Contacts of the helix formed by residues 542 - 551 (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 ASN 542 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A HIS* 2.9 27.7 + - - +
285A ALA* 4.2 5.6 - - + -
286A MET* 4.6 16.9 - - - +
531A CYS* 4.6 2.5 - - - -
534A GLN* 4.7 4.1 + - - +
541A LEU* 1.3 80.1 - - - +
543A VAL* 1.3 57.4 + - - +
544A PHE* 3.2 12.7 + - - +
545A GLN* 2.9 51.3 + - - +
546A THR* 3.0 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A MET* 5.2 3.0 - - - +
291A LEU* 4.9 0.9 - - + -
527A SER* 6.1 0.4 - - - -
531A CYS* 4.3 15.0 - - - -
541A LEU* 4.0 21.1 - - + +
542A ASN* 1.3 68.9 + - - +
544A PHE* 1.3 66.7 + - - +
546A THR* 3.2 1.2 + - - -
547A VAL* 2.9 29.4 + - + +
564A TYR* 4.1 12.6 - - + -
567A CYS* 3.9 26.7 - - + +
568A TYR* 3.8 55.2 + - + +
571A ILE* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A MET* 6.4 0.4 - - + -
294A TYR* 5.1 4.0 - - + +
306A GLU* 3.8 22.7 - - + +
309A ASP* 5.7 4.0 - - + -
310A ILE* 3.6 27.3 - - + +
542A ASN* 3.2 8.4 + - - +
543A VAL* 1.3 80.3 - - - +
545A GLN* 1.3 67.3 + - + +
547A VAL* 4.1 0.7 - - - +
548A SER* 2.8 50.6 + - - -
564A TYR* 3.3 25.7 + - - +
568A TYR* 4.0 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLY* 3.6 17.3 + - - +
283A PRO* 2.3 40.9 + - - +
284A HIS* 4.5 2.0 - - - +
542A ASN* 2.9 39.3 + - - +
544A PHE* 1.3 82.1 - - + +
546A THR* 1.3 67.2 + - - +
548A SER* 3.8 3.3 - - - -
549A ARG* 2.9 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A HIS* 3.3 17.8 + - + -
527A SER* 3.9 32.8 - - - +
530A ILE* 3.9 31.0 - - + +
531A CYS* 3.8 15.1 - - - -
534A GLN* 5.5 2.3 + - - -
542A ASN 3.0 20.0 + - - -
543A VAL* 3.2 4.5 + - - -
545A GLN* 1.3 78.5 - - - +
547A VAL* 1.3 56.9 + - - +
549A ARG* 4.7 1.5 + - - +
550A MET* 2.8 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR* 5.6 1.1 - - + -
310A ILE* 4.2 7.9 - - + -
527A SER* 3.8 20.9 - - - +
543A VAL* 2.9 26.4 + - + +
544A PHE 4.2 1.1 - - - +
546A THR* 1.3 73.5 - - - +
548A SER* 1.3 67.3 + - - +
550A MET* 3.2 6.4 + - - +
551A ARG* 3.0 40.5 + - + +
557A SER* 4.2 0.4 - - - +
558A ILE* 3.8 30.1 - - + -
564A TYR* 3.8 28.7 - - + -
567A CYS* 5.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE* 4.0 11.7 - - - +
544A PHE* 2.8 48.3 + - - -
545A GLN* 3.9 5.2 - - - -
547A VAL* 1.3 77.5 - - - +
549A ARG* 1.3 64.9 + - - +
551A ARG* 3.3 15.5 + - - +
552A THR* 3.5 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A VAL* 3.3 37.9 + - + +
279A HIS* 3.6 22.7 + - + +
280A VAL* 2.8 35.1 + - - +
282A GLY 2.9 23.4 + - - -
283A PRO* 4.1 5.7 - - - +
545A GLN* 2.9 53.0 + - - +
546A THR* 5.8 1.0 + - - +
548A SER* 1.3 77.4 - - - +
550A MET* 1.3 63.5 + - - +
552A THR* 2.7 31.1 + - - -
553A GLN* 3.9 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A HIS* 3.9 9.1 - - + +
363A MET* 3.6 31.4 - - + -
364A ASP 5.4 1.3 - - - +
523A GLY* 3.7 18.8 - - - +
526A CYS* 3.5 11.7 - - + -
527A SER* 3.2 41.7 - - - +
530A ILE* 3.5 21.8 - - + -
546A THR* 2.8 16.3 + - + +
547A VAL* 3.2 6.3 + - - +
549A ARG* 1.3 77.3 - - - +
551A ARG* 1.3 57.9 + - - +
553A GLN* 2.9 10.3 + - + +
554A ARG 2.9 27.0 + - - +
557A SER* 3.7 13.0 - - - +
558A ILE* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR* 4.0 9.9 + - - -
310A ILE* 3.5 33.3 + - - +
311A ARG* 3.9 27.8 + - - +
313A GLU 5.5 2.0 + - - -
315A PRO* 5.7 3.1 - - - +
316A VAL 5.3 3.5 + - - +
339A LEU* 4.1 3.5 - - - +
547A VAL* 3.0 26.2 + - - +
548A SER* 3.7 6.3 - - - +
549A ARG 3.2 0.6 - - - -
550A MET* 1.3 75.9 - - - +
552A THR* 1.3 58.5 + - + +
553A GLN 3.2 1.6 - - - -
554A ARG 3.5 7.9 - - - +
555A ALA* 3.4 19.1 - - - +
556A PHE* 3.5 29.4 + - - +
557A SER* 2.8 48.3 + - - +
558A ILE 3.0 16.4 + - - -
----------------------------------------------------------
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