Contacts of the helix formed by residues 713 - 734 (chain A) in PDB entry 2VWU
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 THR 713 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711A GLN 5.8 0.2 - - - +
712A PHE* 1.3 76.8 - - - +
714A VAL* 1.3 64.9 + - - +
715A ILE* 3.5 8.8 + - - +
716A GLN* 3.0 35.6 + - - +
717A LEU* 3.0 21.7 + - - +
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Residues in contact with VAL 714 (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 PHE 4.1 0.2 + - - -
713A THR* 1.3 72.1 - - - +
715A ILE* 1.3 58.1 + - + +
717A LEU* 3.2 11.0 + - + +
718A VAL* 2.9 35.2 + - + +
814A MET* 4.4 10.3 - - + -
844A ASP* 4.5 9.4 - - + +
846A PRO* 3.7 38.4 - - + -
884A LEU* 4.1 25.1 - - + +
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Residues in contact with ILE 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A THR* 3.1 7.9 + - - +
714A VAL* 1.3 79.3 - - + +
716A GLN* 1.3 60.8 + - + +
718A VAL* 3.4 3.8 + - + +
719A GLY* 3.0 24.4 + - - -
878A ILE* 4.5 29.2 - - + +
881A PRO* 4.1 19.7 - - + -
884A LEU* 3.8 25.6 - - + -
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Residues in contact with GLN 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A GLN 4.6 0.7 - - - +
712A PHE* 3.4 25.1 - - + -
713A THR* 3.0 45.4 + - - +
715A ILE* 1.3 79.3 - - + +
717A LEU* 1.3 62.8 + - - +
719A GLY* 3.2 3.7 + - - -
720A MET* 3.1 31.4 + - + +
752A LEU* 3.8 22.8 - - + +
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Residues in contact with LEU 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A LEU* 4.1 22.2 - - + -
712A PHE* 4.2 10.5 - - + +
713A THR 3.0 18.1 + - - +
714A VAL* 3.2 10.1 + - + +
716A GLN* 1.3 72.6 - - - +
718A VAL* 1.3 61.8 + - - +
720A MET* 3.3 14.7 + - - +
721A LEU* 3.0 31.9 + - - +
813A VAL* 3.9 22.7 - - + +
814A MET* 3.7 36.6 - - + +
816A PHE* 3.8 35.7 - - + -
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Residues in contact with VAL 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A VAL* 2.9 28.6 + - + +
715A ILE* 3.9 6.1 - - - +
717A LEU* 1.3 76.4 - - - +
719A GLY* 1.3 52.4 + - - +
721A LEU* 3.6 6.9 - - + +
722A ARG* 2.8 32.6 + - - +
814A MET* 5.2 1.8 - - - -
849A LEU* 3.6 33.7 - - + -
874A LEU* 4.1 23.8 - - + +
877A MET* 4.8 6.7 - - + -
878A ILE* 3.7 27.4 - - + -
884A LEU* 4.3 10.8 - - + -
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Residues in contact with GLY 719 (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 ILE 3.0 14.8 + - - -
716A GLN* 3.2 4.5 + - - -
717A LEU 3.2 0.4 - - - -
718A VAL* 1.3 77.6 - - - +
720A MET* 1.3 59.1 + - - +
722A ARG* 3.4 8.1 + - - +
723A GLY* 3.1 19.2 + - - -
878A ILE* 4.6 7.8 - - - +
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Residues in contact with MET 720 (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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701A LEU* 4.3 21.3 - - + -
704A PHE* 4.6 5.8 - - + -
705A LEU* 4.3 4.7 - - - -
712A PHE* 4.0 26.5 - - + -
716A GLN* 3.1 20.2 + - + +
717A LEU* 3.3 23.3 + - + +
719A GLY* 1.3 75.3 - - - +
721A LEU* 1.3 62.4 + - - +
723A GLY* 3.2 3.7 + - - -
724A ILE* 3.0 29.5 + - + +
748A VAL* 5.8 0.4 - - + -
752A LEU* 3.8 43.5 - - + +
754A CYS* 3.6 24.8 - - - +
813A VAL* 5.0 6.3 - - + -
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Residues in contact with LEU 721 (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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717A LEU 3.0 21.2 + - - +
718A VAL* 3.6 8.3 - - - +
720A MET* 1.3 76.2 - - - +
722A ARG* 1.3 57.6 + - - +
724A ILE* 3.4 11.4 + - + +
725A ALA* 2.9 19.1 + - - +
806A TYR* 2.6 34.0 + - + +
809A VAL* 4.2 2.7 - - + +
810A MET* 3.7 50.5 - - + +
813A VAL* 3.7 24.0 - - + -
814A MET* 4.1 23.3 - - + -
849A LEU* 4.8 5.8 - - + -
874A LEU* 3.8 6.1 - - + -
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Residues in contact with ARG 722 (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 ASN* 5.6 1.0 - - - +
718A VAL 2.8 20.2 + - - +
719A GLY* 3.6 6.5 - - - +
720A MET 3.3 0.2 - - - -
721A LEU* 1.3 71.7 - - - +
723A GLY* 1.3 60.6 + - - +
725A ALA* 3.2 2.6 + - - +
726A SER* 2.9 48.6 + - - -
729A ARG* 4.4 9.7 - - - +
871A VAL* 3.5 19.0 - - + +
874A LEU* 3.7 25.5 - - + +
875A ASP* 2.7 43.2 + - - +
878A ILE* 4.1 14.4 - - + -
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Residues in contact with GLY 723 (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 ASN* 3.1 46.5 - - - +
719A GLY 3.1 13.6 + - - -
720A MET* 3.2 4.0 + - - -
722A ARG* 1.3 80.2 - - - +
724A ILE* 1.3 61.1 + - - +
726A SER* 3.3 2.6 + - - -
727A GLY 3.1 7.6 + - - -
754A CYS* 4.3 4.5 - - - -
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Residues in contact with ILE 724 (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 ASN* 5.2 0.2 - - - -
701A LEU* 3.7 29.8 - - + -
720A MET* 3.0 20.3 + - + +
721A LEU* 3.7 14.1 - - + +
723A GLY* 1.3 73.7 - - - +
725A ALA* 1.3 62.8 + - - +
727A GLY* 3.3 2.9 + - - -
728A MET* 3.1 22.5 + - + +
741A LEU* 4.4 12.1 - - + -
746A ILE* 4.0 27.4 - - + -
754A CYS* 3.7 17.9 - - + +
756A VAL* 4.3 7.4 - - + +
806A TYR* 3.8 21.3 - - + -
809A VAL* 4.2 16.4 - - + -
813A VAL* 4.8 0.7 - - + -
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Residues in contact with ALA 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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721A LEU 2.9 17.6 + - - +
722A ARG 3.7 3.1 - - - +
724A ILE* 1.3 73.7 - - - +
726A SER* 1.3 60.0 + - - +
728A MET* 3.4 5.5 + - - +
729A ARG* 2.8 29.1 + - - +
806A TYR* 3.6 18.3 - - + +
867A PHE* 4.3 4.6 - - + -
870A VAL* 3.7 20.0 - - + -
871A VAL* 3.5 20.7 - - + +
874A LEU* 4.0 5.4 - - + -
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Residues in contact with SER 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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673A HIS* 3.1 25.8 + - - -
675A ASN* 3.9 10.4 + - - -
722A ARG* 2.9 34.1 + - - -
723A GLY* 3.6 5.2 - - - -
725A ALA* 1.3 73.8 - - - +
727A GLY* 1.3 66.3 + - - +
729A ARG* 3.2 23.8 + - - +
730A TYR 3.0 18.2 + - - -
871A VAL* 3.7 8.4 - - - +
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Residues in contact with GLY 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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673A HIS* 3.7 12.7 - - - -
675A ASN* 4.0 9.2 - - - -
676A ILE* 3.7 20.7 - - - +
723A GLY 3.1 10.5 + - - -
724A ILE 3.3 4.0 + - - -
726A SER* 1.3 77.1 - - - +
728A MET* 1.3 56.7 + - - +
730A TYR* 3.2 6.2 + - - +
731A LEU* 3.0 29.7 + - - +
756A VAL* 4.7 1.8 - - - -
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Residues in contact with MET 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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724A ILE* 3.1 20.2 + - + +
725A ALA 3.8 1.1 - - - +
727A GLY* 1.3 71.5 - - - +
729A ARG* 1.3 60.0 + - - +
731A LEU* 3.2 23.5 + - + +
732A ALA* 2.9 32.9 + - + +
736A TYR 5.5 0.4 - - - +
738A HIS* 4.3 10.1 - - + -
741A LEU* 3.9 37.7 - - + -
756A VAL* 4.1 9.6 - - - -
802A ASP* 3.7 37.5 - - + +
806A TYR* 4.7 0.7 - - + -
867A PHE* 3.5 33.0 - - + -
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Residues in contact with ARG 729 (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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673A HIS* 5.0 2.6 + - - -
722A ARG* 4.4 10.3 - - - +
725A ALA 2.8 18.5 + - - +
726A SER* 3.2 28.7 + - - +
728A MET* 1.3 77.1 - - - +
730A TYR* 1.3 54.9 + - - +
732A ALA* 3.6 2.6 + - - +
733A GLU* 3.0 29.2 + - + +
867A PHE* 3.6 15.4 - - + +
868A PRO* 3.8 41.1 + - + +
871A VAL* 3.5 29.5 - - + +
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Residues in contact with TYR 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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670A GLN 4.0 0.9 + - - -
671A PHE* 3.3 35.9 - + + -
672A GLU* 3.0 35.4 + - - +
673A HIS* 3.4 41.1 - + + -
676A ILE* 4.0 10.8 - - + -
726A SER 3.0 7.0 + - - +
727A GLY 3.4 6.5 - - - +
728A MET 3.2 0.2 - - - -
729A ARG* 1.3 76.2 - - - +
731A LEU* 1.3 69.4 + - + +
733A GLU* 3.4 8.7 + - + +
734A MET* 3.1 58.8 + - + +
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Residues in contact with LEU 731 (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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671A PHE* 3.6 46.7 - - + -
676A ILE* 3.9 19.7 - - + -
727A GLY 3.0 13.3 + - - +
728A MET* 3.7 34.3 - - + +
730A TYR* 1.3 77.2 - - + +
732A ALA* 1.3 62.2 + - - +
734A MET* 3.1 10.6 + - - +
736A TYR* 2.8 47.6 + - + +
738A HIS* 4.5 4.3 - - + -
756A VAL* 4.4 3.4 - - + -
759A PHE* 3.9 19.3 - - + -
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Residues in contact with ALA 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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728A MET* 2.9 17.4 + - + +
729A ARG* 3.9 4.5 - - - +
731A LEU* 1.3 76.2 - - - +
733A GLU* 1.3 57.5 + - - +
735A SER* 3.0 19.5 + - - +
736A TYR 4.0 4.0 + - - +
799A SER* 3.5 33.2 + - - +
867A PHE* 4.3 13.5 - - + +
868A PRO* 6.1 2.0 - - + -
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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 ARG* 3.0 19.9 + - + +
730A TYR* 3.6 10.5 - - + +
731A LEU 3.3 0.2 - - - -
732A ALA* 1.3 75.8 - - - +
734A MET* 1.3 61.5 + - + +
735A SER* 3.2 5.8 + - - -
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Residues in contact with MET 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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670A GLN* 4.0 17.0 - - + +
671A PHE* 4.3 12.8 - - + -
730A TYR* 3.1 54.5 + - + +
731A LEU* 3.1 10.6 + - - +
733A GLU* 1.3 78.7 - - + +
735A SER* 1.3 68.0 + - - +
736A TYR* 3.3 7.8 + - + +
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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
------------------------------------------------------------
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