Contacts of the strand formed by residues 477 - 484 (chain A) in PDB entry 1ASZ
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 GLU 477 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A HIS* 3.1 26.8 + - - -
333A ARG* 3.0 32.0 + - - +
427A GLU* 3.4 4.9 - - - -
428A LYS* 3.5 23.1 - - + -
473A PHE* 3.2 5.7 - - - -
474A MET* 2.6 42.7 + - - +
475A ARG 3.6 10.5 - - - +
476A GLY* 1.3 78.4 - - - +
478A GLU* 1.3 62.4 + - - +
479A ILE* 3.9 1.6 - - - +
534A MET* 4.6 0.5 - - - +
535A PHE* 2.9 40.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ARG* 3.9 1.9 - - - +
427A GLU* 3.1 18.5 + - - +
471A ASP* 3.9 17.8 - - - +
472A PHE 3.6 7.9 - - - +
473A PHE* 3.7 8.4 - - + -
477A GLU* 1.3 71.0 - - - +
479A ILE* 1.3 62.9 + - - +
480A LEU 3.8 15.3 - - - +
481A SER* 4.2 4.5 - - - -
531A ARG* 3.2 32.7 + - - +
535A PHE* 4.0 0.9 - - - -
701A ATP 2.8 71.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A PHE* 3.1 46.4 - - + -
442A PHE* 5.0 2.2 - - + -
472A PHE* 3.1 21.7 + - + -
473A PHE 4.2 0.4 - - - +
474A MET* 3.5 40.6 - - + -
477A GLU 3.6 0.8 + - - +
478A GLU* 1.3 73.9 - - - +
480A LEU* 1.3 60.4 + - - +
527A ILE* 3.3 21.3 - - - +
528A GLY 3.5 3.3 + - - -
531A ARG* 4.2 10.3 - - + +
532A VAL* 4.0 7.6 - - + -
535A PHE* 3.5 32.8 - - + -
701A ATP 2.6 16.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LEU* 4.1 16.2 - - + -
362A PHE* 3.7 12.1 - - + -
470A TYR* 4.2 8.7 - - + +
471A ASP* 3.3 12.5 - - - +
472A PHE* 3.2 69.7 + - + -
478A GLU* 3.8 4.7 - - - +
479A ILE* 1.3 81.3 - - + +
481A SER* 1.3 93.0 + - - +
482A GLY* 3.5 9.0 - - - +
525A GLY* 4.4 4.5 - - - -
526A GLY 3.3 18.4 - - - +
527A ILE* 4.0 12.6 - - + -
701A ATP 3.0 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ARG* 3.5 12.1 + - - -
471A ASP* 3.0 20.0 + - - -
478A GLU* 4.2 3.8 + - - -
480A LEU* 1.3 80.3 - - - +
482A GLY* 1.3 58.0 + - - +
525A GLY* 3.0 1.2 - - - -
526A GLY 2.9 27.9 + - - -
701A ATP 3.8 36.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ARG* 3.4 18.0 + - - -
470A TYR* 2.9 32.0 + - - -
480A LEU* 3.5 1.8 - - - +
481A SER* 1.3 75.0 + - - +
483A ALA* 1.3 67.8 + - - +
485A ARG* 4.5 3.4 - - - -
524A GLY 2.9 15.3 - - - -
525A GLY* 3.5 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ARG* 5.3 0.2 - - - +
456A TYR* 5.5 1.1 - - + -
457A THR* 3.9 28.0 - - + +
468A ASN 3.6 3.8 - - - -
469A SER* 3.9 3.1 - - - -
470A TYR* 3.0 18.6 + - - -
482A GLY* 1.3 76.2 - - - +
484A GLN* 1.3 56.8 + - - +
485A ARG* 3.6 20.3 - - - +
523A ALA* 2.7 36.1 - - - +
524A GLY 2.8 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PHE* 2.8 32.1 - - + -
351A TYR* 3.7 15.4 - - + +
457A THR* 3.9 1.9 - - - -
458A MET* 2.8 77.9 + - - +
468A ASN* 3.5 16.2 + - + -
483A ALA* 1.3 76.9 - - - +
485A ARG* 1.3 58.9 + - - +
487A HIS* 6.5 0.2 - - - -
521A PRO* 5.6 1.1 - - + -
522A HIS 3.7 14.4 - - - +
523A ALA* 3.8 0.4 - - + -
81B ILE 3.7 8.3 + - - +
82B GLN* 4.2 0.6 - - - +
83B SER* 2.8 29.5 + - - -
----------------------------------------------------------
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