Contacts of the helix formed by residues 292 - 303 (chain B) in PDB entry 1PT6
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 292 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B LEU* 3.8 33.2 - - + +
285B TYR* 3.7 29.4 - - + -
286B ASN* 3.8 22.3 + - - +
290B LEU 3.8 1.3 - - - +
291B SER* 1.3 73.9 + - - +
293B GLU* 1.3 60.5 + - - +
294B LYS 3.5 1.8 - - - -
295B PHE* 3.8 9.6 - - + -
296B VAL* 2.9 34.5 + - - +
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Residues in contact with GLU 293 (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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291B SER* 3.5 14.6 + - - +
292B THR* 1.3 79.3 + - - +
294B LYS* 1.3 67.1 + - + +
296B VAL* 3.8 4.8 - - - +
297B GLU* 3.1 31.5 + - + +
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Residues in contact with LYS 294 (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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308A GLU* 3.4 41.7 + - + +
255B GLU* 3.4 20.8 - - - +
291B SER* 4.8 4.2 + - - +
292B THR 3.5 0.2 - - - -
293B GLU* 1.3 79.0 - - + +
295B PHE* 1.3 62.9 + - - +
297B GLU* 3.3 7.2 + - - +
298B GLU* 3.0 25.1 + - - +
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Residues in contact with PHE 295 (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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252B THR* 3.7 14.6 - - + -
253B ASP 3.4 9.4 - - - -
254B GLY 3.3 31.2 - - - -
255B GLU* 3.6 31.2 - - + -
280B ALA* 3.8 7.9 - - + -
281B ILE 3.4 18.4 - - - -
282B LEU* 3.9 24.5 - - + -
285B TYR* 3.8 31.0 - + + -
291B SER 5.2 0.6 + - - -
292B THR* 3.2 11.1 + - - +
293B GLU 3.2 0.8 - - - -
294B LYS* 1.3 77.6 - - - +
296B VAL* 1.3 64.4 + - - +
298B GLU* 3.1 4.0 + - - +
299B ILE* 3.1 42.5 + - + +
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Residues in contact with VAL 296 (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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280B ALA* 5.1 0.4 - - - -
282B LEU* 4.2 24.5 - - + -
292B THR* 2.9 22.6 + - - +
293B GLU* 3.8 5.4 - - - +
295B PHE* 1.3 76.3 - - + +
297B GLU* 1.3 67.3 + - - +
299B ILE* 3.4 2.3 + - - +
300B LYS* 2.9 53.2 + - + +
311B PHE* 4.0 17.0 - - + -
313B ASN* 3.8 24.2 - - - +
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Residues in contact with GLU 297 (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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293B GLU* 3.1 21.7 + - + +
294B LYS* 3.7 7.4 - - - +
295B PHE 3.3 0.2 - - - -
296B VAL* 1.3 77.0 - - - +
298B GLU* 1.3 62.8 + - - +
300B LYS* 3.4 26.5 + - - +
301B SER* 3.0 23.4 + - - -
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Residues in contact with GLU 298 (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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306A PRO* 5.6 0.7 - - - +
222B THR* 5.2 0.7 + - - -
255B GLU* 3.6 18.6 - - - +
256B SER* 2.9 40.2 + - - -
259B ASN* 3.4 27.1 + - + +
262B LEU* 3.7 17.5 - - + +
294B LYS 3.0 13.3 + - - +
295B PHE* 3.1 10.5 + - - +
297B GLU* 1.3 75.9 - - - +
299B ILE* 1.3 73.1 + - + +
301B SER* 2.7 26.4 + - - +
302B ILE* 3.4 8.1 + - - +
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Residues in contact with ILE 299 (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* 5.5 2.0 - - + -
250B ILE* 6.1 0.2 - - + -
252B THR* 3.5 22.9 - - + -
254B GLY 4.6 2.5 - - - +
278B SER* 2.9 41.9 + - - +
279B ILE 4.1 4.9 - - - +
280B ALA* 3.9 15.5 - - + +
295B PHE* 3.1 41.1 + - + +
298B GLU* 1.3 87.4 - - + +
300B LYS* 1.3 67.6 + - - +
302B ILE* 3.1 28.9 + - + +
311B PHE* 3.6 20.0 - - + -
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Residues in contact with LYS 300 (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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296B VAL* 2.9 33.2 + - + +
297B GLU* 3.5 25.8 + - - +
299B ILE* 1.3 76.4 - - - +
301B SER* 1.3 60.9 + - - +
303B ALA* 3.2 21.1 + - - +
307B THR* 4.0 26.0 + - + +
311B PHE* 3.3 45.4 - - + -
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Residues in contact with SER 301 (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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262B LEU* 5.1 6.4 - - - +
266B ILE* 4.4 14.2 - - - +
276B ARG* 5.5 0.2 + - - -
297B GLU 3.0 14.2 + - - -
298B GLU* 2.7 23.0 + - - +
299B ILE 3.1 1.0 - - - -
300B LYS* 1.3 77.2 - - - +
302B ILE* 1.3 60.7 + - - +
303B ALA 3.4 5.1 - - - +
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Residues in contact with ILE 302 (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* 3.9 28.0 - - + -
226B THR* 5.1 3.1 - - - +
250B ILE* 3.5 35.2 - - + -
262B LEU* 4.2 19.1 - - + -
266B ILE* 3.7 27.4 - - + -
276B ARG* 2.8 33.0 + - + +
278B SER* 4.3 5.4 - - - -
298B GLU 3.6 14.1 - - - +
299B ILE* 3.1 27.9 + - + +
301B SER* 1.3 78.5 - - - +
303B ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 303 (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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276B ARG* 3.5 12.6 + - - +
278B SER* 3.5 19.9 + - - +
299B ILE 3.5 1.6 + - - -
300B LYS 3.2 16.3 + - - +
301B SER 4.1 4.3 - - - +
302B ILE* 1.3 81.7 - - - +
304B SER* 1.3 67.6 + - - +
305B GLU* 5.3 2.3 - - - +
307B THR* 4.5 6.4 + - - +
310B HIS* 3.6 28.3 - - + -
311B PHE* 4.0 7.0 - - + +
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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