Contacts of the helix formed by residues 544 - 554 (chain A) in PDB entry 2RD0
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 THR 544 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A ARG* 5.9 0.9 - - - +
542A GLU 5.5 1.6 - - - +
543A ILE* 1.3 74.4 - - - +
545A GLU* 1.3 57.5 + - - +
546A GLN* 3.5 29.6 + - - +
547A GLU* 2.6 59.3 + - - +
548A LYS* 3.0 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ILE 4.0 4.3 - - - +
544A THR* 1.3 72.8 - - - +
546A GLN* 1.3 65.4 + - + +
548A LYS* 3.2 35.3 + - + +
549A ASP* 3.1 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A THR* 3.5 27.3 + - - +
545A GLU* 1.3 82.5 + - + +
547A GLU* 1.3 60.8 + - + +
549A ASP* 3.7 9.7 - - - +
550A PHE* 3.4 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU* 6.1 1.3 - - + +
534A ILE* 4.0 14.5 - - + +
537A ARG* 2.8 41.4 + - - -
543A ILE* 3.9 7.5 - - + +
544A THR* 2.6 46.1 + - - +
546A GLN* 1.3 75.1 - - + +
548A LYS* 1.3 63.9 + - - +
550A PHE* 3.1 7.5 + - + +
551A LEU* 3.0 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ILE* 4.1 29.1 + - + +
544A THR 3.0 9.7 + - - +
545A GLU* 3.2 39.6 + - + +
547A GLU* 1.3 77.1 - - - +
549A ASP* 1.3 63.5 + - - +
551A LEU* 4.5 1.3 - - - -
552A TRP* 3.0 22.9 + - - +
570A LEU* 3.9 21.3 + - - +
571A SER* 3.4 39.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A GLU* 3.1 13.7 + - - +
546A GLN* 3.7 12.9 - - - +
548A LYS* 1.3 78.4 - - - +
550A PHE* 1.3 51.8 + - - +
552A TRP* 3.6 9.6 + - - +
553A SER* 2.5 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A GLU* 4.9 5.2 - - - -
531A LEU* 3.5 50.5 - - + -
532A LYS* 3.6 18.8 - - - -
534A ILE* 5.4 0.7 - - + -
546A GLN 3.4 10.8 + - - +
547A GLU* 3.1 12.7 + - + +
549A ASP* 1.3 77.0 - - - +
551A LEU* 1.3 82.4 + - + +
553A SER* 3.0 17.0 + - - -
554A HIS* 3.0 43.9 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU 5.2 1.3 - - - +
532A LYS* 5.6 2.9 - - - +
534A ILE* 3.6 30.1 - - + -
543A ILE* 4.3 13.0 - - + -
547A GLU* 3.0 23.7 + - + +
548A LYS 3.8 0.2 - - - +
550A PHE* 1.3 92.2 - - + +
552A TRP* 1.3 67.9 + - - +
553A SER 3.2 0.2 + - - -
554A HIS* 3.3 4.8 + - - -
555A ARG* 3.0 23.7 + - - +
558A CYS* 4.8 3.8 - - - -
564A ILE* 5.5 7.9 - - + -
567A LYS* 4.0 26.9 - - + +
568A LEU* 3.9 11.2 - - + +
571A SER* 3.4 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A LYS 3.0 17.9 + - - +
549A ASP* 3.8 9.0 - - - +
551A LEU* 1.3 76.0 - - - +
553A SER* 1.3 53.8 + - - +
555A ARG* 2.7 86.4 + - + +
568A LEU* 4.3 7.6 - - + -
571A SER* 4.4 11.7 - - - +
572A VAL* 3.8 20.9 - - + -
579A GLU* 2.9 67.3 + - + +
582A GLN* 4.0 11.7 - - + -
583A MET* 3.6 29.6 - - + -
586A LEU* 5.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A ASP* 2.5 23.4 + - - +
550A PHE* 3.0 12.0 + - - -
552A TRP* 1.3 80.8 - - - +
554A HIS* 1.3 69.3 + - - +
555A ARG* 3.1 15.9 + - - +
556A HIS* 4.9 2.4 + - - -
557A TYR* 5.1 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A GLU* 5.5 11.9 - - + +
532A LYS* 4.6 15.3 - - - +
550A PHE* 3.0 49.3 + + + +
551A LEU* 3.4 4.7 - - - +
553A SER* 1.3 82.7 - - - +
555A ARG* 1.3 63.4 - - - +
556A HIS 3.2 3.1 - - - -
557A TYR* 3.0 44.0 + + + +
558A CYS* 3.3 11.2 - - - -
----------------------------------------------------------
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