Contacts of the helix formed by residues 365 - 372 (chain A) in PDB entry 1RY2
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 TRP 365 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PHE* 3.9 14.8 - + + -
318A LEU* 4.1 4.3 - - - -
360A ALA 5.4 2.0 - - - -
361A GLY* 3.9 9.7 - - - -
362A ASP* 3.3 28.6 + - - +
363A ILE 3.3 0.2 - - - -
364A GLY* 1.3 79.3 - - - +
366A ILE* 1.3 67.0 + - + +
367A THR* 2.7 37.4 + - + -
368A GLY* 2.7 28.6 + - - -
369A HIS* 3.1 13.4 + - - -
413A ALA* 4.8 9.6 - - + -
442A VAL* 4.6 8.3 - - + -
443A GLY* 4.1 28.7 - - - -
472A THR* 5.4 1.3 - - - +
673A SER* 3.9 45.3 - - - +
720A AMP 3.8 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A PHE* 5.0 3.1 - - + -
318A LEU* 3.3 16.1 - - + +
332A HIS* 4.5 8.7 - - + +
337A TYR* 5.2 0.2 - - + -
365A TRP* 1.3 87.2 - - + +
367A THR* 1.3 72.9 + - - +
368A GLY 3.2 0.2 - - - -
369A HIS* 3.5 8.3 - - + -
370A THR* 2.7 40.6 + - - +
470A TRP* 3.6 21.5 - - + -
471A GLN 4.2 1.3 - - - +
472A THR* 3.1 59.9 - - + +
475A GLY* 4.7 3.4 - - - +
720A AMP 3.2 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A THR* 3.5 25.2 - - + +
360A ALA 5.6 0.7 - - - -
361A GLY* 4.7 4.9 - - - -
365A TRP* 2.7 52.4 + - + +
366A ILE* 1.3 79.7 - - - +
368A GLY* 1.3 55.4 + - - +
371A TYR* 2.7 35.2 + - - +
372A VAL 3.6 0.5 + - - -
411A TYR* 4.4 13.0 - - + -
442A VAL* 4.0 12.4 - - + +
470A TRP* 3.8 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A GLY 3.8 4.7 + - - -
362A ASP 3.4 21.2 + - - -
363A ILE* 3.8 5.8 - - - -
365A TRP 2.7 11.3 + - - -
367A THR* 1.3 73.8 - - - +
369A HIS* 1.3 64.5 + - - +
372A VAL* 2.7 42.3 + - - +
373A VAL* 3.3 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A HIS* 4.1 13.2 - + - -
218A VAL* 3.8 25.6 - - + +
316A PHE* 3.7 30.2 - + + -
317A LEU 4.6 1.8 - - - -
318A LEU* 3.7 28.4 - - + +
337A TYR* 3.4 14.4 - - + +
363A ILE* 2.9 40.1 + - + -
365A TRP 3.1 16.9 + - - -
366A ILE* 3.1 9.9 + - - +
368A GLY* 1.3 79.7 - - - +
370A THR* 1.3 58.7 + - - +
373A VAL* 3.4 1.5 - - - +
374A TYR* 2.8 38.7 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A TYR* 2.4 23.4 + - + +
341A ALA* 3.5 27.4 - - + +
366A ILE* 2.7 20.4 + - - +
369A HIS* 1.3 74.4 - - - +
371A TYR* 1.3 88.5 + - + +
374A TYR* 4.2 2.5 - - - -
375A GLY* 2.8 22.9 + - - -
470A TRP* 3.8 1.3 - - - -
475A GLY 2.9 28.0 + - - +
476A SER* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ALA 4.7 0.9 - - - -
344A THR* 3.2 26.9 + - - -
345A MET* 3.9 20.0 - - - -
349A PHE* 4.1 13.7 - + - -
357A PHE* 3.9 8.6 - - + -
359A THR* 2.4 32.7 + - + +
367A THR 2.7 18.5 + - - +
370A THR* 1.3 90.6 - - + +
372A VAL* 1.3 55.9 + - - +
373A VAL 3.5 1.8 - - - -
376A PRO* 3.5 15.9 - - - +
383A THR* 4.5 1.0 + - - -
411A TYR* 3.6 22.2 - + + -
470A TRP* 3.2 36.3 - + - -
476A SER* 3.6 6.1 - - - -
477A HIS* 3.1 46.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A MET* 3.7 29.2 - - + -
203A ILE* 4.5 6.6 - - + +
359A THR* 3.5 32.1 - - - +
361A GLY 4.3 1.1 - - - +
363A ILE* 4.7 1.6 - - + -
367A THR 3.6 1.0 + - - -
368A GLY* 2.7 38.0 + - - +
371A TYR* 1.3 77.6 - - - +
373A VAL* 1.3 68.3 + - + +
376A PRO* 3.9 0.2 - - - -
383A THR* 3.5 23.3 + - - +
384A LEU 3.7 20.6 - - - +
385A VAL* 5.3 4.3 - - + +
----------------------------------------------------------
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