Contacts of the strand formed by residues 526 - 533 (chain A) in PDB entry 1HKC
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 GLY 526 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ASN* 1.3 80.0 - - - +
527A ASP* 1.3 57.3 + - - -
528A PHE* 3.5 15.7 - - - -
543A VAL 3.6 0.2 - - - +
544A LYS* 3.5 0.2 - - - -
545A ILE* 2.5 45.2 + - - -
546A ARG* 2.8 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A GLY* 1.3 70.4 - - - +
528A PHE* 1.3 66.0 + - - +
542A LEU* 4.5 10.7 - - + +
543A VAL 3.5 2.9 - - - -
544A LYS* 3.4 28.3 - - - +
546A ARG* 2.6 39.1 + - - -
596A MET* 4.3 11.8 - - + +
597A PRO* 3.6 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ASN 4.1 8.1 - - - -
526A GLY* 3.5 36.6 - - - -
527A ASP* 1.3 75.0 - - - +
529A LEU* 1.3 67.9 + - - +
542A LEU* 3.4 4.9 - - - +
543A VAL* 2.7 43.7 + - - +
545A ILE* 3.9 20.0 - - + -
596A MET* 5.0 0.2 - - - -
597A PRO* 3.5 33.4 - - + +
902A ALA* 4.4 18.4 - - + +
905A THR* 4.1 10.5 - - + -
906A ALA* 3.5 35.9 - - + -
909A VAL* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A PHE* 1.3 78.4 - - - +
530A ALA* 1.3 61.3 + - - +
540A VAL* 4.5 7.2 - - + -
541A LEU 3.1 17.5 - - - +
542A LEU* 4.5 4.5 - - + -
582A ILE* 5.4 2.7 - - + -
585A PHE* 4.3 17.5 - - + -
586A LEU* 3.9 24.0 - - + -
591A ILE* 4.8 0.4 - - + -
596A MET* 3.6 45.8 - - + -
597A PRO 2.9 12.6 + - - +
598A LEU* 3.2 14.6 - - + -
599A GLY 2.9 22.2 + - - -
649A LEU* 3.9 24.2 - - + -
902A ALA* 5.0 1.5 - - - -
905A THR* 4.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A LEU* 1.3 76.6 - - - +
531A LEU* 1.3 61.3 + - - +
532A ASP 4.1 0.2 - - - -
540A VAL* 3.4 8.1 - - - +
541A LEU* 2.9 48.8 + - + +
543A VAL* 5.2 1.1 - - + -
598A LEU* 4.6 2.9 - - - -
599A GLY 3.2 9.9 - - - +
898A GLY* 4.0 22.2 - - - +
901A ALA* 4.2 11.2 - - + -
902A ALA* 4.5 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A ALA* 1.3 76.3 - - - +
532A ASP* 1.3 61.1 + - - +
533A LEU* 5.0 4.7 - - + +
538A PHE* 4.1 13.2 - - + -
539A ARG 3.6 1.6 - - - +
540A VAL* 4.0 18.4 - - + -
578A ILE* 3.9 25.6 - - + -
582A ILE* 3.8 32.5 - - + -
598A LEU* 4.6 8.5 - - + -
599A GLY 2.9 10.2 + - - +
600A PHE* 3.5 36.6 - - + -
601A THR* 2.8 31.0 + - - +
637A LEU* 4.5 11.2 - - + -
897A SER 4.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A ALA 4.1 0.2 - - - -
531A LEU* 1.3 73.6 - - - +
533A LEU* 1.3 61.7 + - - +
534A GLY* 3.9 2.5 + - - -
538A PHE* 3.0 23.6 - - - +
539A ARG* 2.8 49.3 + - + +
541A LEU* 4.3 5.4 - - + -
601A THR* 3.9 10.4 - - - +
603A SER* 4.8 2.9 + - - -
897A SER* 2.9 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU* 3.8 5.1 + - + -
532A ASP* 1.3 74.3 + - - +
534A GLY* 1.3 59.9 + - - +
535A GLY 4.1 5.8 - - - +
538A PHE* 3.6 21.8 - - + -
562A ILE* 3.9 23.8 - - + -
574A LEU* 5.9 1.6 - - + -
575A PHE* 5.2 3.8 - - + -
578A ILE* 4.0 22.0 - - + -
600A PHE* 4.0 15.5 - - + -
601A THR 3.0 16.3 + - - +
602A PHE* 3.6 30.3 - - + -
603A SER* 2.9 25.7 + - - -
604A PHE* 3.9 11.0 - - + -
619A TRP* 5.6 2.0 - - + -
623A PHE* 4.6 9.6 - - + -
----------------------------------------------------------
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