Contacts of the helix formed by residues 572 - 587 (chain A) in PDB entry 2PKG
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 ASP 572 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A ALA* 4.0 22.0 - - + +
538A PHE* 6.1 1.3 - - - -
570A ASP* 4.4 2.2 - - - +
571A GLN* 1.3 89.3 + - - +
573A VAL* 1.3 64.7 + - - +
574A ASP* 2.9 48.0 + - - +
575A VAL* 2.9 36.4 + - + +
576A LYS* 3.4 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A GLN* 3.0 13.2 + - - +
572A ASP* 1.3 71.5 + - - +
574A ASP* 1.3 54.4 + - - +
576A LYS* 2.9 18.1 + - + +
577A TYR* 2.5 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A PHE* 4.1 24.9 - - + -
572A ASP* 2.9 21.6 + - - +
573A VAL* 1.3 77.7 - - - +
575A VAL* 1.3 65.3 + - - +
577A TYR* 3.1 18.6 + - - +
578A PHE* 3.1 30.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A ALA* 3.9 23.6 - - + +
537A ARG* 4.6 13.2 - - + +
538A PHE* 3.8 14.1 - - + +
541A ALA* 4.9 1.9 - - + +
567A LEU* 3.9 15.3 - - + +
570A ASP* 3.3 43.1 - - + +
572A ASP* 2.9 28.6 + - + +
574A ASP* 1.3 76.6 - - - +
576A LYS* 1.3 52.7 + - - +
578A PHE* 3.7 1.4 - - - +
579A ALA* 2.7 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A LEU 4.7 2.9 - - - -
568A THR* 3.6 28.9 - - - +
569A GLN* 5.4 0.2 - - - +
570A ASP* 4.0 17.4 + - - +
571A GLN 4.6 6.3 + - - -
572A ASP 3.4 1.9 + - - +
573A VAL* 2.9 23.1 + - + +
575A VAL* 1.3 80.8 - - - +
577A TYR* 1.3 66.7 + - - +
578A PHE 2.7 2.9 + - - -
579A ALA* 3.0 17.3 + - - -
580A GLN* 3.3 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A VAL* 2.5 25.3 + - + +
574A ASP* 3.1 24.5 - - - +
576A LYS* 1.3 72.9 - - - +
578A PHE* 1.3 78.4 + + + +
580A GLN* 5.3 0.7 - - - +
581A GLU* 3.5 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A PHE* 3.4 50.0 - + - +
541A ALA* 4.2 5.6 - - + -
542A LYS* 3.6 35.2 - - + +
545A GLN* 5.2 7.0 - - - +
574A ASP* 3.1 26.6 + - + -
575A VAL 3.8 3.6 - - - +
576A LYS 2.7 3.8 + - - -
577A TYR* 1.3 91.1 - + + +
579A ALA* 1.3 67.9 + - - +
580A GLN 3.1 2.2 - - - -
581A GLU* 2.7 26.4 + - + +
582A ALA* 3.1 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ALA* 3.7 15.2 - - + +
564A LEU* 3.0 25.5 - - - +
567A LEU* 3.7 31.6 - - + -
568A THR* 3.8 15.5 - - + +
575A VAL* 2.7 24.8 + - + +
576A LYS 3.6 3.4 - - - +
578A PHE* 1.3 73.2 - - - +
580A GLN* 1.3 60.0 + - - +
582A ALA* 3.2 8.7 - - - +
583A LEU* 3.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A THR* 3.5 25.9 - - + +
576A LYS* 3.3 16.6 + - + +
577A TYR 5.3 0.4 - - - +
578A PHE 2.9 1.2 + - - -
579A ALA* 1.3 74.1 - - - +
581A GLU* 1.3 67.3 + - - +
582A ALA 2.9 2.2 - - - -
583A LEU* 2.8 29.2 + - + +
584A THR* 2.9 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A GLN* 4.6 16.4 - - - +
577A TYR* 3.5 28.7 + - + +
578A PHE* 2.7 27.3 + - + +
580A GLN* 1.3 72.5 - - - +
582A ALA* 1.3 63.1 + - - +
584A THR* 3.2 24.6 + - - +
585A VAL* 3.4 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ALA 4.6 7.9 - - - +
545A GLN* 4.0 35.8 + - + +
564A LEU* 4.1 18.2 - - + -
578A PHE 3.1 6.8 + - - +
579A ALA* 3.2 14.8 - - - +
581A GLU* 1.3 76.3 - - - +
583A LEU* 1.3 53.9 + - - +
584A THR 2.7 0.5 + - - -
585A VAL* 2.7 29.3 + - - +
586A LEU* 3.3 16.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A LYS* 4.6 0.2 - - - -
564A LEU* 3.5 37.9 - - + -
565A GLU* 2.8 32.8 - - - +
568A THR* 3.8 17.0 - - + -
579A ALA 3.8 1.6 - - - +
580A GLN* 2.8 33.1 + - + +
582A ALA* 1.3 71.4 - - - +
584A THR* 1.3 57.2 + - - +
585A VAL 3.2 1.1 - - - -
586A LEU* 4.2 2.9 - - - +
587A SER* 3.4 4.2 + - - -
588A LEU* 2.9 68.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A GLN* 2.9 22.3 + - - +
581A GLU* 3.4 20.5 + - - +
582A ALA 2.7 0.8 + - - -
583A LEU* 1.3 77.0 - - - +
585A VAL* 1.3 62.0 + - + +
587A SER* 4.5 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A GLN* 3.8 23.1 - - + +
549A PRO* 6.2 3.8 - - + -
581A GLU* 3.4 20.2 - - + +
582A ALA* 2.7 6.0 + - - +
584A THR* 1.3 84.2 - - + +
586A LEU* 1.3 67.8 + - + +
587A SER* 3.2 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A LEU 4.5 9.4 - - - +
545A GLN* 4.5 10.8 - - + +
548A GLY* 4.4 22.2 - - - -
549A PRO* 4.5 10.1 - - + -
556A LEU* 4.6 19.8 - - + +
560A VAL* 4.5 11.0 - - + -
564A LEU* 4.4 19.7 - - + -
582A ALA* 3.3 24.2 + - + +
583A LEU 4.7 0.4 - - - +
585A VAL* 1.3 82.8 - - + +
587A SER* 1.3 71.6 + - - +
588A LEU* 4.2 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A LYS* 4.9 0.3 + - - -
583A LEU 3.4 3.9 + - - -
584A THR 5.3 1.6 - - - -
585A VAL 3.2 9.4 + - - +
586A LEU* 1.3 81.9 - - - +
588A LEU* 1.3 71.7 + - - +
----------------------------------------------------------
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