Contacts of the helix formed by residues 725 - 740 (chain F) in PDB entry 4OQB
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 725 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724F SER* 1.3 79.6 - - - +
726F ASP* 1.3 66.3 + - - +
727F SER* 4.0 11.4 - - - -
728F GLN* 3.4 13.8 + - - +
729F ILE* 3.2 21.0 + - - +
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Residues in contact with ASP 726 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D MET* 5.7 7.4 - - + -
724F SER 4.9 2.3 - - - +
725F SER* 1.3 73.5 - - - +
727F SER* 1.3 53.8 + - - +
729F ILE* 3.3 12.5 + - - +
730F LEU* 2.6 44.0 + - + +
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Residues in contact with SER 727 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D VAL* 3.8 33.0 - - - +
319D THR* 4.5 3.6 + - - +
320D LYS 5.4 0.5 + - - -
322D MET* 5.8 8.9 - - - +
725F SER* 3.3 6.8 - - - -
726F ASP* 1.3 75.8 - - - +
728F GLN* 1.3 59.7 + - - +
730F LEU* 3.5 8.7 - - - +
731F ASP* 2.9 32.1 + - - +
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Residues in contact with GLN 728 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715F GLU* 5.0 7.3 + - - +
718F GLN* 5.0 10.5 - - - +
719F ALA* 3.9 16.8 - - + +
724F SER* 3.9 21.9 + - - -
725F SER* 3.4 22.4 + - - +
726F ASP 3.3 0.2 - - - -
727F SER* 1.3 80.8 - - - +
729F ILE* 1.3 61.3 + - - +
731F ASP* 3.6 7.9 + - - +
732F LEU* 3.4 33.1 + - + +
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Residues in contact with ILE 729 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716F VAL* 5.4 2.7 - - + -
719F ALA* 4.3 23.3 - - + +
720F VAL* 4.6 18.8 - - + -
724F SER 4.3 10.1 - - - +
725F SER 3.2 14.5 + - - +
726F ASP* 3.6 13.9 - - - +
728F GLN* 1.3 75.1 - - - +
730F LEU* 1.3 65.2 + - - +
732F LEU* 3.3 8.6 + - - +
733F SER* 2.8 32.8 + - - +
751F LEU* 4.8 9.0 - - + -
752F LEU 3.5 25.8 - - - +
753F ASN* 4.6 13.7 - - + +
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Residues in contact with LEU 730 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D THR* 5.2 5.4 - - + -
322D MET* 4.5 20.4 - - + -
562F ILE* 3.8 25.6 - - + -
563F VAL* 4.2 25.1 - - + -
726F ASP* 2.6 26.2 + - + +
727F SER* 3.2 11.2 + - - +
729F ILE* 1.3 72.6 - - - +
731F ASP* 1.3 56.3 + - - +
733F SER* 3.4 0.9 + - - -
734F ASN* 2.9 52.0 + - - +
751F LEU* 3.6 26.5 - - + -
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Residues in contact with ASP 731 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D THR* 3.3 33.2 + - + +
318D TRP* 3.6 10.2 - - - +
319D THR* 3.3 20.4 - - + +
727F SER 2.9 16.1 + - - +
728F GLN* 3.7 9.9 - - - +
730F LEU* 1.3 76.7 - - - +
732F LEU* 1.3 63.2 + - - +
734F ASN* 3.3 3.1 + - - +
735F ARG* 2.7 55.6 + - - +
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Residues in contact with LEU 732 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712F ILE* 3.2 24.8 - - + +
715F GLU* 3.5 64.6 - - + +
716F VAL* 3.4 24.0 - - + +
719F ALA* 4.3 9.9 - - + -
728F GLN* 3.4 24.2 - - - +
729F ILE* 3.3 6.8 + - - +
731F ASP* 1.3 87.1 - - - +
733F SER* 1.3 56.5 + - - +
735F ARG* 4.1 5.6 - - - +
736F PHE* 2.9 26.5 + - - +
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Residues in contact with SER 733 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562F ILE* 3.3 24.0 - - - -
716F VAL* 4.9 0.4 - - - +
729F ILE* 2.8 23.5 + - - +
730F LEU 3.7 3.1 - - - -
732F LEU* 1.3 75.0 - - - +
734F ASN* 1.3 65.9 + - - +
736F PHE* 3.9 0.7 - - - +
737F TYR* 3.0 33.1 + - - -
751F LEU* 4.0 3.5 - - - +
752F LEU* 3.1 42.5 + - - +
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Residues in contact with ASN 734 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D TRP* 4.5 11.9 + - + +
319D THR* 3.6 25.3 - - + +
560F VAL* 3.2 22.5 - - - +
561F ASP* 4.4 6.7 + - - -
562F ILE* 2.9 34.1 + - - +
730F LEU* 2.9 36.7 + - - +
731F ASP* 3.4 7.2 - - - +
733F SER* 1.3 76.8 - - - +
735F ARG* 1.3 57.6 + - - +
736F PHE 3.2 0.2 + - - -
738F THR* 2.4 34.7 + - - +
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Residues in contact with ARG 735 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D TRP* 3.3 61.8 - - + +
639F TYR* 5.0 7.1 + - - -
708F ALA* 5.4 5.7 - - - +
712F ILE* 3.8 32.4 - - + +
715F GLU* 5.1 7.3 + - - -
731F ASP* 2.7 43.6 + - - +
732F LEU* 3.6 11.4 - - - +
734F ASN* 1.3 72.7 - - - +
736F PHE* 1.3 62.1 + - - +
738F THR* 3.5 5.8 + - - -
739F LEU* 3.1 33.5 + - - +
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Residues in contact with PHE 736 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709F ALA* 3.6 21.5 - - + -
712F ILE* 3.9 13.2 - - + -
713F LEU* 3.4 36.6 - - + -
732F LEU 2.9 17.9 + - - +
733F SER 3.9 3.8 - - - +
734F ASN 3.2 0.2 - - - -
735F ARG* 1.3 77.5 - - - +
737F TYR* 1.3 73.8 + + - +
739F LEU* 3.1 3.6 + - - +
740F ILE* 2.8 51.0 + - + +
742F HIS* 3.6 26.9 - + - -
752F LEU* 4.3 13.9 - - + -
761F LYS* 4.0 17.7 - - + -
764F MET* 4.7 0.2 - - - -
765F LEU* 3.9 13.5 - - + -
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Residues in contact with TYR 737 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560F VAL* 3.8 17.7 - - + +
562F ILE* 4.0 9.6 - - + -
567F ASN* 4.6 8.0 - - - +
733F SER* 3.0 28.0 + - - +
736F PHE* 1.3 85.9 - + - +
738F THR* 1.3 62.7 + - - +
740F ILE 2.9 19.2 - - - +
741F PRO* 3.9 6.4 - - - +
742F HIS* 3.7 32.9 + + + +
744F PHE* 3.6 20.9 - + + -
749F PRO* 3.7 22.9 - - + -
750F PRO* 2.7 35.0 + - - +
752F LEU* 3.2 23.2 - - + +
761F LYS* 3.4 12.4 + - - -
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Residues in contact with THR 738 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D TRP* 3.9 26.6 - - + -
558F GLY* 3.3 36.8 - - - +
559F LEU* 3.9 9.6 - - - +
560F VAL* 2.9 14.6 + - + +
633F LYS* 5.4 2.7 - - - +
639F TYR* 4.4 7.6 - - + -
641F LEU* 3.1 25.0 - - - +
734F ASN* 2.4 31.6 + - - +
735F ARG* 3.6 5.5 + - - -
737F TYR* 1.3 79.8 - - - +
739F LEU* 1.3 61.1 + - - +
740F ILE 4.4 0.9 - - - -
741F PRO* 4.5 1.2 - - - +
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Residues in contact with LEU 739 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D TRP* 5.2 2.2 - - + -
639F TYR* 3.5 31.6 - - + +
641F LEU* 3.9 4.0 - - - +
701F LEU* 4.3 3.3 - - - +
705F GLN* 3.0 60.0 + - + +
708F ALA* 3.8 13.5 - - + -
709F ALA* 3.4 36.1 - - + +
712F ILE* 3.8 10.8 - - + -
735F ARG* 3.1 22.2 + - - +
736F PHE* 3.6 4.7 - - - +
738F THR* 1.3 81.5 - - - +
740F ILE* 1.3 62.0 + - + +
741F PRO* 3.9 5.8 - - - +
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Residues in contact with ILE 740 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691F ILE* 3.3 34.3 - - + -
696F MET* 6.2 0.7 - - - -
701F LEU* 4.2 19.3 - - + -
706F ILE* 5.5 2.5 - - + -
709F ALA* 3.4 32.8 - - + -
736F PHE* 2.8 22.1 + - + +
737F TYR* 2.9 16.0 - - - +
739F LEU* 1.3 79.0 - - + +
741F PRO* 1.3 65.1 - - + +
742F HIS* 2.8 29.8 + - + -
764F MET* 4.9 0.4 - - - -
765F LEU* 3.5 28.9 - - + -
768F LEU* 6.3 2.0 - - + -
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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