Contacts of the helix formed by residues 704 - 711 (chain A) in PDB entry 5MJA
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 ALA 704 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A ASN 3.8 0.7 - - - +
703A GLY* 1.4 69.1 - - - -
705A LEU* 1.3 60.0 + - - +
706A ASP* 3.4 17.7 - - - +
707A SER* 3.5 10.9 + - - +
708A PHE* 3.1 29.3 + - - +
748A ARG* 3.6 19.5 - - + +
750A ILE 3.3 7.6 - - - -
751A LEU* 3.8 7.9 - - + +
901A 7O3 4.5 5.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
703A GLY 3.6 0.6 + - - -
704A ALA* 1.3 70.0 - - - +
706A ASP* 1.3 66.3 + - - +
708A PHE* 3.4 3.2 + - + +
709A LEU* 3.0 48.3 + - + +
724A MET* 4.2 11.7 - - + -
728A ILE* 3.7 23.6 - - + -
747A ALA* 3.3 20.7 + - + +
750A ILE* 2.8 24.8 + - + +
752A VAL* 3.6 26.5 - - + -
758A CYS* 4.1 10.3 - - - -
813A VAL* 4.7 0.4 - - + -
817A VAL* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 706 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A ALA* 3.5 11.1 - - - +
705A LEU* 1.3 78.4 - - - +
707A SER* 1.4 64.3 + - - +
709A LEU* 3.6 1.0 + - - -
710A ARG* 2.8 61.1 + - - +
747A ALA* 3.6 23.8 + - + +
748A ARG* 3.2 32.4 - - + +
816A GLU* 4.4 7.2 - - - +
821A GLY* 3.7 12.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 707 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A ALA* 3.5 19.6 + - - +
706A ASP* 1.4 79.0 + - - +
708A PHE* 1.3 66.1 + - - +
710A ARG* 3.4 23.3 + - - +
711A GLN* 3.1 40.5 + - - +
901A 7O3 5.6 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 708 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A ASN* 3.3 50.2 + - + +
704A ALA 3.1 19.9 + - - +
705A LEU* 3.4 6.3 + - + +
707A SER* 1.3 77.5 + - - +
709A LEU* 1.3 72.7 + - + +
711A GLN* 3.4 4.8 + - - -
712A ASN* 2.7 53.5 + - - +
716A PHE* 3.5 31.9 - + - -
724A MET* 4.8 1.6 - - + -
752A VAL* 4.1 19.5 - - + -
756A LEU* 3.5 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 709 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A LEU* 3.0 42.2 + - + +
706A ASP* 3.9 2.2 - - - +
708A PHE* 1.3 80.0 - - + +
710A ARG* 1.3 65.0 + - - +
712A ASN* 3.1 13.3 + - - +
713A ASP* 3.1 14.7 + - - -
716A PHE* 4.1 23.3 - - + -
721A LEU* 4.1 9.9 - - + -
724A MET* 4.5 3.8 - - - -
747A ALA* 6.1 0.7 - - + -
816A GLU 4.4 0.7 - - - +
817A VAL* 3.7 38.8 - - + +
820A PHE* 3.5 36.4 - - + +
821A GLY* 3.8 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 710 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A ASP* 2.8 52.9 + - - +
707A SER* 3.4 20.9 + - - +
709A LEU* 1.3 77.4 - - - +
711A GLN* 1.3 60.5 + - + +
712A ASN 3.2 1.3 + - - -
713A ASP* 3.8 14.0 + - - +
820A PHE 3.5 10.1 - - - +
821A GLY 2.9 35.8 + - - +
822A GLU* 5.3 1.4 - - - +
823A ARG* 5.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 711 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A SER* 3.1 32.0 + - - +
708A PHE* 3.7 6.9 + - - +
710A ARG* 1.3 76.1 - - + +
712A ASN* 1.3 68.6 + - - +
713A ASP 3.7 0.9 - - - -
----------------------------------------------------------
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