Contacts of the helix formed by residues 700 - 711 (chain A) in PDB entry 2X8A
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 ARG 700 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A VAL* 3.0 45.5 + - + +
657A GLY 4.7 0.2 + - - -
660A GLU* 3.1 29.4 - - - +
664A ARG* 5.5 2.8 - - - +
698A SER* 3.3 17.0 - - - +
699A VAL* 1.3 82.0 - - + +
701A VAL* 1.4 63.2 + - - +
702A VAL 3.2 2.0 - - - -
703A ASN* 3.2 15.1 + - + +
704A GLN* 3.0 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 701 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A VAL* 4.7 2.2 - - - +
659A SER* 4.2 25.1 - - - -
660A GLU* 4.4 11.4 - - - +
663A VAL* 5.0 10.8 - - + +
686A LEU* 4.3 27.8 - - + +
687A CYS* 5.9 0.9 - - - -
698A SER* 3.4 39.0 + - - +
700A ARG* 1.4 86.2 - - - +
702A VAL* 1.3 60.4 + - - +
704A GLN* 3.7 6.8 - - - +
705A LEU* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 702 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A LEU 5.7 0.7 - - - +
687A CYS* 4.2 27.1 - - + -
698A SER 3.9 3.7 + - - +
699A VAL* 3.3 30.1 - - + +
701A VAL* 1.3 80.7 - - + +
703A ASN* 1.4 60.7 + - - +
705A LEU* 3.1 7.9 + - - +
706A LEU* 2.7 53.0 + - + +
731A ASP* 3.4 32.3 - - + +
733A ALA* 5.2 0.2 - - + -
734A ILE* 4.6 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 703 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A VAL 3.0 20.3 + - - +
700A ARG* 3.2 14.7 + - + +
702A VAL* 1.4 81.9 - - - +
704A GLN* 1.4 49.4 + - - +
706A LEU* 3.2 16.3 + - - +
707A THR* 2.6 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 704 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A GLU* 4.0 23.8 - - + +
663A VAL* 3.8 18.4 - - + -
664A ARG* 4.0 20.6 + - - +
700A ARG* 3.0 28.5 + - - +
701A VAL* 3.8 9.0 - - - +
703A ASN* 1.4 71.9 - - - +
705A LEU* 1.3 59.5 + - - +
707A THR* 3.6 17.2 - - - +
708A GLU* 3.1 69.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 705 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A VAL* 4.4 11.2 - - + +
667A PHE* 4.1 10.5 - - + -
680A PHE* 3.7 40.4 - - + -
683A VAL* 4.9 10.8 - - + -
686A LEU* 4.9 7.6 - - + -
687A CYS* 3.6 29.2 - - - -
701A VAL 2.8 17.9 + - - +
702A VAL* 3.1 5.8 + - - +
704A GLN* 1.3 75.4 - - - +
706A LEU* 1.4 58.4 + - - +
708A GLU* 3.8 1.6 - - - +
709A MET* 2.9 44.9 + - - +
734A ILE* 3.8 17.3 - - + -
740A LEU* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 706 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A VAL* 2.7 35.6 + - + +
703A ASN* 3.6 16.8 - - - +
705A LEU* 1.4 70.1 - - - +
707A THR* 1.4 54.5 + - - +
709A MET* 3.4 4.3 + - - +
710A ASP* 2.8 41.7 + - - +
733A ALA* 4.2 15.7 - - + -
734A ILE* 3.7 39.3 - - + +
739A ARG* 3.6 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 707 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A ASN* 2.6 31.0 + - - +
704A GLN* 3.6 25.0 + - - +
705A LEU 3.4 0.2 - - - -
706A LEU* 1.4 71.5 - - - +
708A GLU* 1.3 55.3 + - + +
710A ASP* 3.2 7.0 + - - +
711A GLY* 2.7 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 708 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A VAL* 4.2 5.4 - - + -
664A ARG* 3.2 33.2 - - - +
667A PHE* 3.6 52.3 - - + +
671A LYS* 3.7 15.4 + - - -
704A GLN* 3.1 33.4 + - - +
705A LEU 4.0 0.2 - - - +
707A THR* 1.3 79.0 - - - +
709A MET* 1.3 61.6 + - - +
711A GLY* 3.5 4.6 + - - +
712A LEU* 3.3 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 709 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ALA* 3.7 17.6 - - + +
667A PHE* 4.2 1.8 - - + -
705A LEU* 2.9 34.7 + - - +
706A LEU* 3.7 5.4 - - - +
708A GLU* 1.3 76.4 - - - +
710A ASP* 1.4 61.7 + - - +
712A LEU* 3.3 24.4 + - - +
720A ILE* 3.5 26.7 - - + -
734A ILE* 3.6 23.3 - - + -
738A GLY 5.0 2.4 - - - +
739A ARG* 3.4 37.5 - - + -
740A LEU* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 710 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A LEU* 2.8 20.7 + - - +
707A THR* 3.7 5.6 - - - +
709A MET* 1.4 73.5 - - - +
711A GLY* 1.3 60.2 + - - +
712A LEU 3.2 9.5 + - - +
738A GLY* 5.4 4.3 - - - +
739A ARG* 2.8 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 711 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A LYS* 5.3 4.8 + - - -
707A THR 2.7 19.8 + - - -
708A GLU* 3.8 7.6 - - - -
709A MET 3.2 0.8 - - - -
710A ASP* 1.3 73.1 - - - +
712A LEU* 1.3 57.7 + - - +
713A GLU* 5.1 1.4 - - - +
716A GLN* 3.6 13.0 + - - +
----------------------------------------------------------
Back to top of page
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