Contacts of the strand formed by residues 242 - 247 (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 THR 242 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207F SER* 3.2 5.4 - - - -
208F ARG* 3.0 42.3 + - - +
209F ARG 4.5 3.4 + - - -
211F PRO* 6.1 0.2 - - - +
215F TRP* 3.2 26.4 - - + -
233F ALA 4.6 5.3 + - - +
234F VAL 4.9 3.0 + - - +
236F GLN 3.2 23.4 + - - -
238F TYR* 3.8 8.0 + - + -
241F GLY* 1.3 73.1 - - - -
243F CYS* 1.3 60.2 + - - +
253F ALA* 3.4 9.6 - - + -
254F GLU* 3.4 26.7 - - - +
256F CYS* 3.3 5.4 - - - -
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Residues in contact with CYS 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F TRP* 3.2 37.7 - - + +
203F TRP* 3.3 28.7 - - + -
206F LEU 3.7 4.0 - - - -
207F SER* 3.7 8.7 - - - -
215F TRP* 4.5 0.7 - - - -
242F THR* 1.3 79.3 - - - +
244F ALA* 1.3 60.6 + - - +
252F TYR 3.6 1.4 - - - +
254F GLU* 2.7 33.2 + - - +
256F CYS* 2.0 44.2 - - - -
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Residues in contact with ALA 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F TRP* 3.3 7.6 - - - -
204F MET* 3.2 28.0 + - + +
206F LEU* 3.0 39.8 + - + +
215F TRP* 4.4 7.4 - - + -
230F VAL* 4.6 5.6 - - + -
243F CYS* 1.3 74.3 - - - +
245F TYR* 1.3 61.3 + - - +
251F VAL* 3.8 21.1 - - + -
252F TYR 3.2 6.5 - - - +
253F ALA* 4.5 0.2 - - - +
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Residues in contact with TYR 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F PRO* 3.3 36.6 - - + +
202F PHE 3.1 26.7 - - - +
203F TRP* 3.7 26.9 - + + -
204F MET* 4.3 4.0 - - - -
244F ALA* 1.3 74.9 - - - +
246F ILE* 1.3 62.5 + - - +
247F GLN* 3.9 15.3 + - + -
251F VAL* 3.3 7.2 - - - -
252F TYR* 3.0 64.1 + + + +
253F ALA 5.3 0.5 + - - -
254F GLU* 3.9 28.4 + - + +
260F ALA* 5.6 0.2 - - + -
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Residues in contact with ILE 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F LEU* 4.7 5.8 - - + -
182F ILE* 5.2 0.2 - - + -
188F LEU* 3.3 35.2 - - + -
191F ILE* 4.2 24.0 - - + -
192F GLN* 5.0 6.5 - - + +
195F ILE* 4.1 22.3 - - + +
201F PRO* 3.9 0.7 - - - +
202F PHE* 2.8 47.9 + - + +
204F MET* 3.7 18.5 - - + +
245F TYR* 1.3 72.4 - - - +
247F GLN* 1.3 65.7 + - - +
249F GLY* 4.3 17.3 - - - +
250F ALA 3.3 9.6 - - - +
251F VAL* 4.5 2.0 - - + -
263F ILE* 4.7 0.2 - - + -
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Residues in contact with GLN 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F ILE* 5.4 3.6 - - - -
199F SER 2.5 31.0 + - - +
200F PHE* 3.4 6.0 - - - +
201F PRO* 3.0 34.2 - - + +
245F TYR* 3.9 24.6 + - + -
246F ILE* 1.3 77.9 - - - +
248F ARG* 1.3 89.8 + - + +
249F GLY 2.6 6.6 + - - +
250F ALA 2.6 34.9 + - - +
252F TYR* 3.2 8.8 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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