Contacts of the helix formed by residues 332 - 345 (chain B) in PDB entry 4KIK
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 332 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ASP 3.3 6.4 + - - -
331B GLU* 1.3 74.0 - - - +
333B LEU* 1.4 65.9 + - - +
334B GLN* 3.7 17.9 + - - +
335B SER* 2.7 31.3 + - - -
336B LEU 3.3 6.6 + - - -
364B ASP* 5.4 4.2 + - - -
365B LYS 5.0 1.7 + - - -
366B PRO* 4.4 5.4 - - - -
367B ALA* 3.9 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B SER* 1.4 74.4 + - - +
334B GLN* 1.4 52.2 + - + +
336B LEU* 3.3 13.5 + - + +
337B LYS* 2.8 58.1 + - + +
353B LEU* 5.2 1.8 - - + -
361B LEU* 3.7 42.4 - - + +
362B ILE 4.8 0.2 - - - +
363B PRO* 4.0 33.9 - - + -
364B ASP* 6.3 0.2 - - - -
365B LYS 3.9 13.7 + - - +
367B ALA* 3.8 22.1 - - - +
369B GLN* 3.6 19.5 - - + +
370B CYS* 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B SER* 3.2 13.4 - - - +
333B LEU* 1.4 76.6 - - + +
335B SER* 1.4 55.9 + - - +
337B LYS* 3.4 15.6 + - - +
338B ALA* 3.1 23.2 + - - +
348B GLU* 2.9 36.6 + - - +
363B PRO* 5.9 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLU* 3.6 19.5 - - - +
332B SER* 2.7 36.4 + - - -
334B GLN* 1.4 72.7 - - - +
336B LEU* 1.3 64.7 + - - +
338B ALA* 3.3 9.4 + - - +
339B ARG* 3.2 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B VAL* 4.0 23.3 - - + -
314B ILE* 4.7 2.9 - - + -
325B TYR* 3.8 38.8 - - + -
327B VAL* 4.3 12.8 - - + -
331B GLU* 4.0 7.9 + - - +
332B SER 3.3 1.6 + - - -
333B LEU* 3.3 21.9 + - + +
335B SER* 1.3 73.6 - - - +
337B LYS* 1.4 56.0 + - - +
339B ARG* 3.0 8.5 + - + +
340B ILE* 2.8 51.4 + - + +
353B LEU* 5.8 1.6 - - + -
361B LEU* 5.4 1.8 - - + -
367B ALA* 3.9 30.3 - - + +
370B CYS* 4.5 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 2.8 33.9 + - + +
334B GLN* 3.5 23.1 + - - +
336B LEU* 1.4 74.3 - - + +
338B ALA* 1.3 55.8 + - - +
340B ILE* 3.4 2.5 + - - -
341B GLN* 3.0 14.7 + - - +
348B GLU* 3.2 39.7 + - + +
349B GLU* 5.4 0.6 - - - +
351B GLN* 2.9 53.1 + - - +
353B LEU* 3.7 27.6 - - + -
363B PRO* 6.1 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLN 3.1 9.2 + - - +
335B SER* 3.4 13.5 - - - +
337B LYS* 1.3 75.2 - - - +
339B ARG* 1.4 58.8 + - + +
341B GLN* 3.2 27.8 + - - +
342B GLN* 3.4 16.3 - - - +
348B GLU* 3.4 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B TYR* 3.8 36.6 - - + +
326B PRO* 2.8 50.7 + - - +
327B VAL* 4.5 1.6 - - - +
331B GLU* 3.0 32.6 + - - -
335B SER* 3.2 12.3 + - - +
336B LEU* 3.0 10.8 + - - +
338B ALA* 1.4 75.7 - - + +
340B ILE* 1.4 64.2 + - - +
341B GLN 3.3 0.2 - - - -
342B GLN* 3.4 27.1 + - - +
343B ASP* 3.3 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ILE* 4.0 19.7 - - + -
325B TYR* 3.3 28.3 - - + +
336B LEU* 2.8 38.5 + - + +
337B LYS* 3.4 5.6 + - - +
339B ARG* 1.4 74.2 - - - +
341B GLN* 1.3 53.4 + - - +
343B ASP* 3.1 4.0 + - - +
344B THR* 2.7 45.5 + - + +
351B GLN* 3.8 19.5 - - - +
353B LEU* 4.1 18.8 - - + -
389B LEU* 3.5 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LYS 3.0 12.9 + - - +
338B ALA* 3.2 20.7 + - - +
340B ILE* 1.3 75.0 - - - +
342B GLN* 1.3 59.0 + - - +
344B THR* 4.0 0.7 - - - -
345B GLY* 2.8 32.7 + - - -
346B ILE 3.4 22.9 - - - +
347B PRO* 3.7 8.1 - - + +
348B GLU* 3.3 33.3 + - - +
349B GLU* 5.2 0.3 - - - +
351B GLN* 3.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ALA 3.4 14.8 - - - +
339B ARG* 3.4 23.5 + - - +
340B ILE 3.3 1.0 - - - -
341B GLN* 1.3 78.4 - - + +
343B ASP* 1.3 64.7 + - - +
345B GLY* 4.6 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B HIS* 3.6 30.2 + - + +
325B TYR* 2.7 42.7 + - - +
339B ARG 3.3 6.5 + - - +
340B ILE 3.1 2.0 + - - +
342B GLN* 1.3 79.6 + - - +
344B THR* 1.4 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ASN* 3.9 11.9 - - - +
323B HIS* 3.6 29.4 - - + +
340B ILE* 2.7 33.4 + - + +
341B GLN* 4.0 0.5 + - - -
343B ASP* 1.4 75.4 - - + +
345B GLY* 1.3 62.8 + - - +
346B ILE* 3.2 33.7 + - - +
389B LEU* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLN* 2.8 17.7 + - - -
342B GLN 4.5 1.9 + - - -
343B ASP 3.8 0.4 - - - -
344B THR* 1.3 77.6 - - - +
346B ILE* 1.3 60.2 + - - +
347B PRO* 3.6 7.6 - - - +
----------------------------------------------------------
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