Contacts of the strand formed by residues 520 - 526 (chain B) in PDB entry 2YA4
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 TYR 520 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ASP* 3.4 7.3 - - - +
420B MET* 2.9 63.7 + - + +
421B PHE* 5.3 0.2 - - - -
422B PRO* 4.0 2.5 - - + -
437B ALA* 3.6 10.8 - - + +
438B TYR* 3.2 34.3 - + - -
447B GLN* 3.7 13.6 + - - -
515B ILE* 3.6 18.4 - - + +
516B ALA* 2.7 47.3 + - - +
518B ASP* 3.8 21.1 - - + -
519B SER* 1.3 78.7 + - - +
521B LEU* 1.3 65.8 + - - +
522B TRP* 4.2 7.6 - - - +
538B ASP* 4.4 3.1 - - - -
540B THR* 3.4 8.3 - - + +
551B LEU 4.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B ILE* 4.9 2.9 - - + -
418B TYR 3.6 4.9 - - - +
419B ASP* 3.5 24.5 - - - +
520B TYR* 1.3 73.5 - - - +
522B TRP* 1.3 64.9 + - - +
539B ILE* 3.0 37.1 + - + -
540B THR* 2.9 19.4 + - + +
543B VAL* 4.1 12.3 - - + -
551B LEU* 3.9 44.6 - - + +
552B GLY* 3.9 5.8 - - - -
553B VAL* 3.9 15.9 - - + -
574B VAL* 4.4 9.2 - - + -
592B ILE* 4.1 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B THR* 4.4 0.9 - - + -
384B LEU* 3.8 34.8 - - + -
400B ASN* 3.6 15.9 - - - -
416B SER 3.9 0.2 - - - +
417B ILE* 3.4 7.1 - - - +
418B TYR* 2.9 53.7 + + + +
419B ASP 5.1 0.2 - - - -
420B MET* 3.6 38.2 - - + +
490B LYS* 3.7 22.7 - - + -
504B TYR* 3.5 28.9 - + - -
520B TYR* 4.2 9.1 - - + +
521B LEU* 1.3 82.6 - - - +
523B MET* 1.3 62.7 + - - +
536B PRO* 3.6 23.8 - - + -
537B GLN 3.3 4.9 - - - +
538B ASP* 3.7 29.2 + - - +
539B ILE* 4.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B PHE* 3.7 30.7 - - + -
416B SER 3.3 4.7 - - - +
417B ILE* 3.7 25.8 - - + -
522B TRP* 1.3 77.0 - - - +
524B SER* 1.3 82.0 + - - +
525B TYR* 3.9 14.6 - - + -
536B PRO* 3.4 1.1 - - - +
537B GLN* 2.7 67.7 + - + +
539B ILE* 4.1 15.9 - - + -
598B GLY 4.3 13.2 - - - +
601B TRP* 4.7 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ILE* 3.4 28.4 - - - +
382B THR* 3.6 2.6 + - - -
415B PHE* 3.5 2.4 - - - -
416B SER* 2.8 32.9 + - - -
418B TYR* 2.7 28.9 + - - -
523B MET* 1.3 77.1 + - - +
525B TYR* 1.3 61.8 + - - +
533B TRP* 3.7 6.0 - - - -
534B SER* 3.5 19.4 + - - -
535B ALA 4.5 0.2 - - - -
536B PRO* 3.7 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ARG* 3.3 60.0 + - + -
414B ILE 3.0 12.1 - - - +
415B PHE* 4.0 3.4 - + + -
523B MET* 3.9 24.2 - - + -
524B SER* 1.3 74.7 - - - +
526B SER* 1.3 62.4 + - - +
527B ASP* 3.5 10.1 - - - -
533B TRP* 3.4 7.1 - - - -
534B SER* 2.8 60.7 + - - -
537B GLN* 4.5 16.3 + - + -
1784B FMT 3.6 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LYS 4.1 0.5 - - - +
413B ARG* 3.6 2.8 - - - -
414B ILE* 2.8 39.5 + - - +
525B TYR* 1.3 73.2 - - - +
527B ASP* 1.3 62.7 + - - +
528B ASP* 2.9 14.4 + - - -
529B ASP 4.9 0.2 - - - -
530B GLY* 2.9 23.2 + - - -
532B THR 2.9 21.9 + - - -
533B TRP* 3.8 20.6 - - - -
1784B FMT 3.4 4.9 - - - -
----------------------------------------------------------
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