Contacts of the helix formed by residues 364 - 374 (chain A) in PDB entry 1YY9
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 364 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ALA* 5.2 0.8 - - - +
362A PRO 3.6 4.8 + - - -
363A LEU* 1.3 73.4 - - - +
365A PRO* 1.3 66.5 - - - +
366A GLN* 3.1 28.0 + - - +
367A GLU* 2.7 44.6 + - + +
368A LEU 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 4.1 18.6 - - + -
363A LEU* 3.0 12.5 - - + +
364A ASP* 1.3 89.4 - - - +
366A GLN* 1.3 63.5 + - - +
368A LEU* 2.9 31.5 + - + +
387A PRO* 3.8 32.3 - - + +
394A HIS* 5.1 3.3 + - - -
3891A NAG 6.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ASP* 3.1 22.2 + - - +
365A PRO* 1.3 76.6 - - - +
367A GLU* 1.3 63.1 + - + +
368A LEU 3.0 1.6 + - - -
369A ASP* 2.9 54.5 + - - +
390A ARG* 5.5 3.2 - - - +
394A HIS* 6.1 0.4 + - - -
3891A NAG 4.9 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ALA* 4.6 6.6 - - - +
332A ILE* 3.5 21.3 - - + +
333A LYS* 5.7 2.6 + - - +
363A LEU* 4.3 13.2 - - + +
364A ASP* 2.7 37.4 + - + +
366A GLN* 1.3 74.5 - - + +
368A LEU* 1.3 62.3 + - - +
369A ASP* 3.0 0.9 - - - -
370A ILE* 3.0 50.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ILE* 4.7 5.4 - - + -
332A ILE* 4.1 13.2 - - + -
347A ILE* 4.8 15.5 - - + -
352A PHE* 4.3 12.6 - - + -
363A LEU* 4.3 15.0 - - + -
365A PRO* 2.9 21.1 + - + +
367A GLU* 1.3 78.7 - - - +
369A ASP* 1.3 61.3 + - - +
370A ILE 3.0 0.4 - - - -
371A LEU* 3.0 33.8 + - + +
386A TRP* 4.2 16.6 - - + -
387A PRO* 3.9 28.7 - - + -
394A HIS* 4.5 7.2 - - + +
395A ALA* 3.1 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A GLN* 2.9 44.6 + - - +
367A GLU* 3.0 1.2 - - - -
368A LEU* 1.3 75.9 - - - +
370A ILE* 1.3 61.2 + - - +
372A LYS* 3.0 57.3 + - + +
390A ARG* 4.3 3.5 + - - -
394A HIS* 3.7 15.1 + - - -
395A ALA* 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 4.0 23.6 - - + +
333A LYS* 4.8 7.0 - - + -
335A PHE* 3.8 40.9 - - + +
336A LYS* 4.0 30.7 - - + +
337A ASN 4.9 1.9 + - - -
367A GLU* 3.0 49.8 + - + +
369A ASP* 1.3 76.5 - - - +
371A LEU* 1.3 60.5 + - + +
372A LYS 3.2 1.7 + - - -
373A THR* 3.4 17.5 + - - +
374A VAL* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ILE* 4.0 30.5 - - + -
332A ILE* 4.5 7.6 - - + -
335A PHE* 4.2 28.0 - - + -
345A LEU* 4.7 7.6 - - + -
347A ILE* 4.8 1.8 - - + -
368A LEU* 3.0 39.8 + - + +
370A ILE* 1.3 72.3 - - + +
372A LYS* 1.3 58.1 + - - +
373A THR 3.1 3.4 - - - -
374A VAL* 2.9 40.7 + - + +
395A ALA* 3.2 18.8 - - + +
396A PHE* 4.2 24.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
368A LEU 4.3 0.2 + - - -
369A ASP* 3.0 50.3 + - + +
370A ILE 3.2 0.4 - - - -
371A LEU* 1.3 75.7 - - - +
373A THR* 1.3 60.8 + - + +
374A VAL 3.2 2.0 + - - -
390A ARG* 4.6 5.1 - - - +
394A HIS* 3.9 24.0 - - - +
395A ALA* 3.3 17.0 + - - +
396A PHE* 5.6 0.2 - - - +
397A GLU* 3.0 29.4 - - + +
398A ASN* 2.8 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PRO* 4.0 28.0 - - + +
335A PHE 4.7 0.2 + - - -
336A LYS* 6.4 0.2 - - + -
337A ASN* 3.8 18.8 - - - +
338A CYS 2.8 31.7 + - - +
339A THR* 3.5 16.2 + - - -
370A ILE 3.4 16.2 + - - +
371A LEU 4.4 0.2 - - - -
372A LYS* 1.3 77.9 - - + +
374A VAL* 1.3 61.8 + - - +
375A LYS* 3.5 12.7 + - - +
398A ASN* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A PHE* 5.5 1.8 - - + +
338A CYS* 3.7 18.6 - - + +
339A THR 3.5 5.2 - - - +
341A ILE* 3.8 34.1 - - + -
345A LEU* 5.1 1.6 - - + -
370A ILE 5.1 0.2 - - - +
371A LEU* 2.9 37.0 + - + +
372A LYS 3.2 1.1 - - - +
373A THR* 1.3 78.0 - - - +
375A LYS* 1.3 62.9 + - - +
376A GLU 3.8 17.3 - - - +
377A ILE* 4.1 12.3 - - + -
396A PHE* 5.1 7.4 - - + -
398A ASN* 3.3 21.3 + - - +
399A LEU* 3.4 10.4 + - + +
----------------------------------------------------------
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