Contacts of the strand formed by residues 724 - 728 (chain A) in PDB entry 3ODX
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 ALA 724 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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718A VAL* 3.6 16.2 + - + -
721A ASP* 2.9 41.5 + - + +
723A LYS* 1.3 80.7 - - - +
725A PHE* 1.3 60.6 - - - +
739A GLU* 4.4 15.9 - - + +
740A LEU 3.5 7.2 - - - +
741A VAL* 3.5 15.9 - - + -
748A ARG* 3.3 15.9 + - - -
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Residues in contact with PHE 725 (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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654A LEU* 4.0 17.5 - - + -
715A THR* 4.8 0.9 - - + -
716A ARG 3.1 15.5 - - - +
717A GLU* 4.8 0.4 - - - -
718A VAL* 3.8 9.6 - - - -
723A LYS 5.0 0.2 - - - -
724A ALA* 1.3 74.1 - - - +
726A TYR* 1.3 71.4 + - - +
727A VAL* 3.5 24.5 - - + -
739A GLU* 3.5 6.4 - - - +
740A LEU* 2.8 63.3 + - + -
742A ALA 5.1 0.9 - - - -
748A ARG* 3.8 27.1 - - + +
751A TRP* 3.8 29.4 - + + -
752A CYS* 3.5 25.6 - - - -
755A ILE* 4.3 11.2 - - + -
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Residues in contact with TYR 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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715A THR* 3.1 9.5 - - - -
716A ARG* 2.8 37.6 + - + +
717A GLU 4.3 8.5 - - - -
718A VAL* 3.7 26.2 - - + +
725A PHE* 1.3 73.7 - - - +
727A VAL* 1.3 63.3 + - - +
728A LEU 4.3 0.2 - - - -
737A ILE* 3.8 11.0 - - + -
738A TYR 3.5 1.6 - - - -
739A GLU* 3.3 43.9 + - + -
476B ASP* 5.3 5.4 - - - -
479B MET* 3.5 47.8 - - + -
480B LYS* 4.3 18.9 - - + +
483B GLN* 4.2 21.9 - - + +
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Residues in contact with VAL 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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675A LEU* 5.8 7.4 - - + -
708A LEU* 5.8 0.4 - - + -
710A LEU* 6.0 0.2 - - + -
713A ALA* 4.5 9.9 - - + -
714A MET 3.4 9.2 - - - +
715A THR* 4.4 4.3 - - + -
725A PHE* 3.5 29.2 - - + -
726A TYR* 1.3 74.4 - - - +
728A LEU* 1.3 65.0 + - - +
729A PHE* 3.3 30.7 - - + -
736A GLN 3.6 3.3 - - - +
737A ILE* 3.9 1.2 - - - -
738A TYR* 3.0 40.6 + - + +
740A LEU* 4.5 9.9 - - + -
755A ILE* 4.2 17.5 - - + -
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Residues in contact with LEU 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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712A SER 3.6 2.6 - - - +
713A ALA* 3.4 6.9 - - - -
714A MET* 3.0 36.4 + - + +
716A ARG* 6.3 0.7 - - + -
727A VAL* 1.3 75.2 - - - +
729A PHE* 1.3 71.6 + - - +
730A THR* 3.5 29.9 + - + +
735A ALA* 4.5 10.3 - - + -
736A GLN 3.7 4.7 - - - +
737A ILE* 5.1 3.1 - - + -
425B LEU* 3.8 28.5 - - + -
426B VAL* 4.9 2.5 - - + -
429B ALA* 4.4 16.8 - - + -
475B LEU* 4.6 2.0 - - + -
479B MET* 3.6 38.6 - - + -
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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