Contacts of the strand formed by residues 368 - 376 (chain A) in PDB entry 2PA5
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 368 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A SER* 3.5 5.7 - - - -
364A ASP* 3.5 2.6 - - - +
365A GLY* 2.8 35.4 + - - +
366A TYR 3.1 11.4 + - - +
367A LYS* 1.3 81.1 - - - +
369A LYS* 1.3 67.9 + - - +
371A ALA* 3.7 27.8 + - + +
491A GLN* 5.6 0.2 - - - +
508A GLU* 4.0 40.4 + - - +
509A PRO 5.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A SER* 4.2 11.7 - - - +
364A ASP* 3.4 18.5 + - - +
368A GLN* 1.3 77.8 + - - +
370A ASN* 1.3 96.4 + - - +
371A ALA 3.3 0.5 + - - -
508A GLU 5.0 4.2 + - - +
553A GLN* 5.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A PHE* 3.4 49.7 - - + +
363A MET 3.4 8.1 - - - -
364A ASP* 3.0 21.7 + - - +
368A GLN 3.6 0.4 + - - -
369A LYS* 1.3 99.0 + - - +
371A ALA* 1.3 64.8 + - - +
372A TYR 3.3 4.5 - - - -
508A GLU 4.2 7.0 - - - +
510A PRO* 3.5 20.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
363A MET 2.9 3.6 + - - -
365A GLY* 3.5 30.3 - - - +
368A GLN* 3.7 33.1 + - + +
369A LYS 3.3 2.2 + - - -
370A ASN* 1.3 77.3 - - - +
372A TYR* 1.3 76.0 + - + +
491A GLN* 5.7 0.2 + - - -
509A PRO 4.5 0.7 - - - +
510A PRO* 3.4 2.9 - - - +
511A ILE* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A PHE* 3.6 3.5 - - - -
363A MET* 2.8 43.9 + - + +
364A ASP 3.5 25.6 - - - -
365A GLY* 3.8 10.7 - - - -
366A TYR 5.0 0.5 + - - -
370A ASN* 3.3 2.5 - - - -
371A ALA* 1.3 93.2 - - + +
373A ILE* 1.3 64.7 + - - +
374A GLY 4.0 0.2 - - - -
510A PRO* 3.7 7.5 - - - +
511A ILE* 3.1 22.7 - - + +
513A VAL* 4.3 11.4 - - + -
525A PHE* 4.9 4.9 - + - -
526A CYS* 3.7 41.3 - - + -
529A ASP* 2.6 41.0 + - + +
530A ILE* 3.7 15.3 - - + +
550A MET* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A VAL* 3.9 15.9 - - + -
360A ALA* 3.8 28.0 - - + -
361A SER 3.3 6.7 - - - +
362A PHE* 3.9 15.9 - - + -
372A TYR* 1.3 77.3 - - - +
374A GLY* 1.3 62.5 + - - +
375A THR* 3.9 1.9 + - - -
389A MET* 4.0 20.4 - - + -
393A GLN* 4.0 23.1 - - + -
510A PRO* 3.5 26.7 - - + +
511A ILE 2.9 7.3 + - - +
512A VAL* 3.4 17.3 - - + +
513A VAL* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ALA* 3.3 1.7 - - - -
361A SER 2.9 33.7 + - - -
363A MET* 3.5 23.1 - - - -
373A ILE* 1.3 69.8 - - - +
375A THR* 1.3 60.0 + - - -
513A VAL* 3.5 7.2 - - - -
518A GLY 4.6 0.2 - - - -
522A THR* 4.1 9.9 - - - -
554A ARG* 3.4 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ILE* 4.5 8.0 - - - +
359A ASN 2.6 22.4 + - - -
360A ALA* 3.4 15.0 - - - +
373A ILE* 4.5 1.3 - - - +
374A GLY* 1.3 75.7 - - - -
376A GLN* 1.3 71.8 + - - +
386A PHE* 4.3 13.0 - - + -
389A MET* 4.4 4.9 - - + -
512A VAL* 3.8 29.6 - - + -
513A VAL 3.1 7.1 + - - -
514A HIS* 3.0 27.9 - - + +
518A GLY* 3.2 19.8 + - - -
554A ARG* 4.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LYS 2.9 24.5 + - - -
332A ARG* 2.8 32.5 + - + +
333A TYR* 4.6 1.0 + - - -
358A ILE* 6.0 1.8 - - + +
359A ASN* 3.5 35.0 + - - +
375A THR* 1.3 91.3 + - - +
377A GLY* 1.3 69.4 + - - +
378A PRO* 3.2 11.1 - - + +
379A LEU* 3.7 14.3 - - - +
382A THR* 4.4 8.7 + - - +
514A HIS* 3.9 2.2 - - - +
515A CYS 3.5 2.5 - - - -
516A SER 3.4 14.1 - - - +
517A ALA* 3.8 15.3 - - - +
554A ARG* 3.8 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