Contacts of the strand formed by residues 522 - 532 (chain A) in PDB entry 4A9C
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 ILE 522 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A ILE* 3.7 46.7 - - + -
514A VAL* 4.0 15.9 - - + -
518A HIS 3.3 15.0 - - - +
519A GLU 3.5 12.4 + - - +
520A ASN* 3.3 5.7 - - - +
521A ARG* 1.4 76.9 - - - +
523A SER* 1.3 64.5 + - - +
525A VAL* 3.8 14.8 - - + -
548A PHE* 3.7 28.7 - - + -
549A MET 3.4 2.0 - - - +
550A PHE* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ARG 4.7 2.2 + - - -
522A ILE* 1.3 75.8 - - - +
524A HIS* 1.4 82.4 + - - +
525A VAL* 3.6 4.9 - - - -
548A PHE* 3.8 1.7 - - - +
549A MET* 2.8 44.5 + - - +
551A ASN 4.4 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A SER* 1.4 90.9 + - - +
525A VAL* 1.3 61.9 + - - +
526A SER* 3.7 2.8 + - - -
547A SER* 3.4 12.3 + - - +
548A PHE* 3.4 5.5 - - - -
549A MET* 4.0 24.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A ILE* 3.9 20.4 - - + +
501A ALA* 3.7 29.4 - - + -
522A ILE* 3.8 29.6 - - + -
523A SER* 4.4 4.3 - - - -
524A HIS* 1.3 72.8 - - - +
526A SER* 1.3 63.6 + - - +
527A THR* 5.3 1.3 - - + -
546A VAL* 5.4 0.2 - - + -
547A SER 3.3 7.9 - - - +
548A PHE* 4.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A HIS 4.7 2.9 - - - -
525A VAL* 1.3 74.3 - - - +
527A THR* 1.3 71.7 + - - +
546A VAL* 3.5 1.2 - - - +
547A SER* 2.8 51.0 + - - +
584A SER 4.2 4.9 + - - -
585A LEU* 4.0 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ALA* 3.9 16.4 - - + -
502A MET 4.3 7.6 + - - +
503A GLN* 3.2 26.6 + - + +
525A VAL* 5.3 1.6 - - + -
526A SER* 1.3 83.8 + - - +
528A SER* 1.3 62.6 + - - +
545A GLY 3.3 6.5 - - - -
546A VAL* 3.8 23.6 - - + -
584A SER 4.4 2.1 - - - +
585A LEU* 3.8 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A GLN* 3.4 11.4 - - - +
527A THR* 1.3 74.5 - - - +
529A SER* 1.3 63.1 + - - +
545A GLY 2.8 33.1 + - - -
582A LEU 4.6 1.2 + - - -
583A LEU* 3.6 13.2 - - - +
584A SER* 3.3 44.4 + - - -
585A LEU* 3.5 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A GLN* 3.6 21.5 + - - +
504A SER 4.8 0.2 + - - -
505A LEU* 3.8 24.4 - - - +
528A SER* 1.3 78.3 + - - +
530A VAL* 1.3 65.7 + - - +
531A LYS 4.3 0.6 + - - -
543A ALA 3.3 11.9 - - - -
544A VAL* 3.9 8.3 - - - -
583A LEU* 4.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A LEU* 3.4 4.6 - - - +
528A SER* 5.1 0.2 - - - +
529A SER* 1.3 77.5 - - - +
531A LYS* 1.3 69.1 + - - +
532A THR* 4.6 4.7 - - + -
542A GLY* 3.2 4.0 - - - -
543A ALA 2.8 36.1 + - - +
578A ASP* 4.5 1.1 - - + +
579A ILE* 4.0 29.2 - - + +
582A LEU* 3.7 33.2 - - + +
583A LEU* 3.5 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A LEU* 3.9 13.4 - - + +
506A TRP* 3.7 39.0 - - + -
529A SER 4.3 1.2 + - - -
530A VAL* 1.3 77.3 - - - +
532A THR* 1.3 63.7 + - - +
541A LYS 4.0 0.2 - - - -
703B ILE* 6.3 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A TRP* 5.7 0.7 - - - -
530A VAL* 4.6 12.6 - - + -
531A LYS* 1.3 79.5 - - - +
533A GLY* 1.3 64.3 + - - +
540A ASN* 5.1 1.6 - - - +
541A LYS* 3.0 33.7 + - - +
542A GLY* 3.2 24.5 + - - -
561A HIS 4.5 1.0 + - - -
562A LEU* 5.6 0.5 - - - +
563A THR* 5.5 0.2 + - - -
575A ASN* 3.8 37.8 + - + +
578A ASP* 4.9 10.1 - - + +
579A ILE* 4.6 10.9 - - + +
----------------------------------------------------------
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