Contacts of the strand formed by residues 236 - 241 (chain D) in PDB entry 1PYB
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 LYS 236 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D ALA* 3.5 1.8 - - - +
226D GLU* 3.1 68.8 + - + +
228D VAL* 3.7 25.4 - - + +
234D LEU* 3.0 12.7 + - - +
235D LEU* 1.3 70.3 - - - +
237D LEU* 1.3 63.9 + - - +
238D THR 3.4 2.6 + - - -
247D THR* 5.9 2.0 - - - -
248D VAL 3.7 8.3 - - - +
249D VAL* 4.2 26.5 - - + +
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Residues in contact with LEU 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D VAL* 3.3 38.6 - - + -
224D SER 3.6 1.3 - - - -
225D ALA* 4.1 15.0 - - + -
235D LEU 2.8 18.1 + - - +
236D LYS* 1.3 70.2 - - - +
238D THR* 1.3 59.8 + - - +
239D LEU* 3.3 16.8 + - + +
247D THR* 3.6 1.3 - - - -
248D VAL 3.0 32.4 + - - +
250D ALA* 3.9 11.9 - - + -
252D ILE* 4.7 2.2 - - + -
261D LEU* 3.7 32.1 - - + -
266D ILE* 4.1 11.4 - - + -
286D ILE* 3.8 20.4 - - + -
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Residues in contact with THR 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D LYS 3.7 0.2 - - - +
222D VAL* 3.8 1.4 - - - +
223D LEU* 3.0 41.6 + - + +
224D SER* 2.6 48.5 + - - +
226D GLU* 4.4 20.0 - - + -
236D LYS 3.4 0.4 + - - -
237D LEU* 1.3 69.3 - - - +
239D LEU* 1.3 63.7 + - - +
246D ARG 3.5 4.9 - - - +
247D THR* 3.8 22.2 - - + -
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Residues in contact with LEU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D ALA* 4.3 11.7 - - + +
221D LYS 4.0 4.0 - - - +
222D VAL* 4.7 11.7 - - + +
223D LEU* 4.8 1.0 - - - +
237D LEU* 3.8 17.9 - - + +
238D THR* 1.3 71.8 - - - +
240D SER* 1.3 59.0 + - - +
241D LEU* 3.7 7.6 + - + -
245D GLU* 3.4 5.2 - - - +
246D ARG* 2.7 53.4 + - + +
248D VAL* 3.4 32.5 - - + -
266D ILE* 5.8 0.4 - - + -
268D ILE* 3.6 39.0 - - + -
286D ILE* 3.8 21.3 - - + -
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Residues in contact with SER 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D ALA* 3.4 12.2 - - - +
221D LYS* 2.9 23.4 + - - +
223D LEU* 3.9 27.5 - - - +
239D LEU* 1.3 70.9 - - - +
241D LEU* 1.3 53.4 + - - +
242D GLY 2.7 13.8 + - - -
244D GLU 3.6 4.7 - - - -
245D GLU* 4.7 5.8 - - - +
306D GLU* 2.6 47.4 + - - +
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Residues in contact with LEU 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D ARG* 3.8 44.7 + - + +
219D VAL 4.2 3.4 - - - +
220D ALA* 3.5 22.0 - - + -
239D LEU* 4.9 8.3 - - + -
240D SER* 1.3 66.1 - - - +
242D GLY* 1.3 52.2 + - - +
243D ASP 2.7 18.1 + - - -
244D GLU* 2.8 31.2 + - + +
246D ARG* 3.2 51.1 - - + +
268D ILE* 5.0 13.7 - - + +
269D VAL 6.0 0.2 - - - +
270D ALA* 5.2 2.7 - - + -
307D GLY* 4.3 10.1 - - - +
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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