Contacts of the strand formed by residues 250 - 259 (chain D) in PDB entry 2Y7Q
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 THR 250 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434B THR* 6.3 1.8 - - - -
437B SER* 4.9 7.9 - - - -
239D SER* 4.5 1.6 + - - -
248D PRO* 3.0 21.5 - - - +
249D PRO* 1.3 83.8 - - - +
251D ILE* 1.3 62.1 + - - +
252D GLN 4.1 1.5 + - - -
298D THR* 4.0 19.3 - - - -
299D LEU 3.2 11.0 - - - -
300D SER* 4.8 0.7 - - - +
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Residues in contact with ILE 251 (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 GLN* 5.2 1.8 - - + -
239D SER* 3.8 12.1 - - - +
247D PHE* 4.2 18.4 - - + -
248D PRO* 4.3 17.0 - - + +
250D THR* 1.3 77.4 - - - +
252D GLN* 1.3 72.1 + - - +
253D LEU* 3.6 4.6 + - + -
297D LEU 3.8 0.3 - - - +
298D THR* 3.7 1.7 - - - -
299D LEU* 2.8 36.7 + - + +
301D GLN* 4.5 9.6 - - - -
304D TRP* 3.0 74.5 - - + +
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Residues in contact with GLN 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B LYS* 5.2 14.4 - - - -
237B LEU* 5.4 8.5 - - + -
238D GLN* 3.6 4.4 - - - -
239D SER* 2.7 40.6 + - - +
250D THR 4.1 1.8 + - - -
251D ILE* 1.3 73.9 - - - +
253D LEU* 1.3 67.8 + - + +
296D GLU* 3.1 36.8 - - + +
297D LEU 3.6 3.8 - - - -
298D THR* 4.3 14.8 - - + +
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Residues in contact with LEU 253 (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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237B LEU* 3.6 29.2 - - + -
253B LEU* 6.2 1.1 - - - +
255B LEU* 5.2 6.1 - - - -
236D ILE* 3.1 23.6 - - + -
237D LEU* 2.7 49.5 + - + +
238D GLN* 3.8 21.8 - - + +
251D ILE* 4.7 1.3 - - + +
252D GLN* 1.3 84.4 - - + +
254D CYS* 1.3 65.1 + - - +
255D LEU* 3.7 23.1 + - + +
268D TRP* 3.8 34.6 - - + -
294D GLN* 4.1 19.7 - - + -
295D SER 3.8 9.3 - - - +
296D GLU* 3.2 28.1 - - + +
297D LEU* 2.6 43.5 + - + +
299D LEU* 4.1 20.2 - - + -
304D TRP* 4.0 20.0 - - + -
310D TYR* 3.8 21.5 - - + +
325D THR* 5.2 5.4 - - - -
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Residues in contact with CYS 254 (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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234D VAL* 4.2 11.4 - - - -
235D LYS 3.8 1.8 - - - -
236D ILE* 4.3 5.4 - - - +
253D LEU* 1.3 72.1 + - - +
255D LEU* 1.3 65.1 + - - +
256D VAL* 3.6 8.4 + - + +
266D ILE* 4.7 0.4 - - - -
268D TRP* 3.7 12.3 - - + -
294D GLN* 3.2 9.9 - - - +
295D SER* 2.7 45.0 + - - +
312D CYS* 2.0 53.6 - - - -
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Residues in contact with LEU 255 (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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253B LEU* 5.4 2.5 - - - -
233D THR 2.9 15.9 - - - +
234D VAL* 3.5 1.4 - - - -
235D LYS* 2.7 49.4 + - + +
237D LEU* 3.6 31.9 - - + -
253D LEU* 3.7 35.9 - - + +
254D CYS* 1.3 73.6 - - - +
256D VAL* 1.3 61.9 + - - +
257D SER* 3.8 9.0 + - - +
293D THR 4.1 2.2 - - - -
294D GLN* 4.6 7.6 - - + -
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Residues in contact with VAL 256 (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 PRO* 3.6 20.6 - - + -
233D THR 3.6 2.9 - - - -
234D VAL* 4.6 2.0 - - + +
254D CYS* 4.5 8.7 - - - +
255D LEU* 1.3 72.3 - - - +
257D SER* 1.3 58.5 + - - +
259D TYR* 4.2 3.4 - - + -
264D ILE* 3.3 31.2 - - + -
266D ILE* 3.6 31.9 - - + -
292D SER* 3.2 2.9 - - - -
293D THR* 2.6 51.0 + - + +
314D VAL* 3.6 22.7 - - + -
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Residues in contact with SER 257 (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 PRO 3.5 0.3 - - - -
233D THR* 2.6 55.4 + - - -
235D LYS* 5.9 1.4 - - - +
255D LEU* 4.0 10.8 + - - +
256D VAL* 1.3 77.6 - - - +
258D GLY* 1.3 62.3 + - - +
259D TYR* 3.6 2.5 - - - -
291D ALA 4.0 0.4 - - - -
292D SER* 3.6 15.7 - - - +
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Residues in contact with GLY 258 (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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230D THR* 3.9 6.4 - - - +
231D PRO 2.8 18.5 - - - +
233D THR* 4.4 4.7 + - - -
257D SER* 1.3 76.2 - - - +
259D TYR* 1.3 57.9 + - - +
290D LEU* 4.2 17.5 - - - -
291D ALA 3.1 10.0 + - - -
292D SER* 4.1 1.8 - - - -
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Residues in contact with TYR 259 (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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230D THR 3.4 6.3 - - - +
232D PRO* 3.5 28.3 - - + -
256D VAL* 4.0 14.8 - - + -
257D SER 4.2 3.6 - - - -
258D GLY* 1.3 77.9 - - - +
260D THR* 1.3 76.1 + - - +
261D PRO* 3.3 2.6 - - + -
262D GLY* 4.4 15.1 + - - -
264D ILE* 3.8 36.0 - - + +
280D SER* 5.1 4.0 + - - -
290D LEU* 4.2 6.2 - - - +
291D ALA* 2.8 60.9 + - + +
292D SER* 3.4 22.0 + - - -
293D THR* 3.8 18.4 - - + +
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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