Contacts of the strand formed by residues 543 - 546 (chain C) in PDB entry 3KSA
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 TYR 543 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 3.7 15.5 + - - -
541C PRO* 4.5 0.3 - - - +
542C LEU* 1.3 106.7 - - + +
544C LYS* 1.3 61.7 + - - +
545C MET* 4.3 0.4 - - + -
557C TYR* 3.3 8.7 - - - +
558C ALA* 2.8 50.5 + - + +
560C THR 4.9 0.9 - - - -
561C ASP* 4.1 26.6 + - - -
564C LEU* 3.2 30.2 - - + +
577C LEU* 3.6 21.1 - - + -
578C GLN 3.3 1.3 - - - -
579C ARG* 3.2 50.0 + - + -
580C TYR* 4.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 544 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C LEU 4.3 0.2 + - - -
543C TYR* 1.3 73.5 - - - +
545C MET* 1.3 60.3 - - - +
546C SER* 4.3 11.4 + - - -
555C VAL* 3.6 25.8 - - + -
556C ALA 3.4 15.0 - - - +
557C TYR* 3.2 38.6 - - + +
576C THR 4.0 0.9 - - - +
577C LEU* 3.6 2.7 - - - -
578C GLN* 2.9 68.9 + - + +
580C TYR* 3.5 21.8 + - + +
590C GLN* 4.7 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 545 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASP* 4.7 9.9 - - + +
543C TYR* 4.3 0.4 - - + -
544C LYS* 1.3 73.9 - - - +
546C SER* 1.3 62.8 + - - +
555C VAL* 3.3 5.5 - - - +
556C ALA 3.0 33.2 + - - +
557C TYR* 5.1 0.2 - - - +
564C LEU* 4.1 19.1 - - + -
567C LEU* 4.0 12.6 - - + +
568C ARG* 3.8 42.6 - - + +
571C PHE* 3.3 18.0 - - + -
572C GLY 5.9 0.2 - - - +
575C ALA* 4.1 26.2 - - + +
576C THR 3.4 10.3 - - - +
577C LEU* 4.3 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 546 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C LYS* 4.6 12.3 + - - -
545C MET* 1.3 76.8 - - - +
547C LYS* 1.3 62.8 + - - +
553C GLU* 6.0 1.3 - - - -
554C GLU 3.2 4.7 - - - -
555C VAL* 3.6 20.9 - - - -
571C PHE* 3.6 3.4 - - - -
574C GLY 4.7 0.3 - - - +
575C ALA* 3.4 1.7 - - - -
576C THR* 2.9 48.7 + - - -
----------------------------------------------------------
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