Contacts of the helix formed by residues 231 - 245 (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 VAL 231 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ILE* 5.3 7.4 - - + -
123D LEU* 4.3 12.3 - - + -
124D PRO* 3.7 16.8 - - + -
209F LEU* 3.5 30.3 - - + +
210F VAL 3.1 24.1 + - - +
211F GLY* 3.9 6.3 - - - +
212F ILE* 4.0 23.6 - - + -
229F ALA* 3.9 7.0 - - + +
230F ARG* 1.4 70.6 - - - +
232F THR* 1.3 58.6 + - - +
234F LEU* 3.0 7.2 + - - +
235F VAL* 2.8 37.2 + - + +
238F VAL* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 232 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D PRO* 4.1 6.9 - - + +
125D SER 3.4 17.0 - - - +
126D ALA* 3.3 39.2 - - - +
128D ASP 3.7 19.9 + - - +
130D PHE* 4.1 23.3 - - + -
210F VAL* 4.6 2.3 + - + +
230F ARG* 3.4 24.0 + - + +
231F VAL* 1.3 77.4 - - - +
233F ALA* 1.3 61.9 + - - +
234F LEU 3.4 0.5 + - - -
235F VAL* 3.7 10.6 + - - +
236F ASN 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F ASP 4.5 2.5 - - - +
179F ALA* 3.8 31.4 - - + +
230F ARG* 2.9 20.4 + - + +
232F THR* 1.3 79.4 + - - +
234F LEU* 1.3 62.9 + - - +
235F VAL 3.8 0.2 - - - -
236F ASN* 5.3 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ASN* 4.0 15.3 - - - +
101D ASN* 3.5 43.3 - - + +
103D ILE* 3.8 33.9 - - + -
179F ALA* 4.4 4.5 - - + +
229F ALA* 3.9 25.6 - - + -
230F ARG 3.7 15.9 - - - +
231F VAL* 3.0 6.4 + - - +
233F ALA* 1.3 87.8 - - + +
235F VAL* 1.3 59.6 + - - +
236F ASN 3.3 3.1 - - - -
237F TRP* 3.3 13.1 + - - +
238F VAL* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D LEU* 4.2 23.8 - - + -
124D PRO 3.3 22.7 - - - +
125D SER* 3.8 2.5 - - - -
126D ALA* 3.4 29.6 - - + +
231F VAL* 2.8 22.3 + - + +
232F THR* 3.7 11.2 - - - +
233F ALA 3.8 0.2 - - - -
234F LEU* 1.3 76.1 - - - +
236F ASN* 1.3 65.6 + - - +
238F VAL* 4.0 8.5 - - + -
239F GLN* 2.8 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 236 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ALA* 3.7 28.5 + - - +
232F THR 4.9 1.0 + - - -
233F ALA 5.3 1.8 - - - +
234F LEU 3.3 1.0 - - - -
235F VAL* 1.3 80.0 - - - +
237F TRP* 1.4 58.4 + - - +
239F GLN* 3.3 7.0 + - - +
240F GLN* 2.9 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 237 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D PHE* 3.3 28.5 - - + -
90D LYS 4.0 2.0 - - - -
91D ASN* 3.4 47.8 - - + +
103D ILE* 3.8 20.9 - - + -
105D LEU* 3.8 30.5 - - + -
2300D SO4 3.1 39.1 + - - -
234F LEU* 3.3 12.1 + - - +
236F ASN* 1.4 80.2 - - - +
238F VAL* 1.4 82.0 + - + +
240F GLN* 3.8 14.8 + - + +
241F THR* 2.8 42.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 4.0 17.5 - - + -
53D VAL* 4.8 3.1 - - + -
103D ILE* 3.8 19.1 - - + -
105D LEU* 4.0 15.0 - - + -
123D LEU* 3.9 29.8 - - + -
231F VAL* 5.8 1.6 - - + -
234F LEU 3.1 16.2 + - - +
235F VAL* 3.1 15.0 + - + +
237F TRP* 1.4 93.3 - - + +
239F GLN* 1.3 61.1 + - - +
241F THR* 3.2 1.9 + - - -
242F LEU* 2.9 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 239 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D LEU* 3.9 31.9 - - - +
124D PRO 5.1 1.8 + - - -
235F VAL* 2.8 31.2 + - + +
236F ASN* 3.8 7.0 - - - +
238F VAL* 1.3 74.3 - - - +
240F GLN* 1.3 57.2 + - + +
242F LEU* 3.4 12.5 + - - +
243F ALA* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 240 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236F ASN* 2.9 38.1 + - - +
237F TRP* 3.8 15.9 - - + +
239F GLN* 1.3 74.2 - - + +
241F THR* 1.4 64.1 - - - +
243F ALA* 3.4 6.3 + - - +
244F ALA* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 241 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D TRP* 4.2 6.5 - - + -
89D PHE* 3.8 35.2 - - + -
105D LEU* 3.7 21.5 - - + -
2300D SO4 4.5 3.8 + - - +
237F TRP* 2.8 43.5 + - - -
238F VAL 3.6 3.8 - - - -
240F GLN* 1.4 77.7 - - - +
242F LEU* 1.4 62.2 + - - +
244F ALA* 3.4 1.4 + - - -
245F ASN* 2.9 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 3.8 15.9 - - + -
48D ASN* 3.3 28.3 - - - +
51D TRP* 3.5 48.2 + - + +
105D LEU* 3.8 17.5 - - + -
123D LEU* 5.6 2.0 - - + -
238F VAL* 2.9 24.0 + - + +
239F GLN* 4.0 13.7 - - - +
241F THR* 1.4 78.0 - - - +
243F ALA* 1.3 62.6 + - - +
244F ALA 3.3 0.3 + - - -
245F ASN 3.3 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239F GLN 3.0 18.7 + - - +
240F GLN* 3.8 5.8 - - - +
242F LEU* 1.3 76.0 - - - +
244F ALA* 1.3 59.2 + - - +
245F ASN 3.7 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F GLN 3.1 16.7 + - - +
241F THR* 4.9 0.7 - - - -
242F LEU 3.3 0.2 - - - -
243F ALA* 1.3 78.2 - - - +
245F ASN* 1.3 72.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 245 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D TRP* 3.7 23.3 + - + -
87D LYS* 5.5 0.7 + - - -
89D PHE* 3.5 35.8 - - + -
107D LYS* 3.5 26.3 + - - -
241F THR* 2.9 32.4 + - - +
242F LEU 3.3 13.4 + - - +
243F ALA 4.3 2.8 - - - +
244F ALA* 1.3 93.5 - - - +
----------------------------------------------------------
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