Contacts of the helix formed by residues 367 - 376 (chain B) in PDB entry 2YTZ
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 PRO 367 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B TYR* 3.7 20.4 - - + +
365B SER 4.3 1.6 - - - +
366B ALA* 1.3 89.8 - - + +
368B TYR* 1.3 68.2 + - - +
369B GLU* 4.4 5.6 - - + +
370B VAL* 2.8 35.4 + - + +
371B PHE* 3.0 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR* 2.6 49.0 + - + +
257B GLY 4.0 2.2 - - - -
258B LYS* 3.9 44.4 - - + -
322B TYR* 3.5 43.8 + + - +
327B ILE* 4.4 4.3 - - + +
367B PRO* 1.3 70.7 - - - +
369B GLU* 1.3 86.8 + - + +
371B PHE* 3.0 14.4 + - + +
372B ILE* 3.0 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LYS* 5.5 1.9 - - - +
367B PRO* 3.2 5.9 - - + +
368B TYR* 1.3 102.9 - - + +
370B VAL* 1.3 63.0 + - + +
372B ILE* 3.7 9.4 + - - +
373B GLU* 3.3 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 4.2 8.7 - - + -
348B GLN* 3.8 21.5 - - - +
350B TYR* 4.1 23.8 - - + +
366B ALA* 4.1 9.0 - - + -
367B PRO* 2.8 38.7 + - + +
369B GLU* 1.3 74.9 - - + +
371B PHE* 1.3 63.9 + - - +
373B GLU* 3.4 11.3 + - + +
374B THR* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B TYR* 3.4 54.5 - + + -
324B THR* 3.7 25.4 - - - -
327B ILE* 3.9 12.3 - - + -
341B ILE* 3.9 18.4 - - + -
345B LEU* 3.8 28.2 - - + +
362B ILE* 4.1 13.7 - - + -
364B THR* 4.4 4.7 - - + -
366B ALA* 5.1 0.9 - - + +
367B PRO 3.0 10.9 + - - +
368B TYR* 3.0 9.8 + + - +
370B VAL* 1.3 78.4 - - - +
372B ILE* 1.3 74.4 - - + +
374B THR* 3.0 11.8 + - - -
375B ILE* 3.1 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ILE* 3.4 33.7 - - + -
368B TYR* 3.0 50.1 + - + +
369B GLU* 4.0 11.4 - - - +
370B VAL 3.4 0.2 - - - -
371B PHE* 1.3 83.5 - - + +
373B GLU* 1.3 63.2 + - - +
374B THR 3.2 0.7 + - - -
375B ILE* 3.2 19.4 - - + +
376B LYS* 3.2 44.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLN* 5.2 5.2 - - - +
369B GLU 3.3 17.2 + - - +
370B VAL* 3.7 11.0 - - - +
371B PHE 3.3 0.2 - - - -
372B ILE* 1.3 80.5 - - - +
374B THR* 1.3 60.1 + - - +
376B LYS* 4.0 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LYS* 3.1 24.3 + - - +
341B ILE* 4.0 22.3 - - + +
344B ALA* 3.4 32.5 - - + -
345B LEU* 3.8 8.1 - - + +
348B GLN* 2.8 24.5 + - - +
370B VAL 2.8 17.2 + - - -
371B PHE 3.0 10.1 + - - -
373B GLU* 1.3 79.8 - - - +
375B ILE* 1.3 60.1 + - - +
376B LYS 3.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B THR* 4.2 9.6 - - + +
327B ILE* 3.9 29.4 - - + +
328B GLY* 4.7 7.6 - - - +
334B GLU 3.7 21.1 - - - +
335B THR* 4.0 0.5 - - - -
336B LYS* 3.2 23.5 + - - +
341B ILE* 3.7 30.1 - - + -
371B PHE* 3.1 35.0 + - + +
372B ILE* 3.2 21.8 - - + +
374B THR* 1.3 75.0 - - - +
376B LYS* 1.3 77.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLU* 4.6 19.3 - - - +
335B THR 5.9 0.2 - - - -
336B LYS* 3.2 22.7 - - - +
372B ILE* 3.2 38.4 - - - +
373B GLU* 4.0 16.1 - - + +
374B THR 3.4 1.7 - - - +
375B ILE* 1.3 91.3 - - + +
----------------------------------------------------------
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