Contacts of the helix formed by residues 361 - 373 (chain B) in PDB entry 2A79
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 ILE 361 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B SER* 3.9 16.4 - - - +
344B SER* 5.4 2.7 - - - -
347B TYR* 3.6 47.1 - - + +
360B SER* 1.3 74.1 - - - +
362B PRO* 1.3 70.6 - - + +
363B ASP 3.0 2.2 - - - -
364B ALA* 2.6 31.8 + - - +
365B PHE* 3.0 29.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B SER* 3.7 13.7 - - - +
361B ILE* 1.3 98.7 - - + +
363B ASP* 1.3 58.8 + - - +
365B PHE* 3.2 28.2 - - + +
366B TRP* 3.8 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B GLN 5.3 8.7 - - - +
358B PHE* 6.0 2.7 - - - -
359B PRO* 5.9 3.5 - - + +
360B SER* 2.6 27.9 + - - +
361B ILE 3.0 0.8 - - - -
362B PRO* 1.3 76.0 - - - +
364B ALA* 1.3 64.0 + - - +
365B PHE 3.1 2.1 + - - -
366B TRP* 3.3 17.6 + - - +
367B TRP* 3.4 12.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
343B SER* 2.8 45.5 + - - +
346B VAL* 6.1 2.0 - - + -
347B TYR* 4.9 5.8 - - + +
358B PHE* 5.9 8.3 - - + +
360B SER 3.9 6.8 + - - +
361B ILE* 2.6 25.2 + - - +
363B ASP* 1.3 74.2 - - - +
365B PHE* 1.3 56.4 + - - -
367B TRP* 3.6 12.4 + - + +
368B ALA* 3.1 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B PHE* 5.4 9.0 - + - -
339B VAL* 3.8 11.0 - - + -
340B ILE* 3.4 38.6 - - + -
343B SER* 3.3 17.9 - - - -
361B ILE* 3.0 44.5 + - + -
362B PRO* 3.2 15.9 - - + +
364B ALA* 1.3 75.9 - - - +
366B TRP* 1.3 65.8 + - - +
368B ALA* 3.4 2.3 + - - +
369B VAL* 3.0 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B PRO 3.8 4.0 + - - +
363B ASP* 3.3 14.2 + - - +
365B PHE* 1.3 75.5 - - - +
367B TRP* 1.3 68.3 + - - +
369B VAL* 3.2 15.9 + - + +
370B VAL* 2.8 44.0 + - + +
377B TYR* 3.7 29.9 - + - -
379B ASP* 2.8 34.3 + - - -
380B MET* 5.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B PHE* 4.1 11.0 - - + -
343B SER* 5.1 1.1 - - - -
346B VAL* 3.6 35.0 - - + -
363B ASP 3.4 9.1 + - - +
364B ALA* 3.7 16.8 - - + +
365B PHE 3.3 0.2 - - - -
366B TRP* 1.3 82.1 - - - +
368B ALA* 1.3 75.1 + - + +
370B VAL* 2.9 10.7 + - + +
371B SER* 2.6 53.5 + - - -
380B MET* 3.4 38.5 + - + -
382B PRO* 3.6 29.4 - - + +
391B GLY* 4.0 19.1 - - - -
394B CYS* 4.0 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B VAL* 3.5 23.3 - - + +
342B PHE* 4.5 7.2 - - + -
343B SER* 3.2 26.0 - - - +
364B ALA 3.1 4.8 + - - +
367B TRP* 1.3 90.1 - - + +
369B VAL* 1.3 57.7 + - - +
371B SER* 2.9 10.6 + - - -
372B MET* 2.8 36.8 + - + +
394B CYS* 4.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 4.7 13.7 - - + -
339B VAL* 3.7 24.0 - - + -
365B PHE* 3.0 21.5 + - + +
366B TRP* 3.7 16.6 - - + +
368B ALA* 1.3 75.5 - - - +
370B VAL* 1.3 62.4 + - + +
372B MET* 4.9 2.5 - - - -
373B THR* 2.9 34.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
366B TRP* 2.8 66.0 + - + +
367B TRP* 3.3 7.2 - - + +
369B VAL* 1.3 79.4 - - + +
371B SER* 1.3 59.3 + - - +
373B THR* 4.0 5.2 - - - -
374B THR 3.9 0.3 - - - -
375B VAL* 3.2 13.3 + - + -
376B GLY* 3.0 43.0 + - - +
377B TYR* 3.6 21.8 - - + +
379B ASP* 4.9 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B TRP* 2.6 38.4 + - - -
368B ALA* 2.9 20.8 + - - -
370B VAL* 1.3 76.0 - - - +
372B MET* 1.3 61.6 + - - +
374B THR* 3.6 12.0 + - - +
376B GLY* 5.7 1.1 - - - -
391B GLY 5.7 1.1 - - - -
394B CYS* 3.1 25.5 - - - -
395B ALA* 4.1 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PHE 5.3 2.0 - - - +
335B LEU* 4.2 13.7 - - + +
338B GLY* 3.8 13.9 - - - -
339B VAL* 3.8 33.7 - - - -
342B PHE* 3.6 30.3 - - + -
368B ALA 2.8 16.7 + - - +
369B VAL* 4.7 2.9 - - - +
371B SER* 1.3 75.5 - - - +
373B THR* 1.3 59.3 + - + +
374B THR* 3.0 13.8 + - - +
394B CYS* 3.7 16.6 - - - -
395B ALA* 5.3 0.4 - - - +
397B ALA* 4.3 5.4 - - + +
398B GLY* 3.6 37.1 - - - +
399B VAL 4.0 0.2 + - - -
401B THR* 4.8 8.5 - - - +
402B ILE* 3.0 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 5.2 12.3 - - + -
369B VAL* 2.9 29.9 + - + +
370B VAL* 4.0 1.0 - - - -
372B MET* 1.3 77.2 - - + +
374B THR* 1.3 74.4 + - - +
375B VAL* 3.2 28.9 + - - +
402B ILE* 3.7 15.6 - - + +
----------------------------------------------------------
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