Contacts of the helix formed by residues 235 - 246 (chain B) in PDB entry 1YZ3
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 SER 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B LEU* 3.6 7.2 - - - -
218B GLU* 3.9 19.5 - - - -
234B VAL* 1.3 73.7 - - - +
236B GLU* 1.3 66.2 + - - +
237B GLU* 3.6 11.7 + - - +
238B GLU* 3.1 33.6 + - - +
239B VAL* 3.1 25.3 + - - +
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Residues in contact with GLU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLU* 4.5 0.8 - - - +
253A LEU 3.9 2.6 - - - +
254A ARG* 3.5 23.2 - - - +
255A THR* 3.0 34.7 + - - +
217B LEU* 3.7 17.1 - - + +
235B SER* 1.3 72.4 - - - +
237B GLU* 1.3 66.3 + - + +
239B VAL* 2.9 8.5 + - - +
240B ARG* 2.9 41.2 + - - +
253B LEU* 3.8 27.3 - - + +
255B THR* 2.7 28.9 + - - +
273B PHE* 5.5 1.8 - - + -
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASN* 5.5 2.8 - - - +
56A TRP* 3.5 24.0 + - - +
59A ARG* 3.3 40.7 + - - +
254A ARG* 4.4 20.5 + - - +
235B SER* 3.3 9.9 + - - +
236B GLU* 1.3 82.0 - - + +
238B GLU* 1.3 57.5 + - + +
240B ARG* 3.5 11.1 + - - +
241B GLU* 2.9 31.5 + - - +
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Residues in contact with GLU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B LEU* 3.6 41.9 - - + +
194B PHE* 5.8 0.7 - - - -
233B PRO 3.9 5.1 - - - +
234B VAL* 3.3 15.2 - - + +
235B SER* 3.1 33.5 + - - +
236B GLU 3.2 1.0 - - - -
237B GLU* 1.3 79.8 - - + +
239B VAL* 1.3 57.9 + - - +
241B GLU* 3.7 14.9 - - - +
242B ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B PHE* 4.6 11.6 - - + -
213B LEU* 4.7 5.4 - - + -
217B LEU* 4.6 0.7 - - + -
234B VAL* 4.0 13.9 - - + -
235B SER 3.1 14.9 + - - +
236B GLU* 2.9 9.2 + - - +
238B GLU* 1.3 73.2 - - - +
240B ARG* 1.3 68.1 + - - +
242B ALA* 3.2 6.2 + - - +
243B LEU* 2.9 41.7 + - + +
253B LEU* 4.8 5.4 - - + -
273B PHE* 3.7 54.1 - - + -
275B ALA* 4.7 1.8 - - + -
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Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASP* 3.9 21.1 + - - -
253A LEU 4.1 6.3 + - - -
254A ARG* 4.1 20.6 - - - +
236B GLU* 2.9 30.4 + - - +
237B GLU* 3.7 10.7 - - - +
239B VAL* 1.3 76.0 - - - +
241B GLU* 1.3 65.2 + - - +
243B LEU* 3.0 20.3 + - - +
244B VAL* 3.1 18.9 + - + +
250B VAL* 4.0 29.3 - - + +
253B LEU* 3.4 37.9 + - + +
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Residues in contact with GLU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B LEU* 4.8 7.3 - - - +
195B GLN* 5.2 0.9 - - - +
237B GLU 2.9 17.9 + - - +
238B GLU* 3.7 20.3 - - - +
240B ARG* 1.3 77.8 - - - +
242B ALA* 1.3 57.3 - - - +
244B VAL* 3.4 6.6 + - - +
245B ARG* 2.7 68.0 + - - +
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B LEU* 5.8 2.7 - - + -
194B PHE* 4.2 20.6 - - + -
195B GLN* 3.1 36.7 - - - +
198B LEU* 3.8 12.8 - - + -
238B GLU 2.9 19.5 + - - +
239B VAL 3.7 3.8 - - - +
241B GLU* 1.3 76.9 - - - +
243B LEU* 1.3 63.5 + - - +
245B ARG 3.2 0.3 + - - -
246B SER* 3.1 21.7 + - - -
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LEU* 3.9 18.6 - - + -
211B LEU* 4.1 14.6 - - + -
213B LEU* 4.2 9.2 - - + -
239B VAL* 2.9 31.5 + - + +
240B ARG* 3.0 7.6 + - - +
242B ALA* 1.3 76.8 - - - +
244B VAL* 1.3 61.5 + - - +
246B SER 3.2 6.8 + - - -
248B TYR* 3.1 39.0 + - + -
250B VAL* 4.1 23.8 - - + -
253B LEU* 5.3 1.1 - - + -
275B ALA* 3.7 29.2 - - + -
277B ALA* 4.1 19.3 - - + -
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ARG* 3.1 18.7 + - + +
241B GLU* 3.8 8.7 - - - +
243B LEU* 1.3 76.1 - - - +
245B ARG* 1.3 63.1 + - - +
246B SER 3.0 0.2 - - - -
247B GLY* 3.0 15.1 + - - -
248B TYR 3.7 16.9 + - - +
249B LYS* 5.7 0.2 - - - -
250B VAL* 4.4 13.7 - - + +
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Residues in contact with ARG 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B GLN* 3.5 32.8 - - + +
199B ASP* 4.4 3.8 - - - +
241B GLU* 2.7 57.1 + - - +
242B ALA 3.2 0.6 + - - +
244B VAL* 1.3 76.8 - - - +
246B SER* 1.3 58.8 + - - +
247B GLY 3.4 0.4 + - - -
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Residues in contact with SER 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLN* 3.0 14.0 + - - -
198B LEU* 3.4 15.0 - - - +
199B ASP* 2.5 26.8 + - - +
202B THR* 4.0 19.9 - - - +
242B ALA 3.1 9.7 + - - -
243B LEU 3.7 5.6 - - - -
244B VAL 3.0 1.0 - - - -
245B ARG* 1.3 77.8 - - - +
247B GLY* 1.3 59.5 + - - +
248B TYR* 3.7 18.1 - - - -
279B LYS* 5.6 1.0 - - - +
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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