Contacts of the strand formed by residues 323 - 328 (chain B) in PDB entry 1KEK
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 VAL 323 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLU 3.1 7.1 + - - +
271B ARG* 3.5 8.1 - - + -
272B VAL* 3.1 22.2 + - - +
321B ALA* 4.7 0.2 - - - +
322B LYS* 1.3 88.9 + - + +
324B ILE* 1.3 70.6 - - - +
356B PRO 3.2 3.8 - - - -
357B LYS* 3.4 13.9 - - + +
359B LEU* 3.7 22.0 - - + -
382B MET* 3.6 47.8 - - + +
386B LYS* 4.4 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B VAL* 3.1 16.8 - - + +
274B VAL* 3.4 31.0 - - + -
300B ILE* 5.5 0.2 - - + -
313B PHE* 3.9 18.4 - - + -
317B LEU* 4.7 4.9 - - + -
321B ALA* 4.5 13.5 - - + -
323B VAL* 1.3 79.5 - - - +
325B THR* 1.3 63.6 + - - +
326B VAL* 4.1 8.1 - - + -
344B VAL* 4.0 13.2 - - + -
348B PHE* 4.1 10.1 - - + -
356B PRO* 4.2 25.8 - - + +
357B LYS 2.9 8.8 + - - +
358B ILE* 3.4 8.4 - - + -
359B LEU* 2.8 27.7 + - - +
382B MET* 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B VAL 2.9 8.5 + - - -
273B ILE* 3.1 8.1 - - - +
274B VAL 2.7 31.2 + - - +
324B ILE* 1.3 72.3 - - - +
326B VAL* 1.4 59.3 + - - +
327B LEU* 3.5 22.5 - - - +
359B LEU* 3.2 24.4 + - + -
378B VAL* 3.9 12.0 - - + +
381B ASN* 5.2 0.4 - - - +
382B MET* 3.2 41.7 - - + -
390B PHE* 3.7 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B VAL* 3.6 15.0 - - + -
324B ILE* 4.1 9.6 - - + -
325B THR* 1.4 74.0 - - - +
327B LEU* 1.3 63.2 + - - +
328B ASP* 3.9 3.9 + - - +
340B LEU* 3.5 38.1 - - + +
341B TYR* 3.5 25.9 - - + +
344B VAL* 3.8 30.1 - - + -
358B ILE* 4.2 12.3 - - + -
359B LEU 2.8 10.0 + - - +
360B ALA* 3.7 3.8 - - - +
361B GLY 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TYR* 5.1 0.3 + - - -
273B ILE* 3.6 31.9 - - + -
274B VAL 3.0 11.7 + - - +
275B SER* 3.9 9.0 + - - +
276B MET* 4.9 1.6 + - - +
283B ILE* 4.2 9.0 - - + -
325B THR* 3.5 23.3 - - - +
326B VAL* 1.3 73.5 - - - +
328B ASP* 1.3 59.3 + - - +
340B LEU* 3.7 19.5 - - - +
361B GLY* 3.2 12.8 - - - +
363B TYR* 3.7 25.3 + - + -
370B PHE* 3.9 25.1 - - + -
378B VAL* 4.4 8.1 - - + -
390B PHE* 3.9 19.7 - - + -
392B VAL* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TYR* 2.8 27.2 + - - -
326B VAL* 4.5 1.7 - - - +
327B LEU* 1.3 73.5 - - - +
329B ARG* 1.3 57.5 + - - +
330B THR* 3.2 10.0 + - + +
338B ASP* 3.2 35.0 - - + +
339B PRO* 3.3 6.4 - - - +
340B LEU* 2.8 19.4 + - - +
341B TYR* 3.0 29.5 + - - +
361B GLY 3.0 9.4 + - - +
362B ARG* 3.4 6.8 - - - -
363B TYR* 3.3 24.5 + - - -
----------------------------------------------------------
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