Contacts of the strand formed by residues 730 - 736 (chain E) in PDB entry 2JDQ
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 ASP 730 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699E LYS* 5.9 1.9 - - - +
725E LEU* 3.7 1.0 - - - -
726E ILE* 2.9 41.8 + - - +
727E GLY* 2.8 17.6 + - - +
728E GLN* 3.7 16.8 + - + +
729E GLY* 1.3 74.0 - - - +
731E VAL* 1.3 64.2 + - - +
732E VAL* 3.8 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 731 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699E LYS* 3.9 5.0 - - - +
700E GLU* 3.1 56.3 + - + +
707E ALA* 3.8 22.2 - - + -
723E ASN* 3.8 10.1 - - + -
724E VAL 3.3 10.3 - - - +
725E LEU* 3.3 27.8 - - + -
729E GLY 3.6 8.4 + - - +
730E ASP* 1.3 74.2 - - - +
732E VAL* 1.3 67.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 732 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696E ILE* 3.1 39.0 - - + -
698E GLY 3.5 9.9 - - - +
699E LYS* 4.8 6.1 - - + -
700E GLU 4.2 0.7 - - - +
723E ASN* 3.4 6.3 - - - -
724E VAL* 2.9 32.5 + - - +
726E ILE* 4.0 22.2 - - + -
730E ASP* 3.8 18.2 - - - +
731E VAL* 1.3 80.0 - - - +
733E LEU* 1.3 64.3 + - - +
734E VAL* 3.8 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 733 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696E ILE* 3.5 4.2 - - - -
697E LEU* 2.6 56.5 + - + -
698E GLY* 2.8 19.6 + - - +
699E LYS 3.9 8.8 + - - +
701E ASP* 4.0 18.8 - - + +
704E TYR* 3.8 35.7 - - + -
721E LYS* 4.2 7.6 - - + -
722E ALA 3.5 24.2 - - - +
723E ASN* 3.3 21.5 - - - +
732E VAL* 1.3 71.7 - - - +
734E VAL* 1.3 56.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 734 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691E LEU* 4.8 5.4 - - + -
694E PHE* 3.9 22.4 - - + -
695E LEU 3.2 8.7 - - - +
696E ILE* 4.1 14.6 - - + -
697E LEU* 4.0 4.5 - - - -
713E LEU* 3.8 18.8 - - + -
716E LEU* 4.4 4.1 - - + +
721E LYS* 3.3 7.8 - - - +
722E ALA 3.0 39.2 + - - +
724E VAL* 3.7 29.2 - - + -
726E ILE* 5.4 0.2 - - + -
732E VAL* 3.8 12.6 - - + -
733E LEU* 1.3 79.0 - - - +
735E MET* 1.3 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 735 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A TRP* 4.3 24.7 - - + -
694E PHE* 3.2 8.6 - - - -
695E LEU* 2.8 39.6 + - + +
697E LEU* 4.1 26.7 - - + -
716E LEU* 4.3 3.4 - - - -
719E GLY* 4.7 19.1 - - - +
720E GLU 3.6 17.9 - - - +
721E LYS* 4.3 15.9 - - + +
734E VAL* 1.3 75.2 - - - +
736E LYS* 1.3 73.8 + - - +
739E ARG* 4.5 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 736 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ASN* 5.8 2.4 + - - +
402A TRP* 4.6 0.9 - - - -
693E GLY 3.6 7.6 - - - +
694E PHE* 3.3 25.2 - - + -
713E LEU 3.8 16.6 - - - -
714E SER* 3.0 22.3 + - - +
715E ASN 4.5 0.2 - - - -
716E LEU* 2.7 35.1 + - + +
717E ALA 4.9 0.9 - - - +
718E LYS* 4.3 31.1 - - + +
719E GLY 5.2 3.0 + - - +
720E GLU 4.6 1.4 + - - -
735E MET* 1.3 92.5 - - - +
737E ARG* 1.3 63.9 + - - +
738E LYS* 3.5 20.0 + - + +
739E ARG* 4.1 3.1 - - - +
----------------------------------------------------------
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