Contacts of the helix formed by residues 329 - 341 (chain A) in PDB entry 5PHY
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 GLN 329 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A MET* 3.1 21.2 - - + +
304A GLY 3.3 9.9 + - - +
305A LYS 3.2 23.2 + - - +
307A ALA 2.8 26.8 + - - +
309A GLN* 2.6 31.9 + - - +
325A VAL* 2.8 25.3 + - + +
328A LEU* 1.3 79.2 - - - +
330A PRO* 1.4 64.3 - - - +
331A GLU 3.2 2.9 - - - -
332A ARG* 2.9 35.5 + - + +
333A TYR* 3.2 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A VAL 3.6 0.2 - - - -
326A ARG 3.8 16.2 - - - +
327A ILE 3.5 12.1 - - - +
328A LEU 3.4 8.5 - - - +
329A GLN* 1.4 87.2 - - - +
331A GLU* 1.3 62.8 + - - +
333A TYR* 3.3 17.8 + - + +
334A ASP* 4.6 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLN 3.1 1.2 + - - -
330A PRO* 1.3 81.1 - - - +
332A ARG* 1.3 82.4 + - + +
333A TYR 3.6 0.2 + - - -
334A ASP* 4.7 4.3 + - - +
335A LEU* 5.3 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LYS 5.0 1.6 + - - -
306A MET* 4.1 6.9 + - - +
307A ALA 3.0 30.1 + - - -
308A SER* 3.9 11.8 + - - +
309A GLN* 4.7 11.8 - - + +
325A VAL* 4.6 4.7 - - + -
329A GLN* 2.9 33.6 + - + +
331A GLU* 1.3 93.5 + - + +
333A TYR* 1.3 63.0 + - - +
334A ASP 3.5 0.9 - - - -
335A LEU* 3.4 10.6 + - - +
336A TRP* 3.1 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ASP* 2.6 44.8 + - - -
325A VAL* 3.9 14.8 - - + -
326A ARG* 3.6 44.6 - - + -
329A GLN 3.2 8.8 + - - +
330A PRO* 3.5 18.2 - - + +
331A GLU 3.3 2.0 - - - -
332A ARG* 1.3 76.1 - - - +
334A ASP* 1.3 74.6 + - - +
336A TRP* 3.3 6.8 + + - +
337A LYS* 2.9 62.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PRO 4.6 2.5 + - - -
331A GLU 4.7 3.7 + - - +
332A ARG 3.5 0.8 - - - -
333A TYR* 1.3 90.1 - - - +
335A LEU* 1.3 63.7 + - - +
337A LYS* 3.3 15.9 + - - +
338A ARG* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A SER* 3.8 27.5 - - - +
331A GLU 5.3 1.7 + - - +
332A ARG* 3.4 10.3 + - - +
333A TYR 3.4 0.6 - - - -
334A ASP* 1.3 79.8 - - - +
336A TRP* 1.3 61.7 + - - +
338A ARG* 3.4 10.9 + - + +
339A GLY 3.3 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLN* 4.0 23.0 + - + -
310A CYS 3.5 21.4 + - - +
311A SER* 3.7 13.0 + - - +
317A VAL* 4.0 6.1 - - + +
318A THR 5.3 0.7 - - - -
319A PHE* 6.3 0.9 - + - -
321A MET* 3.8 31.1 - - + +
322A ASP* 3.6 48.2 - - + -
325A VAL* 3.9 24.2 - - + -
332A ARG* 3.1 18.2 + - + +
333A TYR* 3.8 10.8 - + - +
335A LEU* 1.3 74.6 - - - +
337A LYS* 1.3 74.8 + - + +
339A GLY* 3.0 16.5 + - - -
340A GLN* 3.1 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ASP* 3.8 12.6 - - - +
333A TYR* 2.9 59.4 + - + +
334A ASP* 3.8 13.9 + - - +
336A TRP* 1.3 84.5 - - + +
338A ARG* 1.3 61.0 + - - +
340A GLN* 2.9 24.4 + - + +
341A ASP* 3.0 18.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ASP 3.1 12.9 + - - +
335A LEU* 3.4 17.7 - - + +
337A LYS* 1.3 75.2 - - - +
339A GLY* 1.3 60.7 + - - +
341A ASP* 3.2 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A CYS 5.9 0.7 - - - -
311A SER* 3.4 28.6 + - - -
313A GLY* 3.4 26.1 - - - +
316A ARG* 5.6 2.8 + - - +
335A LEU 3.3 5.1 + - - -
336A TRP 3.0 10.8 + - - -
338A ARG* 1.3 78.1 - - - +
340A GLN* 1.3 63.0 - - - +
341A ASP 3.7 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A CYS 5.3 1.9 - - - +
315A ALA* 6.0 0.5 - - - +
316A ARG* 3.9 14.6 + - - +
317A VAL* 3.3 50.4 + - - +
318A THR 4.5 2.2 + - - -
319A PHE* 5.8 6.4 - - + +
322A ASP* 5.7 1.3 - - - +
336A TRP* 3.1 47.6 + - + +
337A LYS* 2.9 17.1 + - + +
339A GLY* 1.3 79.4 - - - +
341A ASP* 1.3 56.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LYS* 3.0 18.1 + - + +
338A ARG* 3.2 17.1 + - - +
339A GLY 4.6 2.1 - - - +
340A GLN* 1.3 79.7 - - + +
----------------------------------------------------------
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