Contacts of the strand formed by residues 202 - 207 (chain B) in PDB entry 2W8B
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 LEU 202 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 4.1 21.8 - - + +
180B TYR* 3.8 25.8 - - + +
181B GLU 3.9 2.9 - - - -
182B LEU* 3.6 35.2 - - + +
196B HIS* 3.9 17.7 - - + +
198B SER* 3.7 18.2 - - - -
200B GLN 4.1 0.9 - - - +
201B PRO* 1.3 77.3 - - - +
203B MET* 1.3 62.3 + - - +
216B TYR* 4.2 9.2 - - + -
217B VAL 3.1 4.7 - - - +
218B THR* 3.4 34.3 - - - +
422B LYS* 5.7 0.3 - - - -
423B PHE* 3.5 19.4 - - - -
151C GLU* 4.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 5.4 0.4 - - - -
201B PRO 5.2 0.2 - - - -
202B LEU* 1.3 79.3 - - - +
204B SER* 1.3 70.6 + - - +
205B PRO* 3.5 5.2 - - - -
216B TYR* 3.6 3.5 - - - +
217B VAL* 2.8 48.0 + - + -
219B PHE* 3.7 29.6 - - + -
245B HIS* 4.2 12.8 - - - -
423B PHE* 3.9 11.2 - - + -
115C PRO* 3.8 30.1 - - + +
116C GLU* 3.6 26.2 - - + +
119C ILE* 4.2 7.9 - - + -
151C GLU* 3.9 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B MET* 1.3 77.8 - - - +
205B PRO* 1.4 76.3 - - - +
206B ALA* 4.2 0.9 - - - +
215B ALA 3.7 1.1 - - - +
217B VAL* 4.5 0.4 - - - -
248B ALA* 4.3 2.7 - - - -
249B PRO* 3.2 34.4 - - - +
423B PHE* 3.4 20.6 - - - -
116C GLU* 2.7 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ALA* 4.2 15.7 - - + +
170B VAL* 4.5 6.3 - - + -
182B LEU* 3.9 27.4 - - + -
203B MET 3.5 3.1 - - - +
204B SER* 1.4 91.9 - - - +
206B ALA* 1.3 58.4 + - - +
214B LEU* 4.6 5.6 - - + -
215B ALA 3.2 10.1 - - - +
216B TYR* 4.1 6.1 - - + -
423B PHE* 3.1 36.1 - - + +
425B ALA* 3.4 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PRO* 1.3 75.3 - - - +
207B TRP* 1.3 63.3 + - - +
214B LEU* 3.4 6.6 - - - +
215B ALA* 2.9 31.6 + - + +
249B PRO* 3.3 42.4 - - + +
250B ALA* 4.2 8.3 - - - -
251B PHE* 3.4 6.8 - - + +
425B ALA* 4.9 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ARG* 3.8 29.8 - - + -
167B ILE 3.9 14.8 - - - -
168B ALA* 3.8 10.4 - - + +
184B VAL* 4.0 18.4 - - + -
206B ALA* 1.3 72.5 - - - +
208B SER* 1.3 61.6 + - - +
209B PRO* 4.3 0.2 - - - +
211B GLY* 3.6 31.2 - - - -
213B LYS 3.6 8.3 - - - -
214B LEU* 3.4 17.0 - - + -
231B LEU* 3.6 14.8 - - + -
251B PHE* 3.4 13.9 + - - +
425B ALA* 2.8 34.7 + - + -
426B TRP 3.5 10.1 - - - +
427B SER* 3.3 35.8 - - - +
428B PRO* 3.6 14.3 - - + +
430B LEU* 5.4 1.6 - - + -
----------------------------------------------------------
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