Contacts of the helix formed by residues 232 - 245 (chain D) in PDB entry 2YPT
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 GLY 232 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230D PRO 3.5 4.9 + - - -
231D GLU* 1.3 74.4 + - - +
233D LYS* 1.3 60.0 + - - -
234D LEU* 3.3 3.1 - - - -
235D LYS* 3.6 4.6 - - - +
236D GLU* 3.1 28.8 + - - +
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Residues in contact with LYS 233 (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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232D GLY* 1.3 70.9 - - - -
234D LEU* 1.3 60.8 + - - +
236D GLU* 4.2 3.7 - - - +
237D GLU* 3.3 25.3 + - - +
326D ASN* 4.3 15.0 - - + +
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Residues in contact with LEU 234 (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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229D LEU* 4.6 10.9 - - + +
232D GLY* 3.3 1.0 - - - -
233D LYS* 1.3 77.4 - - - +
235D LYS* 1.4 58.7 + - - +
237D GLU* 3.6 4.4 + - - +
238D ILE* 3.1 30.4 + - - +
326D ASN* 3.4 35.9 - - + +
329D VAL* 5.9 7.0 - - + -
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Residues in contact with LYS 235 (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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229D LEU* 3.8 20.3 - - + +
230D PRO 3.4 26.8 + - - +
231D GLU* 3.8 16.8 - - - +
232D GLY 3.6 13.1 + - - +
233D LYS 3.5 0.2 - - - -
234D LEU* 1.4 77.4 - - - +
236D GLU* 1.3 61.1 + - - +
238D ILE* 3.8 4.3 + - - +
239D GLU* 3.5 19.2 + - - +
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Residues in contact with GLU 236 (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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231D GLU* 5.7 1.1 + - - -
232D GLY 3.1 18.8 + - - +
233D LYS* 4.2 4.7 - - - +
235D LYS* 1.3 74.4 - - - +
237D GLU* 1.4 62.6 + - - +
239D GLU* 3.3 8.2 + - - +
240D VAL* 3.2 27.4 + - + +
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Residues in contact with GLU 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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233D LYS 3.3 18.4 + - - +
234D LEU* 4.0 4.7 - - - +
236D GLU* 1.4 75.1 - - - +
238D ILE* 1.4 58.9 + - - +
240D VAL* 3.5 11.4 + - - +
241D MET* 3.1 28.9 + - - +
330D LEU* 5.8 8.7 - - + -
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Residues in contact with ILE 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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229D LEU* 5.4 5.2 - - + -
234D LEU 3.1 18.4 + - - +
235D LYS* 3.9 7.9 - - - +
236D GLU 3.3 0.2 - - - -
237D GLU* 1.4 74.8 - - - +
239D GLU* 1.4 53.8 + - - +
241D MET* 3.3 8.3 + - - +
242D ALA* 2.8 35.3 + - - +
249D LEU* 4.8 7.1 - - + +
252D VAL* 5.7 7.4 - - + -
330D LEU* 6.3 1.6 - - - -
333D LEU* 4.5 22.7 - - + -
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Residues in contact with GLU 239 (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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235D LYS 3.5 11.3 + - - +
236D GLU* 3.3 11.8 + - - +
238D ILE* 1.4 74.5 - - - +
240D VAL* 1.4 59.2 + - + +
242D ALA* 3.7 7.8 - - - +
243D LYS* 3.0 30.8 + - - +
249D LEU* 4.6 10.9 - - + +
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Residues in contact with VAL 240 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236D GLU* 3.2 17.4 + - + +
237D GLU* 3.6 12.3 - - - +
239D GLU* 1.4 76.5 - - + +
241D MET* 1.4 57.0 + - - +
243D LYS* 3.9 5.2 - - - +
244D SER* 3.1 27.8 + - - -
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Residues in contact with MET 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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237D GLU 3.1 17.5 + - - +
238D ILE* 3.5 8.1 - - - +
240D VAL* 1.4 75.6 - - - +
242D ALA* 1.4 57.9 + - - +
244D SER* 3.3 8.3 + - - -
245D ILE* 3.1 29.5 + - + +
330D LEU* 3.5 45.1 - - + +
333D LEU* 4.6 6.3 - - - -
334D GLY* 4.4 6.3 - - - -
337D LEU* 4.2 24.9 - - + +
425D LEU* 5.5 16.2 - - + -
427D LYS* 3.8 19.1 - - + -
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Residues in contact with ALA 242 (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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238D ILE 2.8 20.0 + - - +
239D GLU* 3.7 5.4 - - - +
241D MET* 1.4 72.5 - - - +
243D LYS* 1.3 57.9 + - - +
245D ILE* 3.7 0.6 + - - -
246D ASP 3.2 4.9 + - - -
247D PHE* 2.8 45.7 + - + +
249D LEU* 3.9 35.7 - - + -
337D LEU* 5.6 6.0 - - + +
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Residues in contact with LYS 243 (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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239D GLU 3.0 17.7 + - - +
240D VAL* 3.9 6.7 - - - +
242D ALA* 1.3 74.7 - - - +
244D SER* 1.3 62.9 + - - +
246D ASP* 3.4 20.3 + - - +
247D PHE 5.4 0.4 - - - -
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Residues in contact with SER 244 (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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240D VAL* 3.1 19.3 + - - -
241D MET* 3.3 11.9 + - - -
243D LYS* 1.3 78.8 - - - +
245D ILE* 1.3 56.9 + - - +
246D ASP* 3.3 8.8 + - - +
425D LEU* 5.7 6.0 - - - +
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Residues in contact with ILE 245 (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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241D MET* 3.1 15.3 + - + +
242D ALA* 3.7 2.6 + - - +
244D SER* 1.3 73.6 - - - +
246D ASP* 1.4 69.4 + - - +
247D PHE* 3.4 9.3 + - + +
337D LEU* 5.2 15.3 - - + -
340D TRP* 3.5 19.3 - - + -
421D PHE* 5.5 10.3 - - + -
425D LEU* 5.4 12.3 - - + -
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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