Contacts of the strand formed by residues 510 - 515 (chain A) in PDB entry 1PDR
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 510 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ARG* 2.7 34.0 + - - -
490A PHE* 3.2 4.6 - - - -
491A ILE* 2.9 39.9 + - + +
506A LEU* 3.4 14.2 - - - +
507A ARG* 3.0 37.9 + - - +
508A LYS 3.4 0.4 - - - -
509A GLY* 1.3 78.8 - - - +
511A ARG* 1.3 59.4 + - - +
543A ALA* 4.2 6.7 - - + -
544A GLN 3.6 2.5 - - - -
545A TYR* 3.1 22.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A GLY 4.7 3.2 + - - -
487A GLU 3.3 21.4 + - - -
488A GLY* 3.5 10.4 - - - +
489A ILE 3.3 14.8 - - - +
490A PHE* 3.8 23.3 - - + -
509A GLY 3.6 0.2 + - - -
510A ASP* 1.3 74.4 - - - +
512A ILE* 1.3 68.2 + - - +
513A ILE* 3.5 13.4 + - + +
521A ARG* 3.2 40.1 + - - +
543A ALA* 3.1 5.8 - - - -
544A GLN 2.8 38.4 + - - +
546A ARG* 4.0 29.4 - - + +
549A GLU* 3.4 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A PHE* 4.0 19.3 - - + -
480A ILE* 4.0 26.9 - - + -
489A ILE* 2.9 29.9 + - + +
490A PHE 5.2 0.4 - - - -
491A ILE* 4.1 19.7 - - + -
511A ARG* 1.3 76.0 - - - +
513A ILE* 1.3 65.4 + - - +
514A SER 3.7 10.5 - - - +
515A VAL* 3.7 30.3 - - + -
520A LEU* 3.8 27.2 - - + +
521A ARG* 4.4 1.4 + - - -
532A LEU* 5.4 2.5 - - + -
541A ILE* 4.3 15.0 - - + -
542A VAL 3.7 4.5 - - - +
543A ALA* 5.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A PRO* 5.0 3.6 - - + -
511A ARG* 4.2 20.6 - - - +
512A ILE* 1.3 74.8 - - - +
514A SER* 1.3 63.1 + - - +
519A ASP* 3.2 12.1 - - - +
520A LEU 2.8 22.2 + - - -
521A ARG* 3.4 33.8 + - + +
542A VAL* 2.8 34.0 + - + +
544A GLN* 3.3 45.8 - - + +
546A ARG* 4.7 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A ILE* 3.4 5.5 - - - +
513A ILE* 1.3 83.1 - - - +
515A VAL* 1.3 67.7 + - - +
516A ASN 4.1 0.6 + - - -
517A SER* 4.3 14.5 + - - -
518A VAL 3.1 21.5 - - - -
519A ASP* 4.3 2.9 - - - -
520A LEU* 4.2 2.0 - - - +
540A THR 4.3 0.6 + - - -
541A ILE* 3.5 3.6 - - - -
542A VAL* 3.1 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A ILE* 3.7 10.3 - - + -
514A SER* 1.3 80.6 - - - +
516A ASN* 1.3 71.8 + - - +
518A VAL* 3.2 21.0 + - - +
520A LEU* 3.5 26.0 - - + +
531A ALA* 4.3 14.6 - - + +
532A LEU* 4.0 23.8 - - + -
535A ALA* 4.0 14.4 - - + -
539A VAL* 3.6 30.1 - - + -
540A THR 3.4 4.0 - - - -
541A ILE* 4.3 6.7 - - + -
----------------------------------------------------------
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