Contacts of the strand formed by residues 466 - 472 (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 466 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ILE* 3.8 27.6 - - + -
425A SER 3.1 4.3 + - - +
426A VAL* 3.5 16.6 - - + -
427A PHE* 2.7 34.1 + - - +
464A HIS* 4.0 1.6 - - - +
465A ASP* 1.3 86.4 - - + +
467A TYR* 1.3 61.9 + - - +
468A VAL* 3.8 22.7 - - + -
512A VAL* 3.9 19.1 - - + -
513A LEU 3.5 4.9 - - - +
514A VAL* 3.8 11.7 - - + -
548A PHE* 3.8 30.3 - - + -
550A PHE* 3.8 14.8 - - + -
555A PHE* 5.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PHE* 3.5 21.8 - + + -
446A PHE* 3.9 17.8 + - + -
463A PRO* 4.1 6.4 - - - +
464A HIS* 3.3 59.0 + + + -
466A ILE* 1.3 72.7 - - - +
468A VAL* 1.3 61.4 + - - +
469A PHE* 3.6 22.2 - + + -
489A LEU* 3.7 32.9 - - + +
492A LEU* 4.6 5.6 - - + +
493A THR* 4.2 8.1 - - - +
497A TYR* 3.4 33.2 - + - -
511A ALA 3.7 1.6 - - - +
512A VAL* 3.5 4.5 - - - +
513A LEU* 2.8 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A VAL* 4.5 0.7 - - + -
427A PHE* 2.8 21.8 + - - +
428A ILE* 3.4 6.3 - - + -
429A GLY* 2.8 32.1 + - - +
466A ILE* 3.8 12.1 - - + -
467A TYR* 1.3 76.2 - - - +
469A PHE* 1.3 57.9 + - - +
510A VAL* 4.1 7.0 - - + -
511A ALA 3.5 2.5 - - - -
512A VAL* 3.8 25.1 - - + -
557A PHE* 3.6 38.4 - - + -
605A PHE* 3.6 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PHE* 3.6 20.0 - + - -
429A GLY 3.7 2.0 - - - -
445A TRP* 3.8 20.9 - + + -
446A PHE* 3.4 41.7 - + - -
467A TYR* 3.6 34.1 - + + -
468A VAL* 1.3 71.5 - - - +
470A GLY* 1.3 59.0 + - - +
481A TRP* 3.4 22.2 - - + -
485A LEU* 3.6 29.6 - - + -
489A LEU* 4.1 15.9 - - + -
510A VAL* 3.2 7.4 - - - +
511A ALA 2.9 34.1 + - - +
513A LEU* 4.0 13.0 - - + -
605A PHE* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLY 2.7 16.2 + - - +
430A THR* 3.2 5.3 - - - -
431A TRP 2.9 24.4 + - - -
445A TRP* 4.4 0.7 - - - -
469A PHE* 1.3 71.9 - - - +
471A THR* 1.3 63.7 + - - +
472A GLN* 3.8 0.3 + - - -
559A ASN* 3.5 28.3 - - - -
605A PHE* 3.7 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A TRP* 3.3 14.1 - - + +
433A MET* 3.7 21.1 - - + -
445A TRP* 4.1 16.6 - - + -
470A GLY* 1.3 78.9 - - - +
472A GLN* 1.3 63.6 + - - +
474A ASN* 2.9 25.0 + - - -
481A TRP* 3.4 20.8 - - + +
507A ASN 4.4 1.1 - - - -
508A ILE* 3.4 2.8 - - - +
509A LYS* 2.9 44.0 + - - +
559A ASN* 3.0 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A THR* 3.4 17.9 + - - -
431A TRP 3.3 3.1 + - - -
432A ASN* 3.2 40.2 + - - +
433A MET* 2.9 27.9 + - - +
470A GLY 3.8 0.6 + - - -
471A THR* 1.3 84.4 - - - +
473A GLU* 1.4 65.9 + - - +
474A ASN* 3.2 3.1 + - - -
507A ASN 3.8 4.0 - - - -
508A ILE* 4.4 5.4 - - + +
559A ASN* 2.8 26.4 + - - +
560A CYS 3.4 16.4 - - - +
561A HIS* 3.7 22.2 - - + +
606A GLY* 3.4 4.1 - - - -
607A ASP* 3.4 18.9 + - + +
690A ASP* 4.2 1.2 - - - +
----------------------------------------------------------
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