Contacts of the strand formed by residues 685 - 692 (chain D) in PDB entry 5Z58
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 LEU 685 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448D PRO 3.5 5.5 - - - +
449D ALA* 3.5 16.4 - - - +
450D LEU* 4.4 3.6 + - - +
681D ARG* 5.4 6.1 - - + +
683D VAL 3.5 4.7 + - - +
684D PRO* 1.3 74.4 - - - +
686D GLU* 1.3 61.5 + - - +
687D GLN* 3.7 5.9 + - + +
856D ALA* 5.8 7.6 - - + +
865D GLY 3.2 6.3 - - - +
866D GLU* 5.6 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 686 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447D VAL 3.6 11.0 - - - +
448D PRO* 4.1 4.5 - - + -
449D ALA* 4.2 13.6 - - + +
684D PRO 4.2 0.2 - - - -
685D LEU* 1.3 70.3 - - - +
687D GLN* 1.3 61.2 + - - +
688D THR* 3.8 0.9 + - - -
864D LYS* 6.4 0.7 - - + -
865D GLY 2.9 14.7 + - - +
866D GLU* 3.2 12.7 - - + +
867D GLY 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 687 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445D VAL 3.9 0.7 - - - +
446D HIS* 3.6 3.8 - - - +
447D VAL* 2.9 49.1 + - + +
685D LEU* 3.7 8.0 + - + +
686D GLU* 1.3 72.1 - - - +
688D THR* 1.3 59.7 + - - +
689D TYR* 4.3 0.7 - - + -
867D GLY* 3.9 4.3 - - - +
883D LEU* 6.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 688 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445D VAL 3.6 6.1 - - - -
446D HIS* 4.9 2.0 - - - +
686D GLU 5.2 0.4 - - - -
687D GLN* 1.3 74.2 - - - +
689D TYR* 1.3 60.8 + - - +
690D VAL 4.2 0.2 - - - -
867D GLY 2.9 15.9 + - - +
868D ILE* 3.3 14.5 - - - -
869D LEU* 2.9 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 689 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443D GLU 3.9 0.5 - - - +
444D GLU* 3.5 1.5 - - - -
445D VAL* 2.9 46.4 + - + +
687D GLN* 4.3 0.6 - - + -
688D THR* 1.3 75.8 - - - +
690D VAL* 1.3 59.9 + - - +
691D GLY 3.8 2.3 + - - +
869D LEU* 3.5 13.0 - - + +
876D LEU* 5.6 11.7 - - + +
879D TYR* 6.2 4.5 - - + -
880D LEU* 6.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 690 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D TYR* 5.2 7.0 - - + -
443D GLU 3.5 7.2 - - - +
444D GLU* 4.3 11.4 - - + +
688D THR 4.2 0.6 - - - -
689D TYR* 1.3 71.8 - - - +
691D GLY* 1.3 60.8 + - - +
692D ILE* 3.9 0.5 + - - +
707D ILE* 5.9 7.4 - - + -
869D LEU 2.9 12.3 + - - +
870D ILE* 3.6 9.3 - - + +
871D THR* 2.9 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 691 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D TYR* 3.1 5.9 - - - +
443D GLU* 2.9 34.5 + - - -
689D TYR 3.8 3.4 + - - -
690D VAL* 1.3 73.4 - - - +
692D ILE* 1.3 61.1 + - - -
693D THR 4.0 0.2 + - - -
871D THR* 3.3 7.6 - - - -
872D SER 4.0 1.8 - - - -
873D HIS* 3.6 22.1 - - - +
876D LEU* 4.4 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 692 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D GLY 3.4 7.0 - - - +
442D TYR* 3.9 6.5 - - + -
690D VAL 5.3 0.7 - - - +
691D GLY* 1.3 72.6 - - - -
693D THR* 1.3 61.5 + - - +
694D GLU* 3.3 11.1 + - + +
700D ARG* 5.8 6.7 - - + -
703D ILE* 5.9 7.6 - - + -
704D MET* 6.5 0.7 - - + -
871D THR 2.9 16.0 + - - +
872D SER* 4.1 5.6 - - - -
873D HIS* 3.1 18.8 + - - +
----------------------------------------------------------
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