Contacts of the strand formed by residues 250 - 255 (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 ALA 250 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188H LEU* 5.9 0.2 - - - -
228H PHE* 6.0 2.5 - - - -
231H ARG* 3.5 25.6 - - - +
246H ILE* 3.4 2.9 - - - +
247H GLN 2.8 33.6 + - - +
248H ARG* 4.6 3.1 - - + +
249H GLY* 1.3 80.4 - - - +
251H VAL* 1.3 65.1 + - - +
252H TYR* 3.4 18.3 - - + +
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Residues in contact with VAL 251 (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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188H LEU* 5.5 0.4 - - + -
204H MET* 4.2 11.2 - - + -
228H PHE* 3.5 53.5 - - + +
229H ARG 3.4 10.3 + - - +
230H VAL* 4.1 9.2 - - + -
231H ARG* 2.8 28.7 + - - +
244H ALA* 3.8 26.2 - - + -
245H TYR 3.4 8.7 - - - +
246H ILE* 4.1 14.4 - - + -
250H ALA* 1.3 76.6 - - - +
252H TYR* 1.3 69.6 + - - +
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Residues in contact with TYR 252 (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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230H VAL* 4.3 1.3 - - - -
231H ARG* 3.4 35.4 - - + +
232H GLY* 4.4 6.7 - - - +
243H CYS 3.7 0.5 - - - +
244H ALA* 3.3 5.5 - - - +
245H TYR* 3.1 65.0 + + + +
247H GLN* 3.2 40.0 + - + -
248H ARG* 4.3 10.2 - - - +
250H ALA* 3.4 23.4 - - + +
251H VAL* 1.3 79.3 - - - +
253H ALA* 1.3 61.1 + - - +
254H GLU 3.8 0.5 + - - -
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Residues in contact with ALA 253 (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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215H TRP* 3.6 28.5 - - + -
230H VAL* 3.9 1.6 - - + -
231H ARG 2.6 19.1 + - - +
232H GLY* 3.8 1.7 - - - -
233H ALA* 3.0 42.2 + - - +
234H VAL* 3.6 9.4 - - + -
242H THR* 3.7 3.4 - - + -
243H CYS 3.4 4.9 - - - -
244H ALA* 4.6 0.2 - - - +
252H TYR* 1.3 72.8 - - - +
254H GLU* 1.3 62.5 + - - +
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Residues in contact with GLU 254 (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* 4.0 9.2 - - + -
233H ALA* 5.1 3.0 - - - +
238H TYR* 4.4 6.0 + - - -
242H THR* 3.5 6.9 - - - +
243H CYS* 2.7 38.2 + - - +
245H TYR* 3.4 37.2 + - + -
252H TYR 3.8 0.8 + - - -
253H ALA* 1.3 77.8 - - - +
255H ASN* 1.3 82.2 + - - +
258H LEU* 3.6 28.0 - - + +
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Residues in contact with ASN 255 (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 9.9 - - - -
238H TYR* 3.0 53.5 - - + +
239H PRO* 5.2 3.4 - - - +
240H SER* 2.9 26.5 + - - -
254H GLU* 1.3 80.0 + - - +
256H CYS* 1.3 63.1 + - - +
257H ILE* 2.9 27.8 + - + +
258H LEU* 3.3 28.6 + - + +
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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