Contacts of the strand formed by residues 256 - 261 (chain D) in PDB entry 2W8I
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 LYS 256 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D ASP* 2.8 34.8 + - - +
254D ASP 3.4 3.6 + - - -
255D LEU* 1.3 70.9 - - - +
257D VAL* 1.3 68.1 + - - +
258D PHE* 4.1 10.3 - - + -
268D THR* 3.9 17.5 - - + -
269D LEU 3.3 12.1 - - - +
270D LYS* 3.8 23.1 - - + +
336D PRO* 3.4 3.8 - - - +
337D TYR* 2.5 64.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D LEU 4.4 0.4 - - - +
256D LYS* 1.3 81.4 - - - +
258D PHE* 1.3 68.5 + - - +
259D VAL* 4.7 9.9 - - + -
268D THR 3.7 0.2 - - - -
269D LEU* 2.7 47.5 + - + +
271D MET* 3.5 36.6 - - + +
276D MET* 4.2 17.9 - - - -
281D ALA* 4.7 0.7 - - + -
334D LEU* 3.8 28.3 - - + -
335D GLN 4.4 4.9 - - - +
338D ASP* 3.9 11.0 - - + +
340D VAL* 5.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D LYS* 4.1 12.1 - - + -
257D VAL* 1.3 72.9 - - - +
259D VAL* 1.3 56.8 + - - +
260D MET* 3.9 19.3 - - + -
267D SER 4.0 4.0 - - - +
268D THR* 3.4 37.5 - - + -
337D TYR* 3.7 41.7 - + + -
338D ASP 3.1 19.2 + - - +
339D ILE* 3.4 23.3 - - + +
340D VAL* 2.7 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D VAL* 3.9 4.2 + - + -
258D PHE* 1.3 75.7 - - - +
260D MET* 1.3 63.5 + - - +
263D VAL* 4.1 17.3 - - + -
266D GLN* 3.4 6.2 - - - +
267D SER* 3.1 34.2 + - - +
269D LEU* 4.3 15.9 - - + -
281D ALA* 3.8 36.8 - - + +
282D LEU* 5.2 1.3 - - + -
285D ALA* 3.6 26.9 - - + -
340D VAL* 3.3 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 4.6 16.6 - - - +
258D PHE* 3.9 17.9 + - + -
259D VAL* 1.3 83.3 - - - +
261D GLY* 1.3 61.2 + - - +
263D VAL* 4.4 2.7 - - - -
266D GLN* 3.6 17.5 - - + +
267D SER 5.4 1.1 - - - +
268D THR* 5.9 1.1 - - - +
339D ILE* 4.8 21.8 - - + -
340D VAL 2.7 11.4 + - - +
341D TYR* 3.0 37.1 - - + -
342D VAL* 3.2 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 5.2 0.2 - - - -
260D MET* 1.3 75.9 - - - +
262D GLU* 1.3 62.3 + - - -
263D VAL* 2.8 16.8 + - - +
266D GLN* 3.1 24.6 + - - +
341D TYR* 3.5 15.2 - - - -
342D VAL 3.4 10.1 - - - -
----------------------------------------------------------
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