Contacts of the helix formed by residues 702 - 722 (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 702 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642F GLU* 3.0 37.8 + - - +
643F ILE 5.1 3.6 - - - -
644F ASP* 5.2 7.2 - - - +
700F LYS 3.7 1.7 + - - -
701F LEU* 1.3 80.0 - - - +
703F LYS* 1.3 68.1 + - - +
704F ARG* 3.4 17.0 + - - +
705F GLN* 3.5 8.9 + - - +
706F ILE* 3.2 27.1 + - - +
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Residues in contact with LYS 703 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701F LEU 5.8 0.7 - - - +
702F SER* 1.3 78.2 + - - +
704F ARG* 1.3 65.9 + - + +
705F GLN 3.2 0.2 - - - -
706F ILE* 3.4 7.4 + - + +
707F GLN* 3.1 42.3 + - - +
769F LEU* 3.8 39.1 - - + +
773F VAL* 6.2 0.9 - - - -
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Residues in contact with ARG 704 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642F GLU* 6.3 2.5 - - + -
702F SER* 3.4 9.3 + - - +
703F LYS* 1.3 79.1 - - + +
705F GLN* 1.3 61.0 + - - +
707F GLN* 3.7 16.2 + - - +
708F ALA* 3.3 21.3 + - - +
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Residues in contact with GLN 705 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639F TYR* 4.3 1.7 + - - -
641F LEU* 3.6 25.5 - - - +
642F GLU* 2.9 28.3 - - + +
701F LEU* 3.7 29.2 - - + +
702F SER* 3.5 25.7 + - - +
704F ARG* 1.3 76.9 - - - +
706F ILE* 1.3 60.4 + - - +
708F ALA* 3.1 8.1 + - - +
709F ALA* 2.9 23.7 + - - +
739F LEU* 3.0 50.5 + - + +
740F ILE* 5.7 0.9 - - + -
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Residues in contact with ILE 706 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701F LEU* 3.9 33.4 - - + +
702F SER 3.2 19.1 + - - +
703F LYS* 3.4 8.9 + - + +
705F GLN* 1.3 76.3 - - - +
707F GLN* 1.3 57.7 + - + +
709F ALA* 3.2 7.6 + - - +
710F TYR* 2.8 49.5 + - + -
740F ILE* 5.6 2.2 - - + -
765F LEU* 4.4 15.7 - - + +
768F LEU* 4.2 18.6 - - + -
769F LEU* 3.7 30.7 - - + -
772F GLU* 6.0 3.1 - - + -
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Residues in contact with GLN 707 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703F LYS* 3.1 34.9 + - + +
704F ARG* 3.8 15.2 - - - +
705F GLN 3.2 0.2 - - - -
706F ILE* 1.3 77.1 - - + +
708F ALA* 1.3 56.1 + - - +
710F TYR* 3.4 12.3 + - + +
711F SER* 2.9 31.1 + - - -
881F PRO* 6.3 0.4 - - + -
883F GLU* 3.8 35.9 + - + +
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Residues in contact with ALA 708 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704F ARG 3.3 10.9 + - - +
705F GLN* 3.1 11.0 + - - +
707F GLN* 1.3 75.4 - - - +
709F ALA* 1.3 60.8 + - - +
711F SER* 3.2 9.8 + - - -
712F ILE* 2.9 33.9 + - + +
735F ARG* 5.4 6.5 - - - +
739F LEU* 3.8 14.1 - - + -
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Residues in contact with ALA 709 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705F GLN 2.9 12.7 + - - +
706F ILE* 3.2 11.4 + - - +
708F ALA* 1.3 74.7 - - - +
710F TYR* 1.3 62.8 + - - +
712F ILE* 3.5 5.8 + - - +
713F LEU* 3.2 25.6 + - - +
736F PHE* 3.6 10.6 - - + -
739F LEU* 3.4 12.0 - - + +
740F ILE* 3.4 37.0 - - + -
765F LEU* 3.9 6.3 - - + -
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Residues in contact with TYR 710 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706F ILE* 2.8 42.7 + - + -
707F GLN* 3.4 13.9 - - + +
709F ALA* 1.3 76.3 - - - +
711F SER* 1.3 57.4 + - - +
713F LEU* 3.2 8.6 + - + +
714F SER* 3.0 23.6 + - - -
762F VAL* 4.2 8.5 - - + -
765F LEU* 3.4 25.1 + - + +
766F ASP* 2.7 41.3 + - - -
769F LEU* 5.1 6.7 - - + +
881F PRO* 4.2 20.0 - - + +
883F GLU* 3.5 20.8 - - + +
884F ALA* 3.4 28.5 - - + -
885F PRO* 4.0 10.3 - - + +
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Residues in contact with SER 711 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707F GLN 2.9 20.4 + - - -
708F ALA* 3.2 13.4 + - - -
710F TYR* 1.3 75.7 - - - +
712F ILE* 1.3 58.3 + - - +
714F SER* 2.6 22.9 + - - -
715F GLU* 2.9 27.9 + - - +
883F GLU* 3.9 17.1 + - - +
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Residues in contact with ILE 712 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708F ALA* 2.9 21.4 + - + +
709F ALA* 3.7 6.1 - - - +
710F TYR 3.3 0.2 - - - -
711F SER* 1.3 77.2 - - - +
713F LEU* 1.3 62.6 + - - +
715F GLU* 3.2 12.1 + - - +
716F VAL* 3.0 23.2 + - + +
732F LEU* 3.2 42.4 - - + +
735F ARG* 3.8 51.1 - - + +
736F PHE* 3.9 13.5 - - + +
739F LEU* 3.8 22.7 - - + -
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Residues in contact with LEU 713 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709F ALA 3.2 2.8 + - - +
710F TYR* 3.2 9.9 + - + +
712F ILE* 1.3 78.9 - - - +
714F SER* 1.3 61.3 + - - +
716F VAL* 3.1 14.2 + - - +
717F GLN* 3.2 10.7 + - - +
736F PHE* 3.4 36.6 - - + -
752F LEU* 4.0 17.5 - - + -
758F VAL* 3.5 27.6 - - + +
761F LYS* 3.5 23.1 - - + +
762F VAL* 3.5 36.3 - - + +
765F LEU* 4.1 11.2 - - + -
885F PRO* 4.3 6.5 - - + -
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Residues in contact with SER 714 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710F TYR 3.0 5.4 + - - -
711F SER* 2.6 28.2 + - - -
713F LEU* 1.3 75.8 - - - +
715F GLU* 1.3 61.8 + - - +
717F GLN* 3.7 7.1 + - - +
718F GLN* 3.3 21.8 + - - +
883F GLU 3.6 19.0 + - - -
884F ALA 4.4 0.9 - - - -
885F PRO* 4.0 21.5 - - - +
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Residues in contact with GLU 715 (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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711F SER* 2.9 26.6 + - - +
712F ILE* 3.4 11.5 + - - +
714F SER* 1.3 78.3 + - - +
716F VAL* 1.3 58.3 - - - +
718F GLN* 3.5 16.6 + - - +
719F ALA* 2.9 28.1 + - - +
728F GLN* 5.0 7.2 + - - +
732F LEU* 3.5 28.6 - - + +
735F ARG* 5.1 9.0 + - - -
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Residues in contact with VAL 716 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712F ILE* 3.0 22.8 + - + +
713F LEU* 3.1 11.0 + - - +
715F GLU* 1.3 73.9 - - - +
717F GLN* 1.3 56.5 + - - +
719F ALA* 3.0 3.9 + - + +
720F VAL* 2.7 42.1 + - + +
729F ILE* 5.4 3.4 - - + +
732F LEU* 3.4 31.6 - - + -
733F SER* 5.4 0.4 - - - +
752F LEU* 3.1 50.5 - - + +
754F ASN 5.1 0.2 - - - +
758F VAL* 4.8 11.2 - - + -
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Residues in contact with GLN 717 (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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713F LEU 3.2 8.8 + - - +
714F SER* 3.9 12.1 - - - +
716F VAL* 1.3 79.3 - - - +
718F GLN* 1.3 74.8 + - - +
720F VAL* 3.7 6.9 - - - +
721F SER* 2.8 39.0 + - - -
755F ALA* 6.3 1.8 - - + +
758F VAL* 4.5 12.0 - - + +
885F PRO* 5.0 1.3 - - + -
886F VAL* 3.6 30.4 - - - +
887F THR* 3.2 30.2 + - + +
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Residues in contact with GLN 718 (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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714F SER 3.3 11.4 + - - +
715F GLU* 3.6 19.7 + - - +
716F VAL 3.2 0.2 - - - -
717F GLN* 1.3 86.9 + - - +
719F ALA* 1.3 61.3 + - - +
721F SER* 2.7 21.3 + - - +
722F GLN* 3.4 33.0 + - - +
728F GLN* 5.0 9.9 - - - +
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Residues in contact with ALA 719 (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 2.9 19.0 + - - +
716F VAL* 3.4 8.3 - - - +
718F GLN* 1.3 77.9 - - - +
720F VAL* 1.3 61.3 + - - +
722F GLN* 5.0 0.7 - - - +
723F GLY 3.4 1.7 + - - -
724F SER* 2.8 52.0 + - - +
728F GLN* 3.9 20.4 - - + +
729F ILE* 4.3 12.8 - - + +
732F LEU* 4.3 5.2 - - + -
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Residues in contact with VAL 720 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716F VAL* 2.7 36.5 + - + +
717F GLN* 3.8 7.4 - - + +
719F ALA* 1.3 73.3 - - - +
721F SER* 1.3 67.0 + - - +
723F GLY* 3.4 11.4 + - - -
729F ILE* 4.6 11.7 - - + -
752F LEU 4.3 0.7 - - - +
753F ASN* 3.3 36.6 - - - +
754F ASN 4.0 15.0 - - - +
755F ALA* 4.5 10.1 - - + +
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Residues in contact with SER 721 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717F GLN* 2.8 26.6 + - - -
718F GLN* 2.7 27.9 + - - +
720F VAL* 1.3 77.3 - - - +
722F GLN* 1.3 62.3 + - - +
723F GLY 3.6 1.2 + - - -
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Residues in contact with GLN 722 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718F GLN* 3.4 42.5 + - - +
719F ALA* 5.0 0.2 - - - +
720F VAL 3.4 0.2 - - - -
721F SER* 1.3 80.3 + - - +
723F GLY* 1.3 65.6 + - - +
724F SER* 3.3 16.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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