Contacts of the strand formed by residues 287 - 293 (chain B) in PDB entry 2WFD
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 ILE 287 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LYS* 3.5 7.9 - - - +
271B VAL* 2.9 36.9 + - + +
275B TYR* 3.8 26.1 + - + +
279B LEU* 4.1 18.6 - - + -
282B LEU* 3.8 31.0 - - + -
285B LYS 3.5 11.5 + - - +
286B ASN* 1.3 78.1 - - - +
288B PHE* 1.3 69.6 + - - +
323B ILE* 3.4 21.8 - - + +
325B ILE* 3.4 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LYS* 3.7 37.7 - - + -
269B LEU 3.2 5.6 - - - +
270B LYS* 3.5 50.7 - - + -
286B ASN* 4.1 12.8 - - + -
287B ILE* 1.3 75.8 - - - +
289B LEU* 1.3 69.2 + - - +
290B VAL 3.8 0.2 + - - -
322B ASP* 3.6 35.7 - - + -
323B ILE 3.0 7.2 + - - -
324B PHE* 3.2 30.8 - + + -
325B ILE 2.8 24.6 + - - -
502B GLY 5.8 0.9 - - - -
503B ASP* 6.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LYS* 3.8 0.3 - - - -
269B LEU* 2.8 44.8 + - + +
271B VAL* 4.2 15.3 - - + +
288B PHE* 1.3 75.8 - - - +
290B VAL* 1.3 60.0 + - - +
291B ALA 4.4 0.2 - - - -
305B CYS* 4.4 0.2 - - - -
307B VAL* 4.8 2.7 - - + -
325B ILE* 3.3 48.0 - - + +
357B ILE* 4.0 20.0 - - + -
360B ALA* 5.9 0.9 - - + -
362B LEU* 4.0 10.3 - - + -
374B VAL* 3.4 33.9 - - + -
388B VAL* 4.2 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 3.4 25.4 - - + -
267B LEU 3.4 14.8 - - - +
268B LYS* 4.5 3.8 - - + -
288B PHE 4.3 3.8 - - - +
289B LEU* 1.3 78.8 - - - +
291B ALA* 1.3 53.9 + - - +
324B PHE* 4.1 29.4 - - + -
325B ILE 3.3 16.1 + - - +
326B CYS* 3.7 11.9 - - + -
334B MSE 3.6 26.2 - - + -
386B THR* 2.6 24.4 + - - -
388B VAL* 3.5 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B THR 3.7 0.3 - - - +
266B LEU* 3.5 6.0 - - - +
267B LEU* 2.8 43.5 + - + +
269B LEU* 5.0 10.6 - - + +
289B LEU 4.4 0.2 - - - -
290B VAL* 1.3 72.3 - - - +
292B ALA* 1.3 58.4 + - - +
386B THR* 3.5 2.0 - - - -
388B VAL* 3.0 34.1 - - + +
389B VAL* 4.2 0.7 - - - -
390B THR* 4.0 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ALA* 4.0 16.2 + - + -
264B TYR* 4.1 22.2 - - + -
265B THR 3.3 7.9 - - - +
266B LEU* 3.7 12.9 - - + +
267B LEU* 5.4 0.2 - - - -
291B ALA* 1.3 74.4 - - - +
293B THR* 1.3 64.8 - - - +
385B GLY* 5.4 5.4 - - - -
386B THR* 4.2 12.6 + - + +
388B VAL 4.5 1.0 + - - -
389B VAL* 6.0 0.3 - - - -
390B THR* 4.3 7.7 + - - +
507B TYR* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ALA 3.6 13.5 + - - -
259A MSE 4.1 8.7 - - - +
264B TYR* 3.9 5.4 - - - -
265B THR* 2.8 45.7 + - - +
267B LEU* 4.0 15.3 - - + -
292B ALA* 1.3 77.5 - - - +
294B LEU* 1.3 67.8 + - - +
295B ARG 3.3 14.7 + - - +
296B PRO* 3.8 13.7 - - + -
299B MSE 3.3 31.9 - - + +
390B THR* 4.2 3.0 - - - +
----------------------------------------------------------
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