Contacts of the helix formed by residues 561 - 569 (chain B) 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 LYS 561 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B LEU 2.7 17.1 + - - +
557B GLN* 3.8 29.1 + - + +
560B VAL* 1.3 74.5 - - - +
562B PRO* 1.3 63.6 - - + +
564B LEU* 3.2 5.9 + - - +
565B GLU* 2.7 55.8 + - + +
583B LEU* 5.0 0.2 - - - -
588B LEU* 3.3 57.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 562 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B GLN 3.4 21.1 - - - +
558B SER 3.6 12.3 - - - +
559B GLU* 3.8 9.9 - - - +
560B VAL 3.2 4.9 - - - -
561B LYS* 1.3 96.5 - - + +
563B ILE* 1.3 54.0 + - + +
564B LEU 2.8 10.6 + - - -
565B GLU* 2.8 21.5 + - + +
566B LYS* 3.2 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 563 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B LEU* 3.2 51.6 - - + +
527B ARG* 5.7 1.1 - - - -
529B ALA* 4.5 10.6 - - + +
544B LEU* 5.0 2.1 - - - +
559B GLU 3.0 25.6 - - - +
560B VAL 3.0 6.8 + - - +
562B PRO* 1.3 74.9 - - + +
564B LEU* 1.3 56.8 + - + +
566B LYS* 4.2 35.2 - - - +
567B LEU* 3.8 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 564 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B ALA* 5.5 2.7 - - + -
544B LEU* 4.3 18.2 - - + -
560B VAL* 3.3 31.4 - - + +
561B LYS* 3.3 11.4 - - - +
562B PRO 2.8 0.2 + - - -
563B ILE* 1.3 77.8 - - - +
565B GLU* 1.3 68.2 + - - +
566B LYS 3.4 0.2 - - - -
567B LEU* 3.2 24.0 + - + +
568B THR* 3.5 4.7 + - - +
579B ALA* 3.0 29.8 - - - +
582B ALA* 4.4 17.3 - - + -
583B LEU* 3.5 26.5 - - + -
586B LEU* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 565 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B LYS* 2.7 48.7 + - + +
562B PRO* 2.8 10.0 + - + +
564B LEU* 1.3 74.3 - - - +
566B LYS* 1.3 54.7 + - - +
567B LEU 2.5 5.1 + - - -
568B THR* 2.5 45.0 + - - +
569B GLN* 5.0 0.7 - - - +
583B LEU* 3.2 35.9 - - - +
588B LEU 4.3 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 566 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B PRO 3.2 9.4 + - - +
563B ILE* 4.2 31.7 - - - +
565B GLU* 1.3 77.9 - - - +
567B LEU* 1.3 62.0 + - + +
569B GLN* 3.7 23.4 + - - +
570B ASP* 4.3 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 567 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ALA* 3.6 37.7 - - + +
537B ARG* 5.0 6.7 - - + +
540B VAL* 4.5 13.9 - - + -
541B ALA* 4.6 16.6 - - + -
544B LEU* 5.0 5.4 - - + -
563B ILE 3.8 21.5 - - - +
564B LEU* 3.2 19.0 + - + +
565B GLU 2.5 5.9 + - - -
566B LYS* 1.3 75.6 - - + +
568B THR* 1.3 51.2 + - - +
569B GLN 2.7 17.3 + - - -
570B ASP* 2.8 25.0 + - + +
575B VAL* 4.3 13.3 - - + +
576B LYS* 4.7 1.2 - - - -
579B ALA* 4.0 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 568 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B LEU 3.9 6.1 - - - +
565B GLU* 2.5 32.3 + - + +
567B LEU* 1.3 71.3 - - - +
569B GLN* 1.3 63.3 + - - +
570B ASP 3.5 0.2 - - - -
576B LYS* 3.3 30.9 - - - +
579B ALA* 4.1 8.0 - - - +
580B GLN* 4.0 29.1 + - + +
583B LEU* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 569 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B GLU 5.0 1.1 - - - +
566B LYS* 3.7 17.9 + - - +
567B LEU 2.7 2.6 + - - -
568B THR* 1.3 88.9 + - - +
570B ASP* 1.3 65.7 + - - +
571B GLN* 3.5 1.9 + - - -
576B LYS* 5.0 2.2 - - - +
----------------------------------------------------------
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