Contacts of the strand formed by residues 225 - 230 (chain F) in PDB entry 1YPH
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 PRO 225 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F LEU* 3.7 31.2 - - + -
167F ASN 5.6 0.2 - - - +
168F CYS* 4.0 17.0 - - - -
171F TYR* 4.1 17.3 - - + -
172F TRP* 3.0 37.0 + - + +
182F CYS* 4.0 13.2 - - + -
183F ALA 3.9 6.5 - - - +
185F ALA* 3.6 13.9 - - + +
216F GLY* 4.6 1.7 - - - -
217F SER 4.9 1.1 + - - -
223F SER 4.5 0.7 - - - +
224F THR* 1.3 90.1 + - - +
226F GLY* 1.3 59.2 + - - +
227F VAL* 4.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 226 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F CYS* 3.1 7.3 - - - +
183F ALA 2.9 36.5 + - - -
184F GLY* 4.9 0.2 - - - -
185F ALA 4.9 0.2 - - - +
190F SER* 6.0 6.3 - - - -
215F TRP 4.2 4.5 - - - -
216F GLY* 4.6 4.9 - - - -
217F SER 5.7 0.4 - - - -
224F THR 3.6 2.4 + - - -
225F PRO* 1.3 74.8 - - - +
227F VAL* 1.3 59.9 + - - -
228F TYR* 3.6 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F TRP* 3.8 18.2 - - + +
176F ILE* 3.9 11.0 - - + -
180F MET* 3.8 28.5 - - + -
181F ILE 3.8 3.6 - - - +
182F CYS* 4.1 3.8 - - - +
213F VAL* 5.2 0.5 - - - +
214F SER* 3.1 9.0 + - - -
215F TRP* 2.8 91.1 + - + +
225F PRO 4.2 0.4 - - - +
226F GLY* 1.3 76.6 - - - +
228F TYR* 1.4 70.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 228 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D THR* 4.0 16.7 - - - +
160F LEU* 3.7 19.1 - - + +
180F MET* 3.3 6.8 - - - +
181F ILE* 2.8 53.2 + - + +
183F ALA* 3.7 23.4 + - + -
190F SER* 4.1 16.5 + - - -
199F LEU* 3.8 26.7 - - + -
211F GLY* 4.0 2.0 - - - -
212F ILE 3.2 11.7 - - - +
213F VAL* 3.6 41.3 - - + -
214F SER* 3.8 3.1 - - - -
226F GLY* 3.6 26.0 - - - -
227F VAL* 1.4 77.2 - - - +
229F ALA* 1.3 59.8 + - - +
230F ARG 3.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ASP* 3.5 35.7 - - + +
179F ALA 3.7 6.1 - - - -
180F MET* 4.7 1.3 - - - +
211F GLY* 3.1 26.0 - - - -
212F ILE* 2.8 26.1 + - + +
214F SER* 3.7 4.7 - - - -
228F TYR* 1.3 68.6 - - - +
230F ARG* 1.3 61.7 + - - +
231F VAL* 3.2 3.7 + - - +
234F LEU* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 230 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D PHE* 5.3 4.4 + - - +
163F LEU 5.0 2.2 + - - -
164F SER* 5.9 0.4 - - - +
165F ASN* 2.9 35.4 + - - +
178F ASP 3.4 15.7 + - - -
179F ALA* 2.8 23.6 + - - +
180F MET 3.0 20.5 + - - -
181F ILE* 3.6 42.3 - - + +
210F VAL 4.0 1.8 - - - +
228F TYR 3.3 1.8 + - - -
229F ALA* 1.3 68.0 - - - +
231F VAL* 1.4 66.9 + - - +
232F THR* 3.4 24.3 + - - +
233F ALA* 2.9 23.1 + - - +
234F LEU* 3.5 8.7 + - - +
----------------------------------------------------------
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