Contacts of the strand formed by residues 737 - 743 (chain A) in PDB entry 6NFJ
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 737 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A LYS 2.9 9.9 + - - +
687A LEU* 3.3 11.8 - - + -
688A TRP* 2.7 31.4 + - - +
726A TYR* 4.1 0.8 + - - -
736A GLY* 1.3 73.9 - - - +
738A VAL* 1.3 61.5 + - - +
819A ASP* 3.3 22.4 - - + +
820A PHE* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 738 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A PHE* 4.4 9.6 - - + -
688A TRP* 3.3 27.4 - - + +
690A THR* 4.0 22.9 - - + -
723A TRP* 3.3 33.4 + - + +
726A TYR* 3.5 41.1 - - + -
737A ALA* 1.3 80.7 - - - +
739A SER* 1.3 64.8 + - - +
819A ASP* 3.0 28.7 + - - +
820A PHE* 4.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 739 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A TRP 2.9 8.8 + - - -
689A ILE* 3.2 3.3 - - - -
690A THR* 2.8 36.0 + - - +
719A HIS* 3.7 12.1 - - - -
738A VAL* 1.3 76.7 - - - +
740A LEU* 1.3 68.9 + - - +
777A PHE* 5.2 0.3 - - - -
818A VAL* 3.7 10.9 - - - +
819A ASP 4.2 1.3 - - - -
820A PHE* 2.9 54.1 + - - -
821A CYS* 4.7 0.2 - - - -
822A ALA 4.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 740 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A ILE* 3.7 8.1 - - - -
690A THR* 3.2 19.1 - - - +
691A ILE* 3.8 9.6 - - + +
694A PRO* 3.9 15.7 - - + -
715A LEU 6.0 0.4 - - - +
719A HIS* 3.8 19.3 - - + +
739A SER* 1.3 82.0 + - - +
741A SER* 1.3 61.5 + - - +
742A LEU* 3.7 30.2 + - + +
772A PHE* 4.5 3.1 - - + -
776A LEU* 3.7 34.8 - - + -
777A PHE* 4.7 9.6 - - + -
818A VAL* 3.9 12.3 - - + -
822A ALA* 3.2 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 741 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ARG* 3.3 21.8 + - - -
689A ILE* 3.1 27.4 - - - +
691A ILE 3.3 6.5 + - - -
693A GLU 2.8 29.2 + - - -
694A PRO* 3.1 9.0 - - - +
740A LEU* 1.3 72.6 - - - +
742A LEU* 1.3 60.1 + - - +
822A ALA* 3.2 7.8 - - - +
824A ASN* 3.7 7.0 - - - -
888A THR* 2.9 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 742 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A GLU* 4.7 0.2 - - - -
694A PRO* 3.8 14.4 - - + -
695A ASN* 5.1 5.6 - - + +
740A LEU* 3.7 29.2 - - + +
741A SER* 1.3 74.4 - - - +
743A HIS* 1.3 61.8 + - - +
744A ALA* 3.2 0.9 + - - +
768A GLU 5.7 2.2 - - - +
769A ILE* 4.2 18.8 - - + +
772A PHE* 3.7 45.1 - - + +
773A ALA* 4.6 2.9 - - + +
777A PHE* 4.5 20.4 - - + -
822A ALA 3.3 13.4 + - - +
823A LEU* 3.5 9.2 - - + -
824A ASN* 2.6 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 743 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A GLU* 2.8 43.4 + - + +
695A ASN* 4.3 17.2 - - + +
696A ARG* 5.0 4.9 - - + +
742A LEU* 1.3 71.0 - - - +
744A ALA* 1.3 59.3 + - - +
745A ASP* 3.1 40.9 + - + -
764A PHE* 6.1 3.4 - + - -
768A GLU* 4.8 15.5 - - + +
769A ILE* 3.4 14.8 - - - +
824A ASN* 3.6 13.7 + - - +
826A PHE* 4.3 12.3 - + - -
210C ARG 5.3 2.4 + - - -
211C SER* 3.7 16.1 + - - -
212C PRO* 4.6 2.9 - - + -
----------------------------------------------------------
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