Contacts of the strand formed by residues 202 - 208 (chain F) in PDB entry 1YPO
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 PHE 202 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E TYR* 3.7 41.3 - + + -
158F PHE* 4.3 13.9 - + + -
159F SER 4.9 0.2 - - - -
195F ILE* 3.8 35.7 - - + -
198F SER* 3.6 18.6 - - - -
200F PHE 3.6 13.5 - - - -
201F PRO* 1.3 74.4 - - - +
203F TRP* 1.3 64.0 + - - +
245F TYR* 3.1 4.3 - - - +
246F ILE* 2.8 40.0 + - + +
261F PHE* 3.3 25.6 - + + -
262F SER* 3.7 17.0 - - - -
263F ILE* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 203 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F PHE 3.3 11.2 + - - -
165F TRP* 3.3 45.2 - + + +
168F SER* 3.3 23.3 - - - -
179F LEU* 4.4 5.6 - - + +
180F LEU* 4.7 0.5 - - - +
201F PRO 4.3 0.2 - - - -
202F PHE* 1.3 75.9 - - - +
204F MET* 1.3 59.5 + - - +
243F CYS* 3.3 34.3 - - + -
244F ALA 3.3 22.2 - - - -
245F TYR* 3.7 23.3 - + + +
254F GLU* 4.2 5.6 - - + -
255F ASN 3.3 24.2 - - - -
256F CYS* 4.3 1.1 - - - -
258F LEU* 3.2 23.5 + - + -
260F ALA* 3.6 13.1 - - + +
261F PHE 2.7 21.9 + - - +
262F SER* 3.9 8.7 - - - -
263F ILE* 3.5 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 204 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F TRP* 2.7 22.6 + - - -
179F LEU* 3.9 6.3 - - - -
180F LEU* 3.7 23.1 - - + +
182F ILE* 4.0 20.0 - - + -
202F PHE 4.7 0.2 - - - +
203F TRP* 1.3 74.8 - - - +
205F GLY* 1.3 59.2 + - - +
206F LEU* 2.8 21.2 + - + +
217F TRP* 4.1 14.6 - - - -
228F PHE* 4.0 21.5 - - - -
244F ALA 3.2 20.5 + - - +
245F TYR* 4.3 0.4 - - - +
246F ILE* 3.7 34.1 - - + +
251F VAL* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 205 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F TRP* 4.0 6.9 - - - -
179F LEU* 3.5 19.7 - - - +
180F LEU 2.7 20.9 + - - -
204F MET* 1.3 68.1 - - - +
206F LEU* 1.3 57.6 + - - +
207F SER 4.0 0.3 + - - -
216F LEU 3.4 0.2 - - - +
217F TRP* 2.9 33.6 - - - -
218F GLU* 3.1 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F TRP* 4.1 1.6 + - - -
204F MET* 2.8 17.6 + - + +
205F GLY* 1.3 75.4 - - - +
207F SER* 1.3 65.4 + - - +
215F TRP* 4.0 21.3 - - + -
216F LEU 3.3 21.5 - - - +
217F TRP* 3.5 31.6 - - + -
223F LEU* 4.0 16.8 - - + -
228F PHE* 3.7 33.9 - - + -
230F VAL* 4.2 7.6 - - + -
243F CYS* 3.7 0.9 - - - -
244F ALA* 3.0 43.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 207 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F TRP* 3.8 19.6 - - - -
205F GLY 5.0 0.3 + - - -
206F LEU* 1.3 79.9 - - - +
208F ARG* 1.3 63.2 + - - +
215F TRP* 3.3 14.8 - - - -
216F LEU* 2.9 36.3 + - - +
217F TRP 5.4 1.6 + - - -
242F THR 3.2 11.4 - - - -
243F CYS* 3.7 17.7 - - - -
256F CYS* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 208 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F SER* 1.3 79.8 + - - +
209F ARG* 1.3 63.0 + - - +
210F ASN 3.8 11.9 - - - +
211F PRO* 3.6 26.5 + - - +
213F TYR* 3.3 26.8 + - + +
214F PRO* 3.6 17.2 - - - +
215F TRP* 3.6 49.8 - - + +
216F LEU* 6.0 0.4 - - + -
234F VAL* 2.8 38.8 + - - +
241F GLY* 4.0 0.9 - - - -
242F THR* 3.0 30.8 + - - +
----------------------------------------------------------
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