Contacts of the strand formed by residues 242 - 247 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207H SER* 3.5 1.9 - - - -
208H ARG* 3.0 42.3 + - - +
209H ARG 3.9 6.1 + - - -
210H ASN* 5.1 1.6 - - - -
211H PRO* 5.5 0.3 - - - +
215H TRP* 3.5 13.1 - - + -
233H ALA 3.6 23.1 - - - +
236H GLN 3.9 12.1 + - - -
238H TYR* 3.3 23.1 + - + -
241H GLY* 1.3 70.3 - - - -
243H CYS* 1.3 60.9 + - - +
253H ALA* 3.7 17.9 - - + -
254H GLU 3.5 13.7 - - - +
256H CYS* 3.3 4.7 - - - -
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Residues in contact with CYS 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H TRP* 3.3 37.0 - - + +
203H TRP* 3.5 23.6 - - + -
206H LEU 3.9 3.4 - - - -
207H SER* 3.8 11.9 - - - -
215H TRP* 4.4 4.0 - - - -
242H THR* 1.3 75.3 - - - +
244H ALA* 1.3 59.4 + - - +
252H TYR 3.7 0.3 - - - +
253H ALA* 3.4 1.7 - - - -
254H GLU 2.7 41.5 + - - +
256H CYS* 2.0 45.6 - - - -
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Residues in contact with ALA 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203H TRP* 3.4 6.6 - - - -
204H MET* 3.1 31.5 + - + +
206H LEU* 3.0 41.1 + - + +
215H TRP* 4.5 7.2 - - + -
230H VAL* 5.3 1.6 - - + -
243H CYS* 1.3 74.7 - - - +
245H TYR* 1.3 61.6 + - - +
251H VAL* 3.8 20.2 - - + -
252H TYR 3.3 6.1 - - - +
253H ALA* 4.6 0.2 - - - +
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Residues in contact with TYR 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201H PRO* 3.7 24.0 - - + -
202H PHE 3.2 22.9 - - - +
203H TRP* 3.7 16.2 - + + +
204H MET* 4.0 2.9 - - - -
244H ALA* 1.3 75.3 - - - +
246H ILE* 1.3 58.4 + - - +
247H GLN* 3.3 33.8 + - + -
250H ALA 3.6 0.3 - - - +
251H VAL* 3.4 7.1 - - - -
252H TYR* 3.1 59.6 + + + +
254H GLU* 3.4 44.2 + - + -
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Residues in contact with ILE 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180H LEU* 4.4 6.7 - - + -
188H LEU* 4.1 16.4 - - + +
191H ILE* 4.2 19.7 - - + -
192H GLN* 5.7 1.1 - - + +
195H ILE* 4.0 20.6 - - + -
201H PRO* 3.9 0.2 - - - +
202H PHE* 2.9 46.4 + - + +
204H MET* 3.4 23.5 - - + +
245H TYR* 1.3 72.1 - - - +
247H GLN* 1.3 66.3 + - - +
249H GLY* 3.6 11.9 - - - +
250H ALA 3.4 32.8 - - - +
251H VAL* 4.1 10.5 - - + +
263H ILE* 4.5 1.3 - - + -
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Residues in contact with GLN 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195H ILE* 4.8 4.0 - - - -
198H SER 5.7 0.2 - - - +
199H SER 2.8 28.1 + - - +
200H PHE 4.5 4.3 - - - +
201H PRO* 3.5 24.6 - - + +
245H TYR* 3.3 34.4 + - + -
246H ILE* 1.3 80.6 - - - +
248H ARG* 1.3 84.5 + - + +
249H GLY 2.9 4.3 - - - +
250H ALA 2.8 20.2 + - - +
252H TYR* 3.2 18.7 + - + -
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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