Contacts of the helix formed by residues 363 - 374 (chain A) in PDB entry 1RQG
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 PRO 363 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A VAL 4.4 2.5 - - - +
362A PHE* 1.3 93.0 - - + +
364A ALA* 1.3 65.8 + - - +
365A ASP* 3.2 8.1 - - - +
366A TYR* 3.1 53.6 + - + +
367A LEU* 3.5 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG 3.6 24.7 - - - +
85A ALA* 4.6 6.1 - - - +
86A LYS* 4.3 12.1 - - + +
359A LEU* 4.3 16.8 - - + +
362A PHE 3.7 1.0 + - - -
363A PRO* 1.3 73.2 - - - +
365A ASP* 1.3 57.6 + - - +
367A LEU* 3.3 2.3 + - - +
368A ARG* 2.8 35.6 + - + +
510A ASP* 4.2 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO* 3.2 6.9 - - + +
364A ALA* 1.3 78.5 - - - +
366A TYR* 1.3 65.5 + - + +
368A ARG* 4.4 0.9 - - - +
369A TYR* 2.6 38.3 + - - +
396A LEU* 5.0 0.7 - - + -
508A LEU* 3.1 45.9 - - + +
509A PRO* 3.9 2.6 - - - +
510A ASP* 3.4 30.2 + - - +
511A ALA* 3.3 22.0 + - + +
514A LYS* 3.9 9.7 + - - -
545A PHE* 4.5 3.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A PHE* 4.5 4.7 - + + -
363A PRO* 3.1 41.6 + - + +
365A ASP* 1.3 83.9 - - + +
367A LEU* 1.3 61.4 + - - +
370A TYR* 3.1 28.2 + - - +
388A PHE* 3.7 21.4 - + + -
392A ILE* 3.8 26.3 - - + +
396A LEU* 4.0 21.8 - - + -
545A PHE* 3.4 20.7 - + + +
546A LYS* 2.6 43.8 + - - +
548A VAL* 3.8 22.9 - - + -
552A GLN* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 5.1 2.2 - - + -
22A LEU* 4.2 14.8 - - + -
85A ALA* 6.2 0.2 - - + -
353A ILE* 5.1 4.5 - - + -
355A VAL* 4.2 24.9 - - + -
358A PHE* 3.6 36.3 - - + -
359A LEU* 3.6 32.1 - - + -
363A PRO 3.5 2.6 + - - +
364A ALA 3.3 6.6 + - - +
366A TYR* 1.3 78.1 - - - +
368A ARG* 1.3 66.3 + - + +
370A TYR* 5.0 2.2 - - + -
371A LEU* 3.1 53.3 + - + +
383A PHE* 4.4 12.1 - - + -
388A PHE* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 5.8 5.6 - - + -
27A LEU* 3.8 30.3 - - + +
30A ASP* 2.5 24.0 + - - +
34A ARG* 3.5 5.7 - - - +
85A ALA* 2.9 22.8 + - - +
86A LYS* 2.8 30.6 + - - +
87A ILE* 3.7 10.3 - - + +
364A ALA* 2.8 25.3 + - + +
365A ASP* 3.8 3.8 - - - +
367A LEU* 1.3 78.0 - - + +
369A TYR* 1.3 63.6 + - - +
372A THR* 2.9 31.7 + - - -
506A PRO 3.2 24.5 + - - -
507A PHE* 2.8 26.4 + - - +
508A LEU* 3.9 2.2 - - + -
509A PRO* 3.5 16.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ASP 2.6 23.6 + - - +
366A TYR 3.9 2.2 - - - +
368A ARG* 1.3 72.5 - - - +
370A TYR* 1.3 67.9 + - + +
372A THR* 3.1 5.4 + - - -
373A THR* 2.9 36.7 + - - -
391A ARG* 4.4 9.0 - - + -
392A ILE* 4.0 15.3 - - + -
395A GLU* 2.5 44.6 + - + +
396A LEU* 3.8 27.4 - - + -
456A LEU* 3.6 30.7 - - + +
460A MET* 3.4 38.4 - - + +
508A LEU* 3.6 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A TYR 3.1 15.1 + - - +
367A LEU* 4.5 2.2 - - + +
369A TYR* 1.3 82.2 - - + +
371A LEU* 1.3 63.5 + - + +
373A THR* 2.8 32.8 + - + -
374A ILE* 3.1 29.2 + - + +
382A ASP 3.7 1.7 + - - -
383A PHE* 3.3 44.5 - + - -
384A SER 2.9 31.0 + - - -
387A ASP* 2.9 39.3 + - - -
388A PHE* 3.6 35.4 - + + -
391A ARG* 4.1 5.8 - - + -
392A ILE* 4.7 5.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
19A ALA* 4.0 27.4 - - + +
22A LEU* 4.3 12.8 - - + -
23A ALA* 4.4 10.7 - - + +
27A LEU* 3.7 21.3 - - + -
338A LEU* 4.0 21.3 - - + -
367A LEU* 3.1 43.5 + - + +
370A TYR* 1.3 78.2 - - + +
372A THR* 1.3 57.7 + - - +
374A ILE* 3.1 24.5 + - + +
375A MET* 2.9 28.7 + - - +
376A PRO* 5.0 1.2 - - - +
383A PHE* 4.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.8 7.4 - - - +
31A ILE* 3.5 22.6 - - + +
368A ARG 2.9 23.0 + - - -
369A TYR 3.6 4.0 - - - -
371A LEU* 1.3 76.0 - - - +
373A THR* 1.3 61.6 + - - +
374A ILE 3.2 0.7 + - - -
375A MET* 3.3 16.7 + - + +
452A PHE* 3.7 38.4 - - + +
453A LYS* 3.4 16.5 - - - +
456A LEU* 3.7 21.3 - - + -
507A PHE* 4.2 5.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
369A TYR* 2.9 37.3 + - - -
370A TYR* 2.8 18.6 - - + +
372A THR* 1.3 77.3 - - - +
374A ILE* 1.3 59.8 + - + +
375A MET 3.6 0.2 - - - -
391A ARG* 3.0 55.4 + - - +
395A GLU* 4.3 2.5 + - - +
453A LYS* 3.1 20.7 + - - +
456A LEU* 4.3 5.6 - - - +
457A LYS* 5.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 4.3 10.7 - - + +
370A TYR* 3.1 50.3 - - + +
371A LEU* 3.3 22.7 - - + +
373A THR* 1.3 89.0 - - + +
375A MET* 1.3 68.1 + - - +
376A PRO* 3.0 4.7 - - - +
381A SER* 2.9 26.2 + - - -
382A ASP 4.5 4.0 - - - +
383A PHE* 4.2 15.0 - - + +
387A ASP* 4.0 3.4 - - - +
391A ARG* 3.7 23.1 - - - +
453A LYS* 3.6 7.4 - - - +
----------------------------------------------------------
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