Contacts of the helix formed by residues 236 - 247 (chain B) in PDB entry 2YEV
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 ASP 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B VAL* 3.3 4.3 - - - -
235B ALA* 1.3 80.9 - - - +
237B GLU* 1.3 53.4 + - - +
238B ARG* 2.9 15.4 + - - +
239B GLY* 2.8 25.2 + - - -
240B GLN* 2.8 34.0 + - - +
316B ALA* 3.8 17.5 - - - +
319B ARG* 2.7 44.1 + - + -
320B TYR* 3.7 8.0 - - - +
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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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234B VAL* 4.0 20.9 - - + +
236B ASP* 1.3 70.0 + - - +
238B ARG* 1.3 59.5 + - - +
240B GLN* 3.4 11.0 + - - +
241B GLN* 3.0 34.4 + - + +
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Residues in contact with ARG 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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236B ASP* 2.9 9.5 + - - +
237B GLU* 1.3 78.5 - - - +
239B GLY* 1.3 56.9 + - - +
241B GLN* 3.1 9.3 + - + +
242B VAL* 2.9 32.0 + - + +
310B SER* 4.6 2.4 + - - -
312B GLU* 3.2 47.8 + - - +
313B ASP* 2.9 27.0 + - - +
316B ALA* 3.7 15.9 - - + +
319B ARG* 5.7 1.7 - - - +
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Residues in contact with GLY 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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236B ASP* 2.8 13.4 + - - -
238B ARG* 1.3 74.0 - - - +
240B GLN* 1.3 59.0 + - - +
242B VAL* 3.2 4.5 + - - +
243B PHE* 2.9 29.5 + - - +
316B ALA* 3.2 34.4 - - - +
317B LEU* 3.6 7.8 - - - +
320B TYR* 3.7 7.6 - - - -
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Residues in contact with GLN 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B VAL* 3.2 40.3 - - + +
236B ASP 2.8 16.1 + - - +
237B GLU* 3.5 19.1 + - - +
239B GLY* 1.3 71.4 - - - +
241B GLN* 1.3 73.7 + - - +
243B PHE* 3.2 5.0 - - - +
244B GLN* 2.9 36.8 + - + +
320B TYR* 3.6 34.1 + - + +
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Residues in contact with GLN 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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237B GLU* 3.0 20.8 + - + +
238B ARG* 3.1 9.8 + - - +
240B GLN* 1.3 90.8 - - - +
242B VAL* 1.3 66.6 + - - +
244B GLN* 3.2 16.7 + - - +
245B GLN* 3.1 39.3 + - - +
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Residues in contact with VAL 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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238B ARG* 2.9 25.4 + - + +
239B GLY* 3.2 7.6 + - - +
241B GLN* 1.3 75.4 - - + +
243B PHE* 1.3 63.7 + - - +
245B GLN* 3.2 9.0 + - - +
246B ASN* 3.0 42.7 + - + +
309B LEU* 4.5 14.8 - - + -
313B ASP* 3.8 39.5 - - + +
317B LEU* 3.9 31.6 - - + -
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Residues in contact with PHE 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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239B GLY 2.9 13.2 + - - +
240B GLN 3.2 9.4 - - - +
242B VAL* 1.3 78.4 - - - +
244B GLN* 1.3 65.9 + - - +
247B CYS* 2.7 62.1 + - + +
248B ALA* 3.1 30.0 + - + -
251B HIS* 3.9 19.7 - - + -
253B VAL* 3.9 30.1 - - + -
266B LEU* 3.8 19.1 - - + -
317B LEU* 3.8 6.9 - - + +
320B TYR* 3.8 20.4 - + + -
321B LEU* 3.8 21.3 - - + -
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Residues in contact with GLN 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 GLN* 2.9 28.3 + - + +
241B GLN* 3.2 24.0 + - - +
243B PHE* 1.3 87.0 - - - +
245B GLN* 1.3 61.9 + - + +
246B ASN 3.5 0.2 + - - -
247B CYS 4.5 0.2 + - - -
248B ALA* 3.7 31.7 + - - +
249B ALA 5.2 1.0 + - - -
253B VAL* 5.9 2.3 - - - +
320B TYR* 5.4 1.4 + - - -
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Residues in contact with GLN 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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241B GLN* 3.1 30.4 + - - +
242B VAL* 3.6 7.1 - - - +
243B PHE 3.2 0.2 - - - -
244B GLN* 1.3 79.5 - - + +
246B ASN* 1.3 76.8 + - - +
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Residues in contact with ASN 246 (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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242B VAL* 3.0 37.6 + - + +
245B GLN* 1.3 96.5 + - - +
247B CYS* 1.3 68.1 + - - +
249B ALA* 5.2 6.2 - - - +
306B PHE* 3.6 47.3 - - + -
308B GLN* 5.1 2.4 + - - -
309B LEU* 4.2 17.5 - - + +
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Residues in contact with CYS 247 (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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242B VAL 4.4 0.2 - - - -
243B PHE* 2.7 57.8 + - + +
245B GLN 4.0 0.2 - - - -
246B ASN* 1.3 86.6 - - - +
248B ALA* 1.3 64.1 + - - +
249B ALA* 3.0 3.6 - - - +
250B CYS* 2.9 16.0 + - - +
251B HIS* 3.0 23.4 + - + +
266B LEU* 5.6 0.2 - - + -
306B PHE* 5.7 3.8 - - - -
317B LEU* 4.3 17.0 - - - -
321B LEU* 6.3 0.4 - - - -
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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