Contacts of the strand formed by residues 813 - 816 (chain D) in PDB entry 1S77
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 SER 813 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535D ALA* 3.9 19.9 - - - +
536D PHE 3.5 6.7 + - - -
537D ASP* 3.4 19.0 + - - +
791D LEU* 4.4 2.4 - - - +
808D ALA 4.3 1.1 - - - -
809D LEU* 3.6 3.8 - - - -
810D ILE* 3.0 51.0 + - - +
811D HIS 4.3 0.5 + - - -
812D ASP* 1.3 81.9 + - - +
814D PHE* 1.3 66.0 + - - +
1R 3DA 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 814 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535D ALA* 4.6 1.6 - - - -
536D PHE* 2.8 43.6 + - + +
787D ASP 5.6 0.4 - - - -
790D HIS* 4.0 16.8 - + - -
791D LEU* 3.8 37.7 - - + -
794D THR* 3.8 28.5 - - + -
795D VAL* 5.8 0.2 - - + -
808D ALA 3.5 2.5 - - - -
809D LEU* 4.8 9.6 - - + -
811D HIS 4.7 3.4 - - - -
812D ASP* 3.4 24.9 - - - -
813D SER* 1.3 77.0 + - - +
815D GLY* 1.3 58.8 + - - +
824D LEU* 3.5 24.7 - - + +
828D VAL* 3.5 28.7 - - + -
883D ALA* 3.5 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 815 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533D PRO* 5.2 0.4 - - - -
534D LEU 3.4 13.9 - - - -
535D ALA* 4.3 3.4 - - - -
806D SER 3.7 0.2 - - - +
807D PHE* 3.2 10.0 - - - +
808D ALA* 2.6 50.8 + - - -
809D LEU* 4.9 1.0 - - - +
814D PHE* 1.3 75.2 - - - +
816D THR* 1.3 64.1 + - - -
824D LEU* 3.4 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 816 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446D LEU* 3.8 11.0 - - - -
532D LEU 3.3 0.5 - - - +
534D LEU* 2.7 32.4 + - - +
536D PHE* 6.1 0.2 - - - -
804D ILE* 3.5 18.5 - - + +
806D SER* 2.9 28.9 + - - +
815D GLY* 1.3 70.3 + - - -
817D ILE* 1.3 77.3 + - + +
820D ASP* 3.6 21.5 - - + +
821D ALA* 4.5 1.8 - - - +
824D LEU* 2.7 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