Contacts of the helix formed by residues 237 - 252 (chain B) in PDB entry 2Y4T
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 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B ARG* 2.7 44.7 + - - -
232B TYR* 3.0 39.6 + - + +
235B LEU* 3.6 1.9 - - - +
236B GLY* 1.3 77.0 - - - +
238B HIS* 1.3 59.3 + - - +
239B GLU 3.3 2.9 - - - +
240B LEU* 4.3 13.1 - - + +
241B SER* 3.0 28.3 + - - -
304B TYR* 4.5 0.4 - - - -
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Residues in contact with HIS 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 GLY 3.1 15.5 + - - -
237B ASP* 1.3 73.2 - - - +
239B GLU* 1.3 69.8 + - + +
241B SER* 4.1 1.8 - - - -
242B LEU* 2.8 27.0 + - - +
265B VAL* 3.4 25.3 - - + +
268B LEU* 4.7 6.1 - - + -
269B ASN* 2.9 35.2 + - - +
272B ILE* 3.6 47.7 - - + +
273B GLU* 4.0 12.1 - - - -
304B TYR* 4.0 18.6 - + + +
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Residues in contact with GLU 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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237B ASP 3.3 0.8 - - - -
238B HIS* 1.3 85.3 - - + +
240B LEU* 1.3 60.8 + - + +
242B LEU* 3.0 8.4 + - + +
243B SER* 3.0 27.4 + - - -
269B ASN* 3.9 14.1 - - - +
273B GLU* 3.1 24.6 - - - +
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Residues in contact with LEU 240 (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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212B LYS* 4.6 15.7 - - - +
232B TYR* 3.7 43.3 - - + +
237B ASP* 3.7 13.9 + - + +
239B GLU* 1.3 79.3 - - + +
241B SER* 1.3 59.5 + - - +
243B SER* 3.2 13.8 + - - +
244B GLU* 2.8 33.4 + - - +
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Residues in contact with SER 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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229B SER* 2.7 53.7 + - - +
232B TYR* 3.7 5.2 - - - +
233B TYR* 3.3 17.0 - - - +
237B ASP 3.0 22.7 + - - -
238B HIS* 3.6 6.5 - - - -
240B LEU* 1.3 76.5 - - - +
242B LEU* 1.3 60.1 + - - +
245B VAL* 3.3 12.2 + - - +
261B HIS* 3.1 12.3 + - - -
265B VAL* 3.8 5.2 - - - +
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Residues in contact with LEU 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 HIS 2.8 19.3 + - - +
239B GLU* 3.0 5.8 + - + +
241B SER* 1.3 74.4 - - - +
243B SER* 1.3 65.0 - - - +
245B VAL* 3.2 10.5 - - + +
246B ARG* 3.1 35.8 + - + +
262B TYR* 3.7 35.4 - - + +
265B VAL* 4.1 8.7 - - + +
266B LYS* 4.0 27.1 - - + +
269B ASN* 3.5 35.0 - - + +
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Residues in contact with SER 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 GLU 3.0 14.0 + - - -
240B LEU* 3.2 18.3 + - - +
242B LEU* 1.3 78.7 - - - +
244B GLU* 1.3 70.6 + - - +
246B ARG* 3.5 12.3 + - - +
247B GLU* 3.4 24.1 + - - +
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Residues in contact with GLU 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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212B LYS* 2.7 34.1 + - - +
215B SER* 4.8 0.9 + - - -
225B PHE* 3.5 32.4 - - + +
228B ILE* 3.6 33.9 - - + -
229B SER* 3.9 17.0 - - - -
232B TYR* 4.3 3.7 - - + -
240B LEU* 2.8 17.2 + - - +
243B SER* 1.3 86.7 + - - +
245B VAL* 1.3 57.3 + - - +
247B GLU* 3.2 28.3 - - - +
248B CYS 3.5 3.6 + - - -
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Residues in contact with VAL 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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225B PHE 5.1 0.4 - - - -
226B TYR* 5.2 1.1 - - + -
229B SER* 3.4 17.2 + - - +
241B SER 3.3 11.6 + - - +
242B LEU* 3.2 18.8 - - + +
244B GLU* 1.3 73.0 - - - +
246B ARG* 1.3 66.4 + - - +
247B GLU 3.2 1.1 - - - -
248B CYS* 3.1 5.3 + - - +
249B LEU* 3.1 21.9 + - - +
258B CYS* 3.3 42.6 - - + +
261B HIS* 3.7 17.5 - - + -
262B TYR* 3.9 26.9 - - + -
265B VAL* 4.9 1.6 - - + -
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Residues in contact with ARG 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 LEU* 3.1 27.0 + - + +
243B SER* 3.7 12.8 - - - +
244B GLU 3.4 0.2 - - - -
245B VAL* 1.3 75.5 - - - +
247B GLU* 1.3 57.4 + - - +
249B LEU* 3.2 9.2 + - - +
250B LYS* 2.9 52.2 + - + +
262B TYR* 3.9 26.0 + - + -
249C LEU 4.6 3.6 + - - -
250C LYS* 4.5 10.3 + - - +
253C GLN* 3.2 45.2 - - - +
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Residues in contact with GLU 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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225B PHE* 3.7 24.2 - - + -
243B SER 3.4 12.3 + - - +
244B GLU* 3.2 24.8 + - - +
246B ARG* 1.3 79.0 + - - +
248B CYS* 1.3 61.6 + - - +
250B LYS* 3.3 34.2 + - - +
251B LEU* 3.1 29.0 + - - +
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Residues in contact with CYS 248 (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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222B THR* 3.1 28.4 + - - -
225B PHE* 4.0 21.6 - - + +
226B TYR 4.8 0.7 - - - +
244B GLU 3.5 2.6 + - - -
245B VAL* 3.1 12.2 + - - +
247B GLU* 1.3 76.9 - - - +
249B LEU* 1.3 52.4 + - - +
251B LEU* 3.0 11.2 + - - +
252B ASP* 2.8 29.8 + - - +
255B HIS* 3.6 4.9 - - - -
258B CYS* 2.0 50.3 - - - -
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Residues in contact with LEU 249 (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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245B VAL 3.1 11.1 + - - +
246B ARG* 3.2 8.3 + - - +
248B CYS* 1.3 75.2 - - - +
250B LYS* 1.3 62.4 + - - +
252B ASP 3.0 16.9 - - - +
253B GLN* 2.8 41.4 + - + +
255B HIS 3.9 5.2 - - - +
258B CYS* 3.8 12.1 - - + -
259B PHE* 3.6 42.8 - - + +
262B TYR* 3.6 42.4 - - + -
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Residues in contact with LYS 250 (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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246B ARG* 2.9 43.6 + - + +
247B GLU* 3.4 37.7 + - - +
249B LEU* 1.3 75.9 - - - +
251B LEU* 1.3 64.8 + - + +
252B ASP* 4.7 0.2 - - - -
253B GLN 5.0 0.3 + - - -
250C LYS* 5.6 8.9 - - - +
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Residues in contact with LEU 251 (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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219B ASN 3.2 27.6 - - - +
220B ASP* 3.5 19.7 - - - +
221B ASN 4.2 5.2 - - - +
222B THR* 4.3 8.7 - - - +
225B PHE* 4.0 21.8 - - + -
247B GLU* 3.1 14.8 + - - +
248B CYS* 3.0 8.1 + - - +
250B LYS* 1.3 79.6 - - + +
252B ASP* 1.3 60.3 + - + +
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Residues in contact with ASP 252 (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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222B THR* 4.2 20.7 + - + +
248B CYS 2.8 8.9 + - - +
249B LEU* 3.0 18.3 + - - +
251B LEU* 1.3 80.8 - - - +
253B GLN* 1.3 62.6 + - - +
254B ASP* 3.0 23.0 + - - +
255B HIS* 3.2 31.5 + - + +
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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