Contacts of the strand formed by residues 484 - 489 (chain A) in PDB entry 4JF7
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 PHE 484 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A THR* 4.3 12.1 - - + -
415A LEU* 4.5 7.9 - - + -
435A VAL* 6.1 0.7 - - + -
437A THR* 3.8 31.9 - - + -
439A GLN* 4.0 14.6 - - + -
440A VAL* 4.3 1.1 - - + -
466A ALA* 3.8 13.9 - - + -
467A TRP 3.0 19.3 - - - +
468A LEU* 4.2 14.4 - - + -
469A LEU* 4.2 4.3 - - - +
482A ALA* 4.4 7.0 - - + -
483A THR* 1.3 80.9 - - - +
485A THR* 1.3 60.2 + - - +
501A TYR* 3.5 33.6 - + - -
502A ILE* 3.5 3.8 - - - +
503A ALA* 2.9 38.5 + - + +
504A ASN 3.7 24.0 - - - -
505A ASN* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ALA* 3.4 1.4 - - - -
467A TRP* 2.8 38.2 + - + +
469A LEU* 3.9 20.2 - - + -
484A PHE* 1.3 75.5 - - - +
486A GLY* 1.3 57.5 + - - +
501A TYR* 2.8 25.7 + - - -
502A ILE* 3.9 7.2 - - - +
526A THR* 3.8 4.8 - - + +
528A CYS* 3.6 31.0 - - - -
539A CYS* 3.8 6.3 - - - -
541A TYR* 2.7 23.8 + - - +
562A VAL* 5.0 0.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ASP 4.0 6.7 - - - -
485A THR* 1.3 78.8 + - - +
487A SER* 1.3 58.8 + - - -
500A MET* 3.4 0.9 - - - -
501A TYR* 3.0 41.8 + - - -
526A THR* 3.2 16.8 - - - -
541A TYR* 3.3 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A VAL* 5.1 0.3 - - - +
464A ALA* 3.7 19.4 - - - +
465A ASP 4.5 3.6 + - - +
486A GLY* 1.3 75.4 - - - -
488A TYR* 1.3 62.8 + - - +
489A LEU* 6.5 0.4 - - - -
498A PRO* 5.9 1.3 - - - -
499A THR 3.2 14.1 - - - -
500A MET* 4.2 7.6 - - - -
501A TYR* 3.8 6.1 + - - -
524A GLY* 3.7 25.0 + - - +
526A THR* 3.7 5.3 + - - -
541A TYR* 4.6 3.2 - - - +
543A ILE* 3.8 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A VAL* 3.7 20.4 - - + -
441A PRO* 3.3 41.7 - - + +
442A ARG* 5.8 1.1 - - + -
464A ALA* 4.9 9.9 - - + -
487A SER* 1.3 77.9 - - - +
489A LEU* 1.3 73.7 + - - +
490A ASN* 3.3 41.0 + - - -
498A PRO* 3.6 0.4 - - - +
499A THR* 2.8 60.0 + - + +
501A TYR* 3.7 15.0 - + + -
508A ILE* 3.3 29.3 - - + +
511A SER* 5.7 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A PRO 4.8 1.0 - - - +
443A PRO* 3.7 29.3 - - + +
462A VAL* 4.2 11.0 - - + -
487A SER* 6.5 0.2 - - - -
488A TYR* 1.3 84.2 - - - +
490A ASN* 1.3 57.6 + - - +
491A THR 2.8 19.4 + - - +
494A GLN 4.3 0.4 - - - +
495A ARG* 3.6 36.8 - - + -
496A ILE 3.4 15.9 - - - +
497A ASN 3.9 0.7 - - - -
498A PRO* 4.0 12.1 - - + -
521A ALA* 3.8 30.1 - - + +
522A ALA* 3.8 22.4 - - - +
543A ILE* 5.8 1.1 - - + -
----------------------------------------------------------
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