Contacts of the helix formed by residues 728 - 744 (chain A) in PDB entry 2P8Q
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 PHE 728 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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693A MET* 4.1 21.1 - - + -
717A PHE* 4.0 24.9 - - + -
720A ILE* 4.3 1.1 - - + -
721A ALA* 3.9 23.1 - - + -
724A ILE* 3.3 22.5 - - + +
725A GLY 2.8 17.0 + - - +
727A GLU* 1.3 74.8 - - - +
729A LYS* 1.3 65.5 + - - +
730A LYS 2.9 3.4 - - - -
731A TYR* 2.7 27.6 + + + -
732A LEU* 3.2 24.7 + - + -
735A VAL* 3.9 28.7 - - + -
772A ILE* 3.8 26.7 - - + -
776A LEU* 4.6 8.5 - - + -
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Residues in contact with LYS 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A GLY 4.4 0.2 + - - -
726A GLY* 2.7 33.2 + - - +
728A PHE* 1.3 76.2 - - - +
730A LYS* 1.3 61.7 + - - +
732A LEU* 3.0 25.9 + - + +
733A GLU* 4.5 1.4 + - - +
776A LEU* 4.6 9.5 - - + +
786A ASP* 2.8 39.6 + - - +
789A LEU* 4.2 23.8 - - + -
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Residues in contact with LYS 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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690A ASP* 3.3 29.1 + - - +
727A GLU* 3.8 21.2 + - - +
728A PHE 2.8 0.2 + - - -
729A LYS* 1.3 79.7 - - - +
731A TYR* 1.3 88.4 + - + +
733A GLU* 5.3 0.7 + - - +
734A VAL* 5.8 1.9 - - - +
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Residues in contact with TYR 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A CYS* 3.8 5.1 - - + +
690A ASP* 2.7 45.3 + - - -
693A MET* 3.4 39.3 - - + -
694A GLN 5.6 0.2 - - - -
697A LEU* 5.1 8.3 - - + -
724A ILE* 4.4 13.7 - - + -
727A GLU 4.5 2.2 - - - -
728A PHE* 2.7 43.3 + + + +
730A LYS* 1.3 104.7 - - + +
732A LEU* 1.3 66.3 + - - +
733A GLU 3.2 2.9 + - - -
734A VAL* 3.4 9.6 + - + +
735A VAL* 3.1 30.0 + - + +
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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
----------------------------------------------------------
728A PHE* 3.2 19.3 + - + +
729A LYS* 3.0 25.3 + - + +
730A LYS 3.5 0.2 - - - -
731A TYR* 1.3 78.5 - - - +
733A GLU* 1.3 63.7 + - - +
735A VAL* 3.9 0.5 - - - +
736A LEU* 3.0 45.5 + - + +
772A ILE* 4.0 28.7 - - + -
776A LEU* 3.9 18.2 - - + -
789A LEU* 3.8 37.9 - - + -
790A VAL* 4.3 3.8 - - + -
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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
----------------------------------------------------------
729A LYS 4.5 1.4 + - - -
730A LYS 5.3 1.1 + - - +
731A TYR 3.3 0.6 - - - -
732A LEU* 1.3 80.5 - - - +
734A VAL* 1.3 69.7 + - + +
736A LEU* 3.9 5.0 - - - +
737A ASN* 3.0 42.2 + - - +
793A ARG* 5.0 4.9 + - - +
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Residues in contact with VAL 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A LEU* 3.7 35.4 - - + -
730A LYS 5.8 1.3 - - - +
731A TYR* 3.4 10.0 + - - +
733A GLU* 1.3 83.7 - - + +
735A VAL* 1.3 56.7 + - - +
737A ASN* 3.6 6.3 + - - +
738A THR* 2.7 35.3 + - - +
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Residues in contact with VAL 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A MET* 5.1 0.9 - - - -
697A LEU* 4.9 6.5 - - + -
717A PHE* 4.0 42.4 - - + -
728A PHE* 3.9 22.9 - - + -
731A TYR* 3.1 23.9 + - + +
732A LEU 3.9 2.9 - - - +
734A VAL* 1.3 74.4 - - + +
736A LEU* 1.3 59.9 + - - +
738A THR* 3.0 8.2 + - - -
739A LEU* 2.8 34.5 + - + +
772A ILE* 3.9 24.5 - - + -
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Residues in contact with LEU 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A LEU* 3.0 43.2 + - + +
733A GLU* 3.9 4.0 - - - +
735A VAL* 1.3 75.3 - - - +
737A ASN* 1.3 52.3 + - - +
739A LEU* 3.2 4.8 + - - +
740A GLN* 2.7 34.8 + - - +
769A TYR* 3.8 33.1 + - + -
772A ILE* 4.3 14.4 - - + -
789A LEU 4.9 3.4 - - - +
790A VAL* 4.2 18.8 - - + -
793A ARG* 3.8 48.3 + - + +
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Residues in contact with ASN 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A GLU* 3.0 36.9 + - - +
734A VAL* 4.0 5.6 - - - +
735A VAL 3.3 0.6 - - - -
736A LEU* 1.3 73.6 - - - +
738A THR* 1.3 65.6 + - - +
740A GLN* 3.1 9.5 - - - +
741A GLN* 3.1 25.0 + - - +
793A ARG* 3.4 26.8 + - - +
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Residues in contact with THR 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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697A LEU* 4.6 5.2 - - - +
700A LEU* 4.0 27.5 - - + +
710A LYS* 5.0 10.5 + - - +
714A LEU* 4.1 17.0 - - + -
717A PHE* 4.9 2.9 - - + -
734A VAL* 2.7 28.3 + - - +
735A VAL* 3.0 13.0 + - - -
737A ASN* 1.3 76.1 - - - +
739A LEU* 1.3 63.4 + - - +
741A GLN* 3.5 8.6 + - - +
742A ALA* 3.1 22.4 + - - +
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Residues in contact with LEU 739 (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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714A LEU* 4.0 22.4 - - + -
717A PHE* 5.7 0.2 - - + -
735A VAL* 2.8 21.0 + - + +
736A LEU* 3.4 9.2 - - + +
738A THR* 1.3 74.5 - - - +
740A GLN* 1.3 67.2 + - - +
742A ALA* 3.3 4.4 + - - +
743A SER* 2.9 27.2 + - - -
765A CYS* 4.2 18.0 - - + +
768A ALA* 3.4 34.8 - - + -
769A TYR* 3.4 41.5 - - + +
772A ILE* 3.8 20.0 - - + -
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Residues in contact with GLN 740 (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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736A LEU 2.7 16.8 + - - +
737A ASN* 3.1 19.1 - - - +
739A LEU* 1.3 76.0 - - - +
741A GLN* 1.3 62.9 + - - +
743A SER* 3.1 15.2 + - - -
744A GLN* 3.4 22.4 + - - +
769A TYR* 3.7 1.2 + - - -
793A ARG* 3.6 21.2 + - - +
796A PHE* 2.9 68.5 - - - +
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Residues in contact with GLN 741 (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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710A LYS* 5.5 9.1 - - - +
737A ASN 3.1 11.2 + - - +
738A THR* 3.8 8.1 + - - +
740A GLN* 1.3 80.6 - - - +
742A ALA* 1.3 57.1 + - - +
744A GLN* 2.9 37.4 + - - +
745A ALA* 3.7 4.2 + - - +
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Residues in contact with ALA 742 (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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710A LYS* 4.2 21.2 - - - +
714A LEU* 4.1 15.9 - - + -
738A THR 3.1 15.8 + - - +
739A LEU* 3.3 1.8 + - - +
741A GLN* 1.3 77.9 - - - +
743A SER* 1.3 60.2 + - - +
744A GLN 3.3 0.2 - - - -
745A ALA* 3.6 19.1 - - - +
758A LEU* 5.9 0.2 - - - +
761A LEU* 3.7 16.5 - - + +
762A ARG* 5.7 2.8 - - - +
765A CYS* 3.9 22.7 - - - -
800A PHE* 5.5 0.3 - - - -
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Residues in contact with SER 743 (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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739A LEU 2.9 17.2 + - - -
740A GLN 3.2 13.2 - - - -
741A GLN 3.0 0.2 - - - -
742A ALA* 1.3 73.5 - - - +
744A GLN* 1.3 56.4 + - - +
745A ALA 3.1 15.3 + - - +
746A GLN* 5.3 0.2 - - - +
762A ARG* 5.4 0.3 + - - +
765A CYS* 4.3 4.0 - - - -
769A TYR* 3.8 13.5 + - - -
796A PHE* 3.4 18.1 - - - -
800A PHE* 3.6 53.6 - - - -
803A HIS* 6.1 0.7 - - - -
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Residues in contact with GLN 744 (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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740A GLN* 3.6 26.6 - - - +
741A GLN* 2.9 27.0 + - + +
743A SER* 1.3 76.1 - - - +
745A ALA* 1.3 52.3 + - - +
746A GLN* 2.3 50.3 + - - +
796A PHE* 4.4 13.5 - - + -
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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