - +
731B SER* 1.3 78.2 - - - +
733B TYR* 1.3 59.6 + - - +
735B TYR* 4.2 11.8 + - - +
736B GLN* 6.0 0.2 - - - +
869B LEU* 3.2 37.9 - - + +
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Residues in contact with TYR 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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701B ARG* 4.7 24.9 - - + +
703B SER 2.4 33.9 - - - +
704B ASN* 3.6 12.0 - - + +
729B ILE 3.0 14.4 + - - +
730B LEU 3.8 3.6 - - - +
732B TYR* 1.3 78.5 - - - +
734B ARG* 1.3 65.3 + - - +
735B TYR 4.7 1.2 - - - -
736B GLN* 4.7 0.7 - - - +
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Residues in contact with ARG 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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703B SER* 4.4 2.7 - - - -
707B ILE* 4.3 7.3 - - - +
710B LYS 3.8 26.1 - - - +
711B SER* 4.8 10.2 - - - -
714B GLU* 5.4 9.6 - - + -
730B LEU 3.0 14.3 + - - +
731B SER* 3.0 8.2 + - - +
733B TYR* 1.3 79.0 - - - +
735B TYR* 1.3 60.4 + - + +
736B GLN* 2.8 12.3 + - - +
737B LEU 4.8 0.3 + - - -
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Residues in contact with TYR 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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711B SER* 6.3 0.4 - - - -
731B SER 3.1 12.4 + - - +
732B TYR* 4.2 9.4 + - - +
733B TYR 3.4 1.3 - - - -
734B ARG* 1.3 76.8 - - + +
736B GLN* 1.3 57.7 + - - +
739B LEU* 4.7 7.9 - - - +
829B ILE* 5.7 10.1 - - + -
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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