Contacts of the helix formed by residues 718 - 728 (chain A) in PDB entry 2XR9
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 VAL 718 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714A TYR* 2.9 57.9 + - + +
717A ARG* 1.3 106.5 - - + +
719A LEU* 1.3 68.3 + - + +
720A VAL 3.6 1.1 - - - -
721A LYS* 3.6 7.2 + - - +
722A LYS* 3.2 24.2 + - + +
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Residues in contact with LEU 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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714A TYR* 3.2 33.3 + - + +
715A PHE* 3.2 18.6 + - + +
718A VAL* 1.3 77.1 - - + +
720A VAL* 1.3 67.5 + - - +
722A LYS* 3.2 16.9 + - + +
723A TYR* 2.9 47.1 + - + +
815A VAL* 4.5 2.7 - - + -
816A GLU* 3.6 36.8 - - + +
819A MET* 3.5 32.3 - - + -
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Residues in contact with VAL 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A TYR* 4.0 13.5 - - + +
635A ILE* 3.2 36.6 - - + -
682A PRO* 5.6 0.2 - - + -
685A LEU* 3.4 18.8 - - + -
715A PHE* 3.0 48.4 + - + +
716A GLN* 4.2 8.1 - - - +
718A VAL 3.6 0.4 - - - -
719A LEU* 1.3 74.2 - - - +
721A LYS* 1.3 57.8 + - - +
723A TYR* 3.3 9.5 + - + +
724A ALA* 2.9 26.7 + - - +
730A VAL* 4.2 2.2 - - + +
732A VAL* 4.5 11.2 - - + -
771A ILE* 5.5 0.7 - - + -
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Residues in contact with LYS 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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635A ILE* 5.1 2.5 - - + -
637A LYS 3.1 26.4 + - - +
638A GLN* 3.9 3.2 - - - +
639A ALA* 2.7 37.0 + - + +
640A GLU* 5.5 0.6 + - - +
641A VAL* 3.6 31.0 - - + -
685A LEU* 4.8 5.5 - - + +
716A GLN 5.2 0.8 + - - -
717A ARG 4.7 3.1 - - - +
718A VAL* 3.6 8.8 + - - +
719A LEU 3.3 0.6 - - - -
720A VAL* 1.3 77.4 - - - +
722A LYS* 1.3 61.6 + - - +
724A ALA* 3.6 7.1 - - + +
725A SER* 2.8 45.4 + - - +
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Residues in contact with LYS 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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718A VAL* 3.2 19.0 + - + +
719A LEU* 3.2 16.8 + - + +
721A LYS* 1.3 77.4 - - - +
723A TYR* 1.3 63.1 + - - +
725A SER* 3.3 7.3 + - - -
726A GLU* 3.0 59.6 + - + +
816A GLU* 3.4 36.8 + - - -
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Residues in contact with TYR 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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715A PHE* 4.3 7.4 - + - -
719A LEU* 2.9 47.4 + - + +
720A VAL* 3.8 7.2 - - - +
722A LYS* 1.3 80.7 - - + +
724A ALA* 1.3 57.6 + - - +
726A GLU* 3.7 19.3 - - - -
727A ARG* 2.9 48.1 + - - +
730A VAL* 3.8 16.2 - - + -
771A ILE* 3.7 34.1 - - + -
791A SER* 6.0 0.7 - - - -
793A PHE* 5.3 0.2 - + - -
816A GLU* 3.5 28.3 + - - +
819A MET* 4.0 11.3 - - + +
858A TYR* 5.4 6.1 + + - -
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Residues in contact with ALA 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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635A ILE* 3.6 39.3 - - + +
636A SER 3.7 7.9 - - - +
637A LYS* 3.6 8.1 - - - -
720A VAL 2.9 17.1 + - - +
721A LYS* 3.6 7.2 - - + +
723A TYR* 1.3 76.7 - - - +
725A SER* 1.3 59.7 + - - +
728A ASN 3.3 4.9 + - - -
729A GLY* 2.8 27.4 + - - +
730A VAL* 4.0 10.2 - - + +
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Residues in contact with SER 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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637A LYS* 4.1 29.5 + - - +
721A LYS* 2.8 45.2 + - - +
722A LYS* 3.5 8.2 - - - -
724A ALA* 1.3 76.8 - - - +
726A GLU* 1.3 59.9 + - - +
728A ASN 4.5 1.3 + - - -
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Residues in contact with GLU 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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722A LYS* 3.0 46.1 + - + +
723A TYR* 3.7 23.2 - - - +
725A SER* 1.3 79.3 - - - +
727A ARG* 1.3 67.5 + - + +
728A ASN 3.6 0.8 + - - -
777A PHE* 5.4 4.7 - - - +
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Residues in contact with ARG 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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723A TYR* 2.9 29.6 + - - +
726A GLU* 1.3 87.8 - - + +
728A ASN* 1.3 70.3 + - - +
729A GLY 3.5 10.6 - - - +
730A VAL* 3.9 4.0 - - + +
771A ILE* 2.9 40.6 + - - +
773A SER* 2.8 44.0 + - - +
774A CYS 4.9 2.9 + - - +
777A PHE* 4.7 13.7 - - - +
779A GLN 4.9 1.4 - - - +
789A SER* 3.0 25.0 + - - -
790A VAL* 4.0 2.0 - - - +
791A SER* 3.0 26.2 + - - -
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Residues in contact with ASN 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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637A LYS* 3.9 32.1 - - + +
638A GLN* 5.5 1.4 + - - -
724A ALA 3.3 4.8 + - - -
725A SER 4.5 1.6 + - - -
726A GLU 3.6 2.2 + - - -
727A ARG* 1.3 81.5 - - - +
729A GLY* 1.3 57.6 + - - +
777A PHE* 2.9 28.4 + - + +
778A THR* 3.8 7.3 + - - +
779A GLN 3.4 21.2 - - - +
780A PRO* 3.3 16.7 - - - +
781A ALA 3.1 20.6 + - - -
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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