Contacts of the strand formed by residues 302 - 306 (chain A) in PDB entry 1KCZ
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 ALA 302 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ILE* 3.9 26.9 - - + -
262A ALA* 4.2 13.5 - - + -
269A HIS* 4.3 0.2 - - - -
270A LEU* 3.3 17.7 - - + +
272A ILE* 6.0 0.9 - - + -
295A LEU* 4.2 8.5 - - + +
296A ASP* 5.2 0.5 - - - +
300A VAL* 3.0 21.4 + - + +
301A ASP* 1.3 74.5 - - - +
303A GLU* 1.3 64.8 + - - +
326A HIS* 3.7 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ILE* 6.1 0.2 - - - +
269A HIS* 2.8 23.2 + - + +
270A LEU 2.9 7.5 + - - +
271A ARG* 2.8 43.8 + - + -
272A ILE* 2.8 27.5 + - - +
301A ASP* 5.1 3.4 - - - +
302A ALA* 1.3 76.8 - - - +
304A LEU* 1.3 66.4 + - - +
326A HIS* 3.4 32.5 - - + +
327A MET* 4.0 5.0 - - - +
381A ARG* 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ILE* 4.3 10.5 - - + -
272A ILE* 3.3 10.1 - - + +
275A PRO* 4.0 21.1 - - + -
288A MET* 4.0 22.7 - - + +
291A LEU* 3.8 23.8 - - + -
292A ARG* 3.6 33.2 - - + +
295A LEU* 3.8 22.7 - - + -
303A GLU* 1.3 78.8 - - - +
305A VAL* 1.3 61.6 + - - +
325A GLY* 3.7 3.8 - - - -
326A HIS* 2.8 40.0 + - - +
327A MET* 3.2 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A HIS* 4.2 15.0 - - - +
271A ARG* 4.2 20.9 - - + -
272A ILE 2.9 12.0 + - - +
273A GLU* 3.4 20.9 - - + +
274A GLY 2.9 27.4 + - - -
288A MET* 3.7 6.0 - - - +
303A GLU 5.1 0.2 - - - -
304A LEU* 1.3 74.1 - - - +
306A ALA* 1.3 71.8 + - - +
327A MET* 3.4 31.6 - - + +
329A GLN 4.5 1.3 - - - +
356A TYR* 4.3 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A GLY* 5.7 0.2 - - - -
284A GLN* 6.1 0.4 - - - +
288A MET* 3.6 18.1 - - + +
305A VAL* 1.3 76.4 - - - +
307A ASP* 1.3 60.5 + - - +
310A CYS* 4.4 8.1 - - + -
319A PHE* 3.9 31.4 - - + -
324A ALA 4.0 4.0 - - - +
327A MET 2.9 15.1 + - - +
328A VAL* 4.4 11.7 - - + -
329A GLN* 3.2 27.2 + - - +
----------------------------------------------------------
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