Contacts of the helix formed by residues 552 - 560 (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 552 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A GLN* 3.4 28.2 + - - +
518A THR* 5.0 3.5 + - - +
551A LEU* 1.3 75.6 - - - +
553A ASN* 1.3 55.6 + - - +
554A SER* 2.6 20.0 + - - +
555A THR* 2.7 36.4 + - - -
556A LEU* 3.0 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A LEU 4.4 0.2 + - - -
552A ASP* 1.3 69.9 - - - +
554A SER* 1.3 62.9 + - - +
556A LEU* 3.5 13.6 - - - +
557A GLN* 3.3 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ASP* 2.6 15.5 + - - +
553A ASN* 1.3 74.9 - - - +
555A THR* 1.3 70.5 + - - -
556A LEU 2.9 2.3 + - - -
557A GLN* 3.3 1.9 + - - +
558A SER* 3.2 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A THR* 3.6 22.2 - - + +
522A LEU* 3.5 29.6 - - + -
551A LEU* 4.8 3.1 - - + -
552A ASP* 2.7 34.9 + - - -
554A SER* 1.3 77.3 + - - +
556A LEU* 1.3 63.7 + - - +
558A SER* 3.8 6.7 - - - -
559A GLU* 3.1 28.4 + - + +
560A VAL* 3.7 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A GLY* 4.7 15.3 - - - +
551A LEU* 4.8 8.4 - - + +
552A ASP 3.0 15.2 + - - +
553A ASN* 3.5 16.2 - - - +
554A SER 2.9 1.4 + - - -
555A THR* 1.3 76.7 - - - +
557A GLN* 1.3 66.5 + - + +
558A SER 2.9 3.3 + - - -
560A VAL* 2.6 66.4 + - + +
561A LYS 3.2 2.2 + - - +
586A LEU* 4.6 26.0 - - + +
588A LEU* 4.0 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ASN* 3.5 36.5 + - - +
554A SER 3.3 3.9 + - - +
556A LEU* 1.3 84.2 - - + +
558A SER* 1.3 56.7 + - - +
561A LYS* 4.0 17.1 - - + +
562A PRO* 3.1 20.2 - - - +
588A LEU* 4.4 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A SER* 3.2 17.6 + - - -
555A THR* 3.7 9.6 - - - -
556A LEU 2.9 0.6 + - - -
557A GLN* 1.3 79.6 - - - +
559A GLU* 1.3 69.9 + - - +
562A PRO* 3.1 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A THR* 5.6 2.4 - - - +
522A LEU* 4.7 4.3 - - - +
523A PRO* 5.8 4.0 - - - +
526A LEU* 3.8 21.6 - - + +
555A THR* 3.1 23.8 + - + +
558A SER* 1.3 88.0 - - - +
560A VAL* 1.3 69.4 + - + +
562A PRO* 3.6 4.5 - - - -
563A ILE* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A LEU* 4.1 16.6 - - + -
526A LEU* 4.3 7.0 - - + -
544A LEU* 4.8 14.8 - - + +
548A GLY* 6.5 0.7 - - - -
551A LEU* 3.5 32.1 - - + -
555A THR 4.2 2.5 - - - +
556A LEU* 2.6 40.6 + - + +
559A GLU* 1.3 74.1 - - - +
561A LYS* 1.3 71.1 + - - +
562A PRO 3.0 0.3 - - - -
563A ILE* 3.5 1.6 - - - +
564A LEU* 3.1 41.3 + - + +
586A LEU* 4.5 7.2 - - + -
----------------------------------------------------------
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