Contacts of the strand formed by residues 241 - 250 (chain B) in PDB entry 2DW1
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 241 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PHE* 3.6 1.2 - - - -
198B ARG* 3.7 20.4 - - + +
200B VAL* 3.8 27.8 - - + -
233B ASN* 4.5 0.7 - - - +
236B TYR* 2.7 51.7 + - + +
239B MET* 3.5 9.2 - - + +
240B TYR* 1.3 84.7 - - - +
242B HIS* 1.3 73.6 + - - +
243B VAL* 5.0 1.1 - - + -
339B LEU* 3.5 34.3 - - + -
377B CYS* 3.7 22.7 - - - -
378B TRP* 5.0 0.2 - - + -
381B ILE* 4.3 10.3 - - + -
389B ILE* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PHE* 3.2 39.0 - + + -
198B ARG 2.9 7.6 + - - +
199B PHE* 3.4 40.6 - + + +
200B VAL* 2.7 34.5 + - - +
233B ASN* 3.6 21.8 - - - +
237B ARG* 5.3 3.7 - - + +
241B ILE* 1.3 76.0 - - - +
243B VAL* 1.3 58.4 + - - +
244B ALA* 4.0 0.8 + - - +
407B GLU* 3.1 52.2 + - + +
408B LEU* 4.1 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B VAL* 3.7 7.6 - - + +
202B LEU* 3.9 28.5 - - + -
229B VAL* 4.3 12.7 - - + +
232B VAL* 3.7 31.9 - - + -
233B ASN* 2.6 34.1 + - + +
236B TYR* 3.9 24.9 - - + -
241B ILE* 5.0 2.5 - - + -
242B HIS* 1.3 75.5 - - - +
244B ALA* 1.3 61.8 + - - +
335B MET* 4.1 19.5 - - + -
408B LEU* 3.8 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PHE* 6.0 1.6 - - + -
200B VAL 3.0 11.4 + - - +
201B GLU* 3.4 3.7 - - - -
202B LEU* 2.8 33.1 + - - -
229B VAL* 4.9 0.4 - - - -
242B HIS 4.0 1.5 + - - +
243B VAL* 1.3 74.6 - - - +
245B LEU* 1.3 59.0 + - - +
246B VAL* 3.4 3.0 + - + +
393B PRO* 4.2 18.2 - - + -
398B ILE* 4.0 21.1 - - + -
408B LEU* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU* 3.3 17.3 - - + +
204B LEU* 3.8 30.3 - - + +
225B MET* 5.2 1.6 - - + -
226B TYR* 3.9 33.9 - - + -
229B VAL* 4.2 27.2 - - + +
244B ALA* 1.3 69.8 - - - +
246B VAL* 1.3 58.7 + - - +
247B GLY 2.8 27.1 - - - +
248B LEU* 4.4 8.3 - - + -
398B ILE* 3.6 12.8 - - - +
399B ILE* 3.4 29.9 + - + +
400B SER* 4.6 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLU* 3.6 49.6 - - + +
202B LEU 2.8 16.9 + - - +
203B VAL* 3.8 13.0 - - + -
244B ALA* 3.9 6.7 - - + +
245B LEU* 1.3 75.8 - - - +
247B GLY* 1.3 58.4 + - - +
282B LYS* 2.8 36.4 + - - +
283B LYS 4.2 3.4 - - - +
284B HIS* 3.9 7.6 - - + -
393B PRO* 4.8 6.1 - - + -
397B ASP* 3.4 28.4 - - + +
398B ILE* 4.9 1.3 - - - -
399B ILE* 3.7 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU 3.5 3.8 + - - -
203B VAL* 3.9 20.0 - - - -
204B LEU 3.3 4.5 + - - -
245B LEU* 2.8 26.8 - - - +
246B VAL* 1.3 79.7 - - - +
248B LEU* 1.3 60.9 + - - +
282B LYS* 4.5 4.5 - - - -
399B ILE* 3.1 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 4.2 2.4 - - - +
204B LEU* 3.2 32.5 + - + +
206B VAL* 4.2 20.0 - - + -
222B LYS* 3.8 41.5 - - + -
225B MET* 4.6 12.6 - - + -
226B TYR* 4.2 16.8 - - + +
245B LEU* 4.4 4.3 - - + -
247B GLY* 1.3 76.0 - - - +
249B GLU* 1.3 63.9 + - - +
250B ILE* 4.0 11.3 + - + +
399B ILE* 3.4 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 4.9 3.6 - - + +
204B LEU 2.9 8.6 + - - +
205B VAL* 3.2 13.0 - - + +
206B VAL 2.8 25.3 + - - -
248B LEU* 1.3 78.1 - - - +
250B ILE* 1.3 62.8 + - - +
251B TRP* 4.2 8.6 + - + +
256B LYS* 3.8 10.0 + - - -
273B TRP* 3.7 13.1 - - - -
278B LEU* 3.5 17.4 - - + +
281B ARG* 2.5 47.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 3.6 20.9 - - + +
211B VAL* 3.5 28.5 - - + -
218B LEU* 3.7 36.6 - - + -
221B ILE* 4.5 13.0 - - + -
222B LYS* 3.8 31.2 - - + -
248B LEU* 4.0 13.0 + - + +
249B GLU* 1.3 79.1 - - - +
251B TRP* 1.3 64.6 + - - +
252B SER* 2.9 14.7 + - - +
----------------------------------------------------------
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