Contacts of the helix formed by residues 235 - 246 (chain B) in PDB entry 3KCZ
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 ASP 235 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ASN* 5.8 1.8 - - - +
233B SER 3.3 4.9 + - - -
234B MET* 1.3 74.4 - - - +
236B LEU* 1.3 66.9 + - - +
237B ARG* 2.9 48.7 + - - +
238B VAL* 3.1 13.1 + - + +
239B GLN* 2.9 17.8 + - - +
371B PRO* 3.6 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ASN* 6.3 0.4 - - - +
233B SER* 5.7 2.5 - - - +
234B MET 4.4 2.0 - - - +
235B ASP* 1.3 77.2 + - - +
237B ARG* 1.3 62.1 + - + +
239B GLN* 3.2 28.8 + - + +
240B GLU* 2.9 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ASP* 2.9 23.2 + - - +
236B LEU* 1.3 77.2 - - + +
238B VAL* 1.3 60.9 + - - +
240B GLU* 3.4 7.7 + - - +
241B LEU* 3.0 26.7 + - - +
371B PRO* 3.4 24.6 - - + +
372B LEU 3.0 29.1 + - - +
373B ASP* 5.0 1.8 - - - +
374B HIS* 4.0 7.6 - - - -
403B ASP* 3.0 41.1 + - - +
405B PHE* 3.7 15.0 - - + -
574B LYS* 5.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B MET* 3.7 23.8 - - + -
235B ASP* 3.1 14.0 + - + +
237B ARG* 1.3 73.1 - - - +
239B GLN* 1.3 60.9 + - - +
241B LEU* 3.2 3.8 + - + +
242B ILE* 2.9 38.0 + - + +
362B TYR* 4.3 21.3 - - + -
369B LEU* 3.5 26.5 - - + +
371B PRO* 3.7 23.8 - - + -
405B PHE* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B SER* 4.6 5.7 + - - -
234B MET* 2.7 52.4 + - + +
235B ASP 2.9 9.8 + - - +
236B LEU* 3.2 33.4 + - + +
238B VAL* 1.3 78.0 - - - +
240B GLU* 1.3 60.8 + - - +
242B ILE* 3.3 2.5 + - - +
243B LYS* 3.0 38.7 + - - +
356B HIS* 5.7 1.6 - - - -
358B LEU* 4.2 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 2.9 31.9 + - + +
237B ARG* 3.9 6.7 - - - +
238B VAL 3.3 0.2 - - - -
239B GLN* 1.3 74.9 - - - +
241B LEU* 1.3 64.5 + - - +
243B LYS* 3.2 36.0 + - - +
244B LEU* 3.1 24.4 + - - +
574B LYS* 4.4 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ARG 3.0 14.3 + - - +
238B VAL* 3.4 9.0 - - - +
240B GLU* 1.3 73.9 - - - +
242B ILE* 1.3 65.9 + - + +
244B LEU* 3.2 10.3 + - + +
245B ILE* 3.0 31.2 + - + +
369B LEU* 3.8 28.9 - - + -
405B PHE* 3.8 40.2 - - + -
484B LEU* 3.9 38.6 - - + -
572B LEU* 4.1 11.4 - - + -
574B LYS* 5.1 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B MET* 4.2 8.7 - - - -
238B VAL* 2.9 29.5 + - + +
239B GLN* 3.7 5.6 - - - +
241B LEU* 1.3 71.9 - - + +
243B LYS* 1.3 66.6 + - - +
245B ILE* 3.3 11.8 + - + -
246B CYS* 2.9 30.4 + - - +
358B LEU* 3.9 21.8 - - + +
361B HIS* 3.8 27.6 - - + -
362B TYR* 4.0 19.5 - - + -
365B LEU* 4.0 26.5 - - + -
369B LEU* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B GLN* 3.0 23.3 + - - +
240B GLU* 3.2 37.4 + - - +
242B ILE* 1.3 76.3 - - - +
244B LEU* 1.3 61.3 + - - +
246B CYS* 4.0 2.5 - - - -
247B ASN* 3.3 24.1 + - - +
358B LEU* 3.8 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLU 3.1 15.9 + - - +
241B LEU* 3.3 9.0 - - + +
242B ILE 3.1 0.4 - - - -
243B LYS* 1.3 83.5 - - - +
245B ILE* 1.3 62.5 + - + +
246B CYS 3.3 0.2 + - - -
247B ASN* 3.4 18.5 + - + +
250B ALA* 5.4 2.4 - - - +
432B MET* 3.7 27.6 - - + +
482B THR* 4.0 29.4 - - + +
484B LEU* 4.9 9.2 - - + -
574B LYS* 4.4 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 3.0 26.5 + - + +
242B ILE* 3.6 23.6 - - + +
244B LEU* 1.3 77.1 - - + +
246B CYS* 1.3 63.8 - - - +
247B ASN 3.4 0.7 + - - +
251B MET* 3.4 20.8 - - - +
365B LEU* 4.4 6.3 - - + -
432B MET* 4.0 19.2 - - + +
433B SER 5.5 0.3 - - - +
435B TRP* 3.9 13.9 - - + -
436B VAL* 3.5 28.0 + - + +
439B LEU* 3.9 26.5 - - + -
484B LEU* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 2.9 37.1 + - - +
243B LYS* 4.0 3.1 - - - +
245B ILE* 1.3 81.6 - - - +
247B ASN* 1.3 56.9 + - - +
248B VAL* 3.0 20.4 + - - +
251B MET* 4.4 4.2 - - - +
346B LEU* 5.0 2.9 - - - -
347B VAL* 3.8 24.8 - - + +
358B LEU* 6.0 0.2 - - + -
361B HIS* 3.9 26.0 - - + -
365B LEU* 5.9 2.0 - - - -
436B VAL* 4.0 17.0 - - - -
----------------------------------------------------------
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