Contacts of the helix formed by residues 724 - 739 (chain A) in PDB entry 4RG7
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 LYS 724 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A LEU* 3.3 22.5 - - + +
722A ASN* 2.9 13.2 + - + -
723A GLU* 1.3 74.4 - - - +
725A TYR* 1.3 62.0 + - - +
726A LYS 3.5 2.4 + - - -
727A SER* 3.9 14.3 + - - -
728A ALA* 3.8 11.8 + - - +
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Residues in contact with TYR 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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720A PHE* 3.1 52.0 + + + -
721A ALA 5.4 1.1 + - - -
722A ASN 3.3 12.2 - - - -
723A GLU* 3.5 19.7 + - + +
724A LYS* 1.3 69.6 - - - +
726A LYS* 1.3 67.1 + - - +
728A ALA* 3.3 20.5 - - - +
729A LEU* 3.7 7.1 + - - +
752A VAL* 5.9 2.4 - - - +
755A LYS* 5.1 19.1 - - + -
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Residues in contact with LYS 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A TYR* 1.3 75.6 - - - +
727A SER* 1.3 65.6 + - - +
729A LEU* 3.0 38.0 + - + +
730A GLN* 3.6 4.5 + - - +
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Residues in contact with SER 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A LEU* 5.0 5.8 - - - -
724A LYS* 3.9 19.6 + - - -
725A TYR 3.5 0.2 - - - -
726A LYS* 1.3 79.1 - - - +
728A ALA* 1.3 59.7 + - - +
730A GLN* 3.7 7.8 + - - +
731A GLU* 3.5 20.4 + - - +
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Residues in contact with ALA 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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716A ALA* 4.2 15.9 - - + +
719A LEU* 4.0 22.8 - - + +
720A PHE* 4.3 13.7 - - + +
724A LYS 3.8 5.1 + - - +
725A TYR 3.3 13.6 + - - +
726A LYS 3.1 0.6 - - - -
727A SER* 1.3 79.6 - - - +
729A LEU* 1.3 57.6 + - - +
731A GLU* 3.4 5.8 + - - +
732A LEU* 2.8 30.0 + - - +
752A VAL* 6.2 4.3 - - + -
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Residues in contact with LEU 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A TYR 3.7 3.9 + - - +
726A LYS* 3.0 36.9 + - + +
728A ALA* 1.3 76.1 - - - +
730A GLN* 1.3 70.4 + - + +
732A LEU* 3.6 8.1 - - - +
733A GLU* 3.2 23.9 + - - +
752A VAL* 5.7 10.3 - - + -
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Residues in contact with GLN 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A LYS 3.6 4.6 + - - +
727A SER* 3.9 10.5 - - - +
728A ALA 3.4 0.2 - - - -
729A LEU* 1.3 89.2 - - + +
731A GLU* 1.3 62.6 + - - +
732A LEU 3.3 0.2 + - - -
733A GLU* 3.5 3.3 + - - +
734A GLU* 3.4 19.8 + - - +
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Residues in contact with GLU 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A LYS 6.1 0.7 - - - +
715A ARG* 5.8 3.8 - - + +
716A ALA* 5.0 14.1 - - + +
727A SER 3.5 10.1 + - - +
728A ALA* 3.4 8.6 + - - +
730A GLN* 1.3 79.2 - - - +
732A LEU* 1.3 60.7 + - - +
734A GLU* 3.6 8.3 - - - +
735A LEU* 3.3 20.6 + - - +
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Residues in contact with LEU 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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716A ALA* 5.1 10.1 - - + +
728A ALA 2.8 18.9 + - - +
729A LEU* 3.6 10.8 - - - +
730A GLN 3.2 0.2 - - - -
731A GLU* 1.3 74.0 - - - +
733A GLU* 1.3 54.7 + - - +
735A LEU* 2.9 9.6 + - - +
736A LYS* 2.7 33.9 + - - +
745A VAL* 6.0 0.5 - - - +
748A LEU* 6.2 4.0 - - + -
749A ILE* 6.3 3.4 - - + +
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Residues in contact with GLU 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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729A LEU* 3.2 14.1 + - + +
730A GLN* 4.1 3.4 - - - +
732A LEU* 1.3 78.6 - - - +
734A GLU* 1.3 64.5 + - - +
736A LYS* 3.0 21.0 + - + +
737A GLN* 3.1 14.6 + - - +
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Residues in contact with GLU 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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730A GLN 3.4 10.9 + - - +
731A GLU* 3.6 13.5 - - - +
733A GLU* 1.3 77.8 - - - +
735A LEU* 1.3 58.4 + - - +
737A GLN* 3.9 7.1 - - - +
738A ILE* 3.5 16.3 + - - +
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Residues in contact with LEU 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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709A PRO* 5.8 2.5 - - + +
712A LYS* 5.1 15.3 - - + -
713A PHE* 5.9 5.4 - - + +
731A GLU 3.3 9.9 + - - +
732A LEU* 2.9 11.5 + - - +
734A GLU* 1.3 77.0 - - - +
736A LYS* 1.3 54.9 + - - +
737A GLN 3.1 2.0 - - - -
738A ILE* 2.9 10.4 + - + +
739A VAL* 2.8 35.3 + - - +
745A VAL* 5.4 5.0 - - + +
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Residues in contact with LYS 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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732A LEU 2.7 16.7 + - - +
733A GLU* 3.0 14.8 + - + +
735A LEU* 1.3 72.4 - - - +
737A GLN* 1.3 58.7 + - - +
739A VAL 3.6 20.5 - - - +
740A PRO* 3.7 10.9 - - - +
745A VAL* 4.7 13.9 - - + +
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Residues in contact with GLN 737 (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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733A GLU 3.1 13.6 + - - +
734A GLU* 3.9 7.4 - - - +
735A LEU 3.1 0.4 - - - -
736A LYS* 1.3 76.8 - - - +
738A ILE* 1.3 62.8 + - - +
739A VAL* 3.6 0.3 + - - -
740A PRO* 4.7 4.4 - - - +
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Residues in contact with ILE 738 (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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705A ASP 5.6 3.8 - - - +
706A PRO* 5.3 10.5 - - + +
709A PRO* 6.1 6.3 - - + -
734A GLU 3.5 11.7 + - - +
735A LEU* 2.9 15.7 + - + +
737A GLN* 1.3 80.2 - - - +
739A VAL* 1.3 60.2 + - + +
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Residues in contact with VAL 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A PRO* 4.8 18.4 - - + -
735A LEU 2.8 14.6 + - - +
736A LYS* 3.6 7.6 - - - +
738A ILE* 1.3 78.2 - - + +
740A PRO* 1.3 58.2 - - - +
741A LYS* 3.1 10.4 + - + +
742A GLU* 4.0 19.0 + - + +
745A VAL* 4.2 16.8 - - + +
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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