Contacts of the helix formed by residues 359 - 374 (chain A) in PDB entry 2YHS
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 359 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A THR* 4.2 0.9 - - - -
332A PHE* 5.6 1.3 - - - -
354A GLN* 4.8 1.2 + - - -
358A ALA* 1.3 73.7 - - - +
360A SER* 1.3 65.2 + - - +
361A ALA* 3.0 30.5 + - - +
362A SER* 3.0 31.0 + - - +
363A VAL* 3.1 14.2 + - - +
399A LYS* 3.1 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLY* 3.4 21.3 - - - -
331A THR* 3.7 17.6 + - - -
332A PHE* 5.9 0.2 - - - -
358A ALA 3.4 4.6 + - - -
359A ASP* 1.3 72.4 + - - +
361A ALA* 1.3 61.1 + - - +
363A VAL* 3.3 2.1 + - - +
364A ILE* 3.0 28.4 + - - +
396A GLU* 2.7 30.9 + - - -
399A LYS* 2.8 22.5 + - - -
400A ILE* 3.6 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ASP* 3.0 14.6 + - - +
360A SER* 1.3 82.5 + - - +
362A SER* 1.3 56.1 + - - +
364A ILE* 3.4 3.3 + - - +
365A PHE* 2.8 29.8 + - - +
399A LYS* 3.5 22.7 - - + +
400A ILE* 4.3 10.3 - - - +
403A VAL* 3.5 36.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A GLN* 4.0 13.9 - - - -
359A ASP* 3.0 28.5 + - - +
361A ALA* 1.3 74.8 - - - +
363A VAL* 1.3 66.0 + - - +
365A PHE* 3.7 6.1 - - - +
366A ASP* 2.9 31.1 + - - +
403A VAL* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ALA* 4.7 2.9 - - + -
328A ALA 3.8 20.9 - - - +
329A GLY* 4.6 2.2 - - - -
331A THR* 3.6 21.1 - - + -
352A ILE* 3.7 30.2 - - + +
353A ALA* 4.4 2.2 - - - -
354A GLN* 3.6 41.5 - - + +
358A ALA* 4.3 0.7 - - + -
359A ASP 3.1 12.9 + - - +
360A SER 3.7 6.3 - - - +
362A SER* 1.3 75.5 - - - +
364A ILE* 1.3 60.0 + - + +
366A ASP* 3.4 2.3 + - - +
367A ALA* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 4.3 3.1 - - + -
327A ALA* 4.2 8.7 - - + -
329A GLY* 4.5 9.2 - - - -
360A SER 3.0 20.1 + - - +
361A ALA 3.9 2.9 - - - +
363A VAL* 1.3 76.8 - - + +
365A PHE* 1.3 65.5 + - - +
367A ALA* 3.2 6.2 + - + +
368A ILE* 3.0 26.2 + - + +
379A LEU* 5.4 0.7 - - + -
381A ALA* 4.1 20.4 - - + -
382A ASP 4.1 17.5 - - - +
400A ILE* 3.6 36.3 - - + +
403A VAL* 6.3 0.7 - - + -
404A MET* 3.4 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ALA 2.8 19.1 + - - +
362A SER* 3.7 7.6 - - - +
364A ILE* 1.3 75.8 - - - +
366A ASP* 1.3 75.7 + - - +
368A ILE* 3.2 4.5 + - - -
369A GLN* 3.1 45.9 + - + +
403A VAL* 3.6 28.9 - - + +
404A MET* 6.0 0.2 - - - +
406A LYS* 4.2 18.6 - - + -
407A LEU* 3.5 43.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ILE* 4.4 10.7 - - + +
354A GLN* 2.9 24.9 + - - +
362A SER* 2.9 20.0 + - - +
363A VAL 3.6 4.0 - - - +
365A PHE* 1.3 89.6 - - - +
367A ALA* 1.3 57.9 + - - +
369A GLN* 3.4 7.6 + - - +
370A ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A MET* 3.7 4.2 - - - +
327A ALA* 3.5 28.9 - - + -
352A ILE* 3.8 23.3 - - + +
363A VAL 2.9 17.2 + - - +
364A ILE 3.5 5.6 - - - +
365A PHE 3.2 0.4 - - - -
366A ASP* 1.3 74.3 - - - +
368A ILE* 1.3 60.1 + - - +
370A ALA 3.3 0.2 + - - -
371A ALA* 2.8 31.4 + - - +
379A LEU* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PRO* 4.7 5.8 - - + -
295A VAL* 4.3 7.6 - - + -
364A ILE* 3.0 20.1 + - + +
365A PHE* 3.2 6.3 + - - +
367A ALA* 1.3 75.4 - - - +
369A GLN* 1.3 57.7 + - - +
371A ALA* 3.3 4.1 + - - +
372A LYS* 2.9 55.1 + - + +
379A LEU* 3.6 21.3 - - + -
404A MET* 3.6 48.9 - - + +
407A LEU* 3.7 19.7 - - + -
408A ASP* 5.3 3.4 - - + -
411A ALA* 4.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PHE* 3.1 34.9 + - + +
366A ASP* 3.6 11.0 - - - +
368A ILE* 1.3 78.4 - - - +
370A ALA* 1.3 61.2 + - - +
372A LYS* 3.4 15.9 + - - +
373A ALA* 3.0 24.5 + - - +
407A LEU* 3.6 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A MET* 4.0 8.7 - - + -
352A ILE* 3.8 25.1 - - + -
366A ASP 2.9 18.7 + - - +
367A ALA 3.7 3.8 - - - +
369A GLN* 1.3 76.5 - - - +
371A ALA* 1.3 63.2 + - - +
373A ALA* 3.3 6.1 + - - +
374A ARG* 3.0 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PRO* 3.5 28.9 - - + -
325A MET* 3.7 14.5 - - - -
367A ALA 2.8 17.6 + - - +
368A ILE* 3.6 2.9 - - - +
370A ALA* 1.3 77.4 - - - +
372A LYS* 1.3 60.3 + - - +
374A ARG 3.3 0.5 + - - -
375A ASN* 3.2 3.5 + - - -
376A ILE* 3.0 45.9 + - + +
379A LEU* 4.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ALA* 2.9 37.3 + - - +
293A PRO* 3.7 4.6 - - + +
368A ILE* 2.9 40.0 + - + +
369A GLN* 3.7 16.4 - - - +
371A ALA* 1.3 77.3 - - - +
373A ALA* 1.3 62.8 + - - +
374A ARG 3.2 0.7 + - - -
375A ASN* 3.3 18.1 + - - +
407A LEU* 4.7 11.2 + - + -
408A ASP* 3.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A GLN 3.0 17.0 + - - +
370A ALA* 3.7 8.1 - - - +
372A LYS* 1.3 76.7 - - - +
374A ARG* 1.3 62.2 + - + +
375A ASN* 3.5 5.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A MET* 4.0 16.5 - - - +
350A PRO* 3.5 29.3 - - - +
352A ILE* 4.3 17.0 - - - +
370A ALA* 3.0 23.9 + - - +
372A LYS 3.1 0.2 - - - -
373A ALA* 1.3 82.6 - - + +
375A ASN* 1.3 73.8 + - - +
376A ILE* 3.2 19.1 + - + +
----------------------------------------------------------
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