Contacts of the strand formed by residues 291 - 300 (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 ALA 291 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258D GLY 3.1 7.2 + - - -
259D TYR* 2.8 51.3 + - + +
261D PRO* 4.0 14.5 - - + +
290D LEU* 1.3 75.9 - - - +
292D SER* 1.3 65.5 + - - +
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Residues in contact with SER 292 (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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256D VAL 3.2 13.5 - - - -
257D SER* 3.6 17.9 - - - -
258D GLY 4.1 1.3 - - - -
259D TYR* 3.4 8.3 + - - -
291D ALA* 1.3 80.4 - - - +
293D THR* 1.3 63.6 + - - +
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Residues in contact with THR 293 (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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254D CYS 3.8 0.2 - - - +
255D LEU* 3.9 1.4 - - - -
256D VAL* 2.6 57.6 + - + +
259D TYR* 3.8 17.5 - - - +
264D ILE* 4.0 17.7 - - + -
266D ILE* 4.4 6.6 - - + +
280D SER* 3.9 18.9 + - - -
292D SER* 1.3 77.0 - - - +
294D GLN* 1.3 69.5 + - - +
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Residues in contact with GLN 294 (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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253D LEU* 4.1 17.9 - - + -
254D CYS 3.2 10.5 - - - +
255D LEU* 4.6 9.0 - - + -
266D ILE* 4.7 2.6 - - - +
293D THR* 1.3 81.8 + - - +
295D SER* 1.3 60.9 + - - +
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Residues in contact with SER 295 (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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253D LEU* 3.8 2.7 - - - +
254D CYS* 2.7 44.1 + - - +
266D ILE* 3.4 33.7 - - - +
268D TRP* 3.2 26.7 + - - -
276D ASP* 5.5 1.7 + - - -
278D ASP* 6.2 0.3 - - - -
294D GLN* 1.3 73.2 - - - +
296D GLU* 1.3 60.9 + - - +
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Residues in contact with GLU 296 (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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252D GLN* 3.1 36.5 - - + +
253D LEU* 3.2 25.8 - - + +
268D TRP* 4.4 4.3 + - - -
276D ASP* 5.0 7.8 - - - +
295D SER* 1.3 80.2 + - - +
297D LEU* 1.3 69.4 + - - +
298D THR* 4.3 9.4 + - - +
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Residues in contact with LEU 297 (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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251D ILE 3.8 0.7 - - - +
252D GLN* 3.5 0.9 - - - -
253D LEU* 2.6 46.7 + - + +
268D TRP* 3.4 57.1 - - + +
275D MET* 5.8 3.6 - - - -
276D ASP* 5.0 12.3 - - + +
296D GLU* 1.3 76.7 - - - +
298D THR* 1.3 72.0 + - - +
299D LEU* 4.6 5.2 - - + -
310D TYR* 3.8 28.7 - - + -
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Residues in contact with THR 298 (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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437B SER* 3.3 32.4 + - - +
250D THR* 4.0 20.0 - - - -
251D ILE 3.7 3.4 - - - +
252D GLN* 4.3 18.8 - - + -
296D GLU* 4.3 13.9 + - - +
297D LEU* 1.3 83.8 - - - +
299D LEU* 1.3 70.5 + - - +
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Residues in contact with LEU 299 (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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250D THR* 3.2 8.0 - - - -
251D ILE 2.8 40.0 + - - +
253D LEU* 4.1 17.3 - - + -
297D LEU* 4.6 8.1 - - + -
298D THR* 1.3 83.4 - - - +
300D SER* 1.3 67.3 + - - +
303D HIS* 3.9 17.7 - - + +
304D TRP* 3.7 25.8 - - + -
310D TYR* 3.1 62.4 - - + +
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Residues in contact with SER 300 (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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342B ARG* 4.3 23.6 - - - -
436B THR* 6.0 6.1 - - - +
249D PRO 4.2 2.2 - - - -
250D THR* 4.8 1.3 - - - +
299D LEU* 1.3 73.7 - - - +
301D GLN* 1.3 61.2 + - - +
302D LYS* 3.9 7.2 - - - -
303D HIS* 3.1 30.7 + - - +
304D TRP* 2.8 28.4 + - - +
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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