Contacts of the strand formed by residues 683 - 688 (chain D) in PDB entry 6X34
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 683 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681D HIS* 3.1 47.6 + - - +
682D LEU* 1.3 79.9 - - - +
684D VAL* 1.3 60.9 + - - +
704D GLY 5.5 4.0 + - - -
705D ASN 5.6 0.2 - - - -
706D GLY* 4.9 11.1 - - - +
707D VAL* 3.4 39.3 + - + +
709D ASP* 5.6 3.4 - - - +
715D GLY 5.8 0.9 - - - -
716D PHE 5.3 3.8 - - - +
717D ASP* 3.7 18.6 - - + +
722D TRP* 3.3 68.1 - - - +
725D HIS* 5.6 3.4 + - - -
781D VAL* 3.7 2.8 - - - +
782D SER 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 684 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664D PHE* 4.6 23.1 - - + -
666D VAL* 4.7 22.4 - - + -
683D ARG* 1.3 74.5 - - - +
685D GLY* 1.3 64.8 + - - +
707D VAL* 4.7 1.3 - - - -
715D GLY* 4.3 2.7 - - - -
716D PHE 3.2 32.3 + - - +
717D ASP* 5.3 2.5 - - + -
744D VAL* 5.2 12.6 - - + +
745D SER 6.3 1.1 - - - -
746D CYS* 5.7 10.8 - - + +
780D VAL 3.3 14.1 - - - +
781D VAL* 4.2 17.0 - - + -
791D PHE* 5.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 685 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664D PHE* 5.4 0.2 - - - -
684D VAL* 1.3 76.7 - - - +
686D TRP* 1.3 66.3 + - - -
707D VAL* 4.7 8.1 - - - +
714D TYR 3.4 10.5 - - - -
715D GLY* 3.7 6.3 - - - -
746D CYS* 5.5 5.4 - - - -
779D PRO* 3.5 4.7 - - - +
780D VAL* 2.7 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 686 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650D VAL* 5.4 10.3 - - + -
662D TRP* 4.7 23.6 - + + -
664D PHE* 3.6 29.8 - + - -
685D GLY* 1.3 79.2 - - - -
687D ALA* 1.3 59.8 + - - +
707D VAL* 5.9 0.8 - - - +
713D SER* 3.5 2.6 - - - -
714D TYR* 2.7 43.6 + - + +
746D CYS* 3.0 27.0 - - + +
747D CYS 5.0 0.2 - - - -
748D LEU* 3.5 36.0 - - + +
755D ILE* 4.9 11.8 - - + +
777D PHE* 3.2 48.9 - - + -
778D PHE 3.4 4.5 - - - +
779D PRO* 3.5 29.6 - - + -
811D CYS* 6.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 687 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685D GLY 4.3 0.4 + - - -
686D TRP* 1.3 73.9 - - - +
688D LEU* 1.3 61.5 + - - +
692D TYR* 4.1 23.1 - - + -
707D VAL* 5.3 1.3 - - + -
713D SER* 3.9 18.4 - - - +
777D PHE* 4.4 3.6 - - - -
778D PHE* 2.9 55.6 + - + +
780D VAL* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 688 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687D ALA* 1.3 75.0 - - - +
689D THR* 1.3 64.4 + - + +
690D GLU 3.3 16.1 + - - +
692D TYR* 4.0 16.5 + - - +
712D TYR* 3.5 24.4 + - + +
775D GLY* 5.8 2.0 - - - -
776D LEU 3.4 17.5 - - - +
777D PHE* 4.3 14.3 - - + -
778D PHE* 3.2 14.1 - - - -
826D ILE* 5.9 0.2 - - - +
1470D ARG* 5.1 6.5 - - - +
----------------------------------------------------------
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