Contacts of the helix formed by residues 725 - 736 (chain A) 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 GLU 725 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723A GLN 3.0 4.2 + - - -
724A LYS* 1.3 78.1 - - - +
726A ASP* 1.3 66.1 + - - +
727A ARG* 3.2 4.0 + - - +
728A ASP* 3.6 5.6 + - - +
729A ILE* 3.9 5.4 + - - +
861A LYS* 2.9 32.3 - - + +
862A LEU* 3.1 16.3 - - - +
865A GLU* 3.0 29.2 - - + +
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Residues in contact with ASP 726 (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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697A TRP* 3.0 44.8 - - + +
698A LEU* 5.8 0.9 - - - +
701A ARG* 4.2 3.3 - - - +
723A GLN 3.6 9.5 + - - +
724A LYS 2.7 10.5 + - - +
725A GLU* 1.3 72.5 - - - +
727A ARG* 1.3 63.4 + - - +
729A ILE* 3.2 9.7 + - - +
730A LEU* 3.0 19.8 + - - +
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Residues in contact with ARG 727 (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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719A ALA* 6.0 7.0 - - + -
722A GLY* 6.1 4.7 - - - -
723A GLN 5.1 0.6 + - - -
725A GLU* 3.2 2.1 - - - -
726A ASP* 1.3 76.7 - - - +
728A ASP* 1.3 56.2 + - - +
730A LEU* 2.9 10.5 + - - +
731A SER* 2.7 36.6 + - - -
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Residues in contact with ASP 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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725A GLU* 3.6 3.5 + - - +
726A ASP 3.4 0.6 - - - -
727A ARG* 1.3 77.9 - - - +
729A ILE* 1.3 57.7 + - - +
731A SER* 3.3 9.1 - - - -
732A TYR* 3.0 25.8 + - - +
862A LEU 5.1 0.2 - - - +
865A GLU* 3.5 42.0 - - + +
866A VAL* 3.7 11.9 - - + +
869A LEU* 4.2 13.3 - - + +
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Residues in contact with ILE 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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698A LEU* 6.2 0.2 - - - -
701A ARG* 3.3 25.1 - - + +
704A ASN* 4.9 2.3 - - - +
725A GLU 3.9 6.5 + - - +
726A ASP* 3.2 6.8 + - - +
727A ARG 3.1 0.4 - - - -
728A ASP* 1.3 76.4 - - - +
730A LEU* 1.3 66.1 + - - +
732A TYR* 3.1 11.8 + - - +
733A TYR* 3.0 18.0 + - - +
865A GLU* 4.9 3.3 - - + +
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Residues in contact with LEU 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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700A TRP 5.8 0.2 - - - -
701A ARG* 3.6 18.2 - - - +
717A GLN* 5.5 11.7 - - + -
726A ASP 3.0 12.9 + - - +
727A ARG* 2.9 13.2 + - - +
729A ILE* 1.3 75.8 - - - +
731A SER* 1.3 54.2 + - - +
733A TYR* 2.7 32.7 + - - +
734A ARG* 3.1 6.0 + - - +
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Residues in contact with SER 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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727A ARG 2.7 16.3 + - - -
728A ASP* 3.3 13.7 - - - -
730A LEU* 1.3 72.0 - - - +
732A TYR* 1.3 51.7 + - - +
734A ARG* 3.1 10.4 + - - +
735A TYR* 2.7 36.3 + - - +
869A LEU* 6.2 2.2 - - - -
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Residues in contact with TYR 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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704A ASN* 2.9 22.9 - - + +
728A ASP 3.0 12.6 + - - +
729A ILE* 3.2 13.9 - - - +
731A SER* 1.3 73.6 - - - +
733A TYR* 1.3 66.6 + - - +
735A TYR* 2.7 18.7 + - - +
736A GLN* 3.0 6.9 + - - -
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Residues in contact with TYR 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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700A TRP 5.5 0.2 - - - +
701A ARG* 3.6 16.6 - - - +
703A SER 3.1 19.1 - - - +
704A ASN* 2.9 24.0 - - - +
706A GLU 4.1 8.3 - - - +
707A ILE* 4.6 1.6 - - - +
710A LYS* 3.6 17.9 - - + -
729A ILE 3.0 4.9 + - - -
730A LEU* 2.7 21.8 + - - +
732A TYR* 1.3 73.2 - - - +
734A ARG* 1.3 63.0 + - - +
735A TYR 2.9 0.3 + - - -
736A GLN* 3.3 5.0 + - - +
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Residues in contact with ARG 734 (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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707A ILE* 4.0 8.7 - - - +
710A LYS 5.6 0.2 - - - +
711A SER* 3.6 29.5 - - - +
714A GLU* 6.1 1.3 - - + +
730A LEU 3.1 4.9 + - - +
731A SER* 3.1 11.6 + - - +
733A TYR* 1.3 80.2 - - - +
735A TYR* 1.3 62.1 + - - +
736A GLN 3.5 0.3 + - - -
737A LEU* 3.8 9.9 + - - +
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Residues in contact with TYR 735 (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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731A SER 2.7 16.1 + - - +
732A TYR* 2.7 16.6 + - - +
734A ARG* 1.3 74.2 - - - +
736A GLN* 1.3 54.3 + - - +
737A LEU 2.5 27.0 - - - +
739A LEU* 2.9 21.2 - - + +
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Residues in contact with GLN 736 (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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704A ASN 2.9 21.3 - - - +
705A LYS* 2.8 37.8 - - + +
732A TYR 3.0 5.8 + - - +
733A TYR 3.3 2.7 + - - +
735A TYR* 1.3 75.9 - - - +
737A LEU* 1.3 60.6 + - - +
738A ASN 3.2 10.7 + - - +
739A LEU* 4.8 1.8 - - - -
740A PHE* 4.4 8.2 + - - +
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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