Contacts of the strand formed by residues 452 - 457 (chain F) in PDB entry 6Q2J
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 LEU 452 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412F VAL* 4.7 6.1 - - + -
422F ILE* 3.8 20.4 - - + -
442F LEU* 3.6 21.7 - - + +
450F SER* 5.1 3.5 + - - -
451F THR* 1.3 94.4 + - + +
453F GLY* 1.3 60.2 + - - +
465F LEU* 4.6 12.1 - - + -
466F PHE 3.3 14.6 - - - +
467F VAL* 3.8 14.1 - - + -
468F ASN* 4.2 6.3 + - - +
473F LEU* 5.1 0.4 - - + -
481F LEU* 5.1 1.3 - - + -
483F TYR* 3.2 32.5 + - + +
500F LEU* 4.3 9.4 - - + -
502F VAL* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 453 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442F LEU* 3.7 7.0 - - - -
452F LEU* 1.3 77.1 - - - +
454F VAL* 1.3 62.5 + - - -
465F LEU* 3.2 1.0 - - - -
466F PHE* 2.9 52.7 + - - -
468F ASN* 4.3 8.2 - - - +
705F NAG 5.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 454 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425F VAL* 5.5 3.4 - - + -
440F TYR* 3.6 51.3 - - + +
441F LYS* 5.0 2.4 - - - +
442F LEU* 3.7 36.9 - - + +
453F GLY* 1.3 76.8 - - - -
455F VAL* 1.3 69.2 + - - +
463F GLY* 4.3 5.6 - - - -
464F ILE 3.4 13.2 - - - +
465F LEU* 3.7 20.9 - - + -
466F PHE* 5.0 0.2 - - - -
485F VAL* 5.4 4.7 - - + -
705F NAG 5.0 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 455 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454F VAL* 1.3 76.4 - - - +
456F THR* 1.3 74.6 + - - +
457F SER* 3.5 1.4 + - - -
463F GLY* 4.3 1.8 - - - -
464F ILE* 2.9 35.2 + - - +
466F PHE* 3.5 29.1 - - + -
572F VAL* 3.7 29.8 - - + +
573F VAL* 4.8 7.1 - - + +
576F GLN* 4.3 17.3 - - + +
705F NAG 5.0 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 456 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438F VAL 3.3 20.6 - - - +
439F GLN* 3.4 12.7 - - + +
440F TYR* 3.1 33.9 + - + +
454F VAL 4.2 0.8 + - - -
455F VAL* 1.3 82.8 - - - +
457F SER* 1.3 69.0 + - - +
458F ALA* 3.8 10.8 + - + +
461F THR* 5.1 1.8 - - - -
462F SER 3.7 15.3 - - - +
463F GLY* 4.1 2.2 - - - -
572F VAL* 3.9 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 457 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424F LYS* 5.9 0.3 - - - -
455F VAL 3.5 2.7 + - - -
456F THR* 1.3 70.4 - - - +
458F ALA* 1.3 58.7 + - - +
459F GLU* 3.1 12.3 + - - -
460F ASP* 3.5 7.7 + - - +
461F THR* 3.3 11.3 + - - -
462F SER* 2.9 32.4 + - - +
464F ILE* 4.1 24.8 - - - +
571F ASP* 4.9 5.6 - - - -
572F VAL* 3.8 21.8 - - - -
----------------------------------------------------------
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