Contacts of the helix formed by residues 355 - 366 (chain B) in PDB entry 4CEJ
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 355 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A ARG* 6.0 0.4 - - - -
320B ARG* 3.5 35.0 + - + -
323B GLU* 2.4 38.5 + - - -
324B LEU* 3.9 21.0 - - + +
349B ALA* 4.2 16.4 - - + -
351B GLN 4.3 2.2 - - - -
352B PRO* 2.7 15.5 + - + +
354B ASP* 1.3 91.3 - - + +
356B LYS* 1.3 63.5 + - - +
357B ASP 3.4 2.7 - - - -
358B MET* 3.0 10.9 + - + +
359B VAL* 2.9 31.9 + - + +
607B LEU* 4.0 25.6 - - + -
608B GLY* 3.4 19.2 - - - -
670B PRO* 3.6 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A ARG* 6.0 0.2 - - - +
352B PRO* 2.9 20.4 + - + +
353B GLU* 2.4 52.3 + - - +
354B ASP 4.0 0.2 - - - -
355B TYR* 1.3 71.9 - - - +
357B ASP* 1.3 87.2 + - - +
359B VAL* 3.0 18.8 + - - +
360B LYS* 3.1 23.6 + - - +
372B ILE* 4.4 21.6 - - + +
375B LYS 5.8 2.2 + - - -
590B VAL* 5.9 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A SER* 5.9 2.5 - - - +
744A TYR* 4.0 6.9 + - - +
748A ARG* 2.8 47.5 + - - +
355B TYR 3.4 1.0 - - - -
356B LYS* 1.3 93.3 - - - +
358B MET* 1.3 60.0 + - - +
360B LYS* 3.6 14.5 + - - +
361B GLU* 3.5 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A TRP* 4.3 11.0 - - + -
744A TYR* 3.7 26.9 - - + -
745A ASP* 3.5 26.2 - - - +
748A ARG* 4.9 11.4 - - - +
320B ARG* 4.4 9.6 - - + -
321B ARG* 3.7 39.5 - - + +
324B LEU* 3.6 14.4 - - + -
354B ASP 5.4 4.0 - - - +
355B TYR* 3.0 11.8 + - - +
357B ASP* 1.3 77.3 - - - +
359B VAL* 1.3 65.1 + - - +
361B GLU* 3.4 3.5 + - - +
362B VAL* 3.0 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU* 3.6 25.8 - - + -
347B ILE* 5.8 3.6 - - + -
355B TYR* 2.9 31.3 + - + +
356B LYS* 3.0 10.5 + - - +
358B MET* 1.3 77.4 - - - +
360B LYS* 1.3 62.8 + - - +
362B VAL* 4.7 1.8 - - - -
363B PHE* 2.9 54.9 + - + +
370B TYR* 5.0 2.9 - - + -
372B ILE* 4.9 5.4 - - + -
590B VAL* 4.4 28.7 - - + -
607B LEU* 5.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A GLU* 5.4 7.4 - - - +
356B LYS* 3.1 18.4 + - - +
357B ASP* 3.7 17.4 + - - +
359B VAL* 1.3 80.0 - - - +
361B GLU* 1.3 69.1 + - - +
363B PHE 4.0 0.7 - - - -
364B ALA* 3.1 27.4 + - - +
370B TYR* 3.4 33.5 + - - +
372B ILE* 3.9 27.8 - - + +
376B ALA* 4.8 16.0 - - - +
581B ILE* 6.1 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A GLU* 4.4 27.4 - - + +
715A TRP* 3.5 48.5 - - + +
716A GLU* 5.3 0.9 + - - +
719A ARG* 2.5 31.7 + - - -
744A TYR* 4.2 6.1 - - + +
357B ASP 3.5 14.7 + - - +
358B MET 3.4 3.7 + - - +
359B VAL 3.3 0.4 - - - -
360B LYS* 1.3 87.0 - - - +
362B VAL* 1.3 65.3 + - - +
364B ALA* 3.2 6.3 - - - +
365B ASP* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A TRP* 4.0 21.1 - - + -
321B ARG* 4.2 2.7 - - - -
324B LEU* 4.0 22.0 - - + +
325B GLU* 4.0 33.2 - - + +
328B ALA* 4.2 0.9 - - + -
358B MET* 3.0 27.8 + - + +
359B VAL* 4.0 2.0 - - - +
361B GLU* 1.3 76.1 - - - +
363B PHE* 1.3 70.6 + - + +
364B ALA 3.0 0.2 - - - -
365B ASP* 2.8 7.9 + - - -
366B TYR* 2.8 44.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU* 4.2 15.5 - - + -
328B ALA* 4.1 12.3 - - + -
331B ILE* 3.9 11.2 - - + -
347B ILE* 3.4 33.4 - - + -
359B VAL* 2.9 38.3 + - + +
362B VAL* 1.3 84.5 - - + +
364B ALA* 1.3 60.2 + - - +
366B TYR* 3.8 2.9 - - - +
367B GLU* 3.1 2.3 + - - -
368B ILE* 2.8 72.8 + - + +
370B TYR* 3.8 23.3 - - + -
588B VAL* 4.2 16.8 - - + -
590B VAL* 5.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A ARG* 3.8 22.7 - - - +
360B LYS 3.1 21.6 + - - +
361B GLU* 3.2 10.5 - - - +
362B VAL 3.0 0.4 - - - -
363B PHE* 1.3 77.9 - - - +
365B ASP* 1.3 61.2 + - - +
367B GLU* 3.5 14.3 + - - +
370B TYR* 4.9 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A TRP* 3.0 28.5 + - - -
719A ARG* 3.4 33.6 + - - +
321B ARG* 5.5 0.9 + - - -
361B GLU 3.1 8.3 + - - +
362B VAL* 2.8 8.7 + - - +
364B ALA* 1.3 80.0 - - - +
366B TYR* 1.3 65.4 + - + +
367B GLU* 3.3 3.0 + - - +
718B ASN* 3.0 19.6 + - - +
720B SER* 5.5 4.1 - - - -
721B VAL* 3.8 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLU* 2.7 49.7 + - + +
328B ALA* 3.6 14.1 - - + -
329B ARG* 3.9 21.3 + - + -
332B HIS* 3.2 21.8 - - - -
362B VAL* 2.8 27.9 + - + +
363B PHE* 3.7 0.4 + - - -
364B ALA 3.3 0.2 - - - -
365B ASP* 1.3 84.1 - - + +
367B GLU* 1.3 70.4 + - - +
368B ILE* 3.2 21.5 - - + +
717B VAL* 3.4 35.2 - - + -
718B ASN* 3.9 5.4 - - - +
721B VAL* 3.9 15.4 - - + +
725B PHE* 3.4 20.4 - - - -
----------------------------------------------------------
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