Contacts of the strand formed by residues 247 - 251 (chain D) in PDB entry 1PZY
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 CYS 247 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D HIS* 5.5 2.2 - - + +
181D LYS 3.1 1.8 + - - +
182D VAL* 3.4 22.3 - - + -
183D ALA* 3.0 24.2 + - - +
245D TYR* 3.6 0.9 - - - +
246D ASN* 1.3 92.7 + - - +
248D PHE* 1.3 71.9 + - - +
265D ARG* 3.5 11.7 - - + -
266D CYS* 2.0 63.3 - - + +
295D ALA* 4.6 1.1 - - - -
296D LEU 3.9 0.7 - - - -
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Residues in contact with PHE 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D ALA* 3.5 20.6 - - + -
185D ILE* 3.7 19.5 - - + -
236D PHE* 3.3 56.8 - + + -
239D ALA* 4.2 5.6 - - + -
240D LEU* 3.8 21.8 - - + -
245D TYR* 3.9 11.9 - - + -
247D CYS* 1.3 78.0 - - - +
249D VAL* 1.3 62.6 + - - +
250D PHE* 3.7 21.9 - - + -
295D ALA* 3.1 3.6 - - - -
296D LEU* 2.9 44.9 + - + +
297D SER 4.6 0.4 - - - -
298D LYS* 3.9 24.7 - - + -
301D PHE* 5.4 1.6 - - + -
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Residues in contact with VAL 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D VAL* 3.5 21.3 - - + +
183D ALA 3.0 6.7 + - - +
184D ILE* 3.3 18.3 - - + +
185D ILE* 2.8 28.9 + - - +
247D CYS* 4.8 0.2 - - - -
248D PHE* 1.3 72.1 - - - +
250D PHE* 1.3 64.2 + - - +
251D SER* 4.5 0.4 - - - -
264D TYR* 3.6 50.9 - - + +
265D ARG* 4.2 0.9 - - - +
273D ILE* 4.4 2.5 - - + -
293D VAL* 3.9 18.8 - - + -
294D SER 3.4 5.8 - - - +
295D ALA* 3.8 14.1 - - + -
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Residues in contact with PHE 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D ILE* 3.6 23.1 - - + -
228D ARG* 4.9 5.0 + - - +
232D LEU* 3.7 58.8 - - + -
236D PHE* 4.8 4.0 - - + -
248D PHE* 3.7 35.2 - + + -
249D VAL* 1.3 72.3 - - - +
251D SER* 1.3 59.0 + - - +
292D GLY 3.5 2.9 - - - +
293D VAL* 3.1 4.7 - - - -
294D SER* 2.7 44.5 + - - +
296D LEU* 4.2 11.7 - - + -
301D PHE* 3.7 27.4 - + - -
307D PHE* 3.6 26.0 - + + -
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Residues in contact with SER 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ILE* 4.4 17.3 - - - -
185D ILE 3.0 7.5 + - - -
186D ILE* 3.3 10.6 - - - +
187D PRO* 3.0 22.1 - - - +
198D TRP* 3.4 19.9 + - - -
228D ARG* 5.5 0.4 - - - -
249D VAL* 3.9 1.9 + - - -
250D PHE* 1.3 75.3 - - - +
252D ASP* 1.3 76.0 + - - +
255D LEU 4.5 1.2 + - - -
264D TYR* 4.8 3.2 - - - -
292D GLY 3.6 4.3 - - - -
293D VAL* 3.7 23.7 - - - +
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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