Contacts of the strand formed by residues 478 - 486 (chain B) in PDB entry 2E4Y
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 478 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU* 3.2 49.9 + - + +
310B VAL* 4.6 10.8 - - + -
311B LYS* 3.9 16.4 - - - +
314B GLU* 3.2 54.2 + - + +
471B LEU* 4.5 13.5 - - + -
472B GLN 3.9 4.7 - - - -
473B GLN* 4.0 10.7 - - + +
476B GLY 5.5 0.9 - - - -
477B LYS* 1.3 91.7 - - + +
479B SER* 1.3 63.5 + - - +
480B TYR* 5.5 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU* 3.3 13.0 - - - -
471B LEU* 3.5 4.6 - - - +
472B GLN* 2.8 41.2 + - - +
473B GLN* 5.2 0.2 - - - -
474B THR* 5.6 1.9 + - - -
477B LYS* 4.4 7.3 + - - -
478B TYR* 1.3 76.4 - - - +
480B TYR* 1.3 71.2 + - - +
481B LEU* 4.0 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TRP* 2.8 22.9 + - - -
304B GLY 3.4 17.3 - - - -
305B ALA* 3.3 29.6 - - + -
306B GLN 2.4 32.6 + - - -
307B GLU* 3.6 23.4 + - + +
310B VAL* 3.2 16.3 - - + +
322B THR* 3.6 12.1 - - - -
469B PHE* 3.7 24.8 - + + -
470B ASN 3.7 3.1 - - - +
471B LEU* 4.2 26.0 - - + -
478B TYR* 5.5 0.9 - + - -
479B SER* 1.3 82.8 - - - +
481B LEU* 1.3 61.1 + - - +
482B LYS 4.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B PHE* 3.7 3.3 - - - -
470B ASN 3.0 30.9 + - - +
472B GLN* 3.4 42.8 - - + +
479B SER* 4.0 1.1 + - - +
480B TYR* 1.3 74.3 - - - +
482B LYS* 1.3 79.3 + - + +
483B VAL* 3.3 13.9 + - + +
496B SER* 4.7 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ASN* 3.7 30.1 + - - +
468B VAL 3.8 6.5 - - - +
469B PHE* 4.3 22.2 - - + -
480B TYR 4.1 2.0 + - - -
481B LEU* 1.3 84.0 - - + +
483B VAL* 1.3 66.2 + - - +
484B GLY 4.1 20.0 - - - +
485B HIS* 4.8 7.1 + - - +
493B ASP* 4.8 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ILE* 5.8 1.6 - - + -
468B VAL* 3.0 22.5 + - + +
469B PHE 3.9 4.0 - - - +
470B ASN* 3.7 30.3 - - + +
481B LEU* 3.5 22.2 - - + +
482B LYS* 1.3 79.1 - - - +
484B GLY* 1.3 60.0 + - - +
492B LEU* 2.9 22.0 - - + +
493B ASP* 3.9 10.7 + - - +
496B SER* 3.4 36.1 - - - +
497B ILE* 4.5 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ASN* 3.8 1.7 - - - -
468B VAL* 2.8 31.4 + - - +
482B LYS* 3.8 15.4 - - - +
483B VAL* 1.3 75.9 - - - +
485B HIS* 1.3 60.6 + - - +
491B SER* 3.3 14.8 - - - -
492B LEU* 3.5 8.0 - - - +
493B ASP* 4.2 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ARG* 5.7 3.4 - - - -
466B TYR 3.1 15.3 - - - +
467B ASN* 3.5 14.4 - - - +
468B VAL* 3.7 9.6 - - - +
482B LYS* 4.8 7.5 + - - -
484B GLY* 1.3 76.8 - - - +
486B TRP* 1.3 72.6 + - - +
487B ALA* 3.8 24.5 + - + +
489B THR 5.4 0.6 + - - -
490B LEU* 3.6 2.9 - - - +
491B SER* 3.1 54.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B TYR* 3.9 28.3 - + + -
199B LYS* 4.1 25.4 - - + -
200B ALA* 3.3 41.6 - - + +
203B GLU* 3.1 28.8 + - - -
464B GLY 3.3 21.8 - - - -
465B ARG* 3.7 4.9 - - - -
466B TYR* 2.8 41.2 + + + +
468B VAL* 5.1 2.9 - - + -
485B HIS* 1.3 79.7 - - - +
487B ALA* 1.3 69.1 + - - +
488B GLU* 3.4 32.1 - - + -
489B THR 3.7 2.6 - - - +
490B LEU* 3.7 21.1 - - + -
----------------------------------------------------------
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