Contacts of the strand formed by residues 735 - 739 (chain D) in PDB entry 1XSK
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 THR 735 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686D THR 3.1 8.4 + - - -
687D ALA* 5.0 6.7 - - + -
688D PHE* 2.9 34.0 + - - +
733D ASN* 4.7 3.0 + - - -
734D TRP* 1.3 83.1 + - - +
736D LEU* 1.3 76.1 + - - +
737D CYS* 4.5 1.6 - - + +
760D VAL* 3.1 36.2 - - + +
761D VAL 3.5 10.0 + - - +
762D LYS* 4.6 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 736 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668D LEU* 3.7 20.6 - - + -
688D PHE* 3.4 24.0 - - + +
690D LEU* 4.4 9.4 - - + -
714D LEU* 4.9 8.3 - - + -
725D VAL* 5.2 15.9 - - + -
734D TRP* 4.2 13.7 - - + -
735D THR* 1.3 81.7 - - - +
737D CYS* 1.3 64.4 + - - +
738D LEU* 3.2 35.7 - - + -
759D LEU 3.9 0.2 - - - +
760D VAL* 3.5 0.9 - - - -
761D VAL* 2.7 49.1 + - + +
768D LEU* 6.0 2.7 - - + -
770D ILE* 6.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 737 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688D PHE 2.8 16.7 + - - +
689D HIS* 3.6 19.1 - - + +
690D LEU 2.9 26.3 + - - -
735D THR* 5.4 1.6 - - + -
736D LEU* 1.3 80.5 - - - +
738D LEU* 1.3 60.8 + - - +
739D ARG* 3.3 29.2 + - - -
755D SER* 4.8 1.3 - - - -
757D GLN* 4.2 8.1 - - - -
758D GLY 3.6 22.4 - - - -
759D LEU 3.3 4.3 - - - +
760D VAL* 4.3 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 738 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690D LEU* 4.0 24.7 - - + -
723D ILE* 4.3 12.3 - - + -
736D LEU* 3.2 27.4 - - + -
737D CYS* 1.3 71.7 - - - +
739D ARG* 1.3 68.1 + - - +
740D ASN 3.2 0.3 + - - -
741D VAL* 2.8 51.1 + - + +
744D VAL* 5.0 0.4 - - + -
758D GLY* 3.3 8.1 - - - -
759D LEU* 2.6 27.4 + - + +
761D VAL* 4.2 19.1 - - + -
770D ILE* 4.2 24.0 - - + -
772D LEU* 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 739 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637D HIS 4.2 0.8 + - - -
638D LEU* 3.2 32.3 + - - +
641D ASN* 2.8 35.4 + - - +
671D LEU* 4.6 8.7 - - - +
689D HIS* 2.5 45.2 + - + +
690D LEU 3.3 21.1 + - - +
691D PHE* 3.4 43.9 - - + -
692D ASN* 4.7 7.8 + - - +
737D CYS* 3.3 5.9 + - - -
738D LEU* 1.3 71.6 - - - +
740D ASN* 1.3 75.5 + - - +
741D VAL* 3.1 8.5 + - - +
757D GLN* 3.2 35.8 + - - +
----------------------------------------------------------
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