Contacts of the helix formed by residues 261 - 272 (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 ARG 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A ASN* 2.5 50.1 + - - +
223B ALA* 3.6 11.8 + - + +
224B LEU* 3.8 40.2 - - - +
227B ASP* 3.8 21.4 + - - -
231B LYS* 5.8 0.4 - - - +
258B ASP* 3.0 19.9 + - + +
260B HIS* 1.3 100.5 - - + +
262B LEU* 1.3 61.7 + - - +
263B LYS 3.4 2.3 + - - -
264B LYS* 3.4 8.7 + - - +
265B VAL* 3.1 36.5 + - + +
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Residues in contact with LEU 262 (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* 4.6 3.6 - - + +
223B ALA* 3.9 28.9 - - + +
226B THR* 5.2 2.0 - - - +
256B SER* 3.9 13.9 - - - +
259B ASN* 3.1 23.4 + - + +
260B HIS 3.4 0.2 - - - -
261B ARG* 1.3 75.0 - - - +
263B LYS* 1.3 67.6 + - - +
265B VAL* 4.4 4.5 - - + -
266B ILE* 2.8 41.9 + - + +
298B GLU* 3.7 31.6 - - + +
301B SER* 5.1 5.6 - - - +
302B ILE* 4.2 29.4 - - + -
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Residues in contact with LYS 263 (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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270A GLU* 3.8 24.7 - - - +
305A GLU* 3.7 43.2 + - + +
259B ASN 4.6 1.4 + - - -
260B HIS 4.7 3.8 + - - +
261B ARG 3.4 0.8 - - - -
262B LEU* 1.3 77.6 - - - +
264B LYS* 1.3 63.2 + - - +
266B ILE* 3.6 4.2 + - - +
267B GLN* 3.1 24.2 + - + +
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Residues in contact with LYS 264 (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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267A GLN* 4.8 6.9 - - - +
270A GLU* 3.8 32.1 + - + +
271A ASP* 3.1 39.7 + - - +
273A ASN* 5.5 6.1 - - - +
261B ARG* 3.4 9.7 + - - +
262B LEU 3.3 0.2 - - - -
263B LYS* 1.3 78.2 - - - +
265B VAL* 1.3 63.4 + - + +
267B GLN* 3.2 7.4 + - + +
268B ASP* 2.9 57.5 + - - +
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ALA* 3.9 12.8 - - + +
226B THR* 3.7 29.8 - - + -
227B ASP* 3.7 42.6 - - + +
230B ARG* 4.6 0.5 - - - -
261B ARG* 3.1 38.5 + - - +
262B LEU* 3.9 6.5 - - + +
264B LYS* 1.3 80.6 - - + +
266B ILE* 1.3 60.3 + - + +
268B ASP* 3.3 9.2 + - - +
269B CYS* 3.0 28.8 + - - -
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Residues in contact with ILE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 4.6 9.6 - - + -
262B LEU* 2.8 41.6 + - + +
263B LYS* 3.9 4.5 - - - +
265B VAL* 1.3 78.2 - - + +
267B GLN* 1.3 55.9 + - - +
269B CYS* 3.2 6.3 + - - +
270B GLU* 2.9 27.4 + - + +
276B ARG* 3.6 32.0 + - - +
301B SER* 4.4 13.5 - - - +
302B ILE* 3.7 43.5 - - + +
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Residues in contact with GLN 267 (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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263B LYS* 3.1 18.9 + - + +
264B LYS* 3.2 10.9 + - + +
266B ILE* 1.3 76.5 - - - +
268B ASP* 1.3 59.3 + - - +
270B GLU* 3.3 17.6 + - - +
271B ASP* 2.9 63.7 + - - +
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Residues in contact with ASP 268 (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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227B ASP* 4.7 1.7 - - - +
230B ARG* 3.5 37.8 + - - +
264B LYS* 2.9 53.2 + - - +
265B VAL* 3.3 8.3 + - - +
267B GLN* 1.3 80.5 - - - +
269B CYS* 1.3 60.0 + - - +
271B ASP* 3.5 10.8 + - - +
272B GLU* 3.1 31.4 + - - +
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Residues in contact with CYS 269 (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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226B THR* 4.0 16.6 - - - -
230B ARG* 4.1 19.1 - - - +
248B MET* 3.9 26.7 - - - -
265B VAL* 3.0 20.6 + - - -
266B ILE* 3.2 8.3 + - - +
268B ASP* 1.3 73.0 - - - +
270B GLU* 1.3 65.6 + - - +
272B GLU 3.1 7.8 + - - -
274B ILE* 3.0 33.6 + - + +
276B ARG* 3.9 23.1 - - - +
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Residues in contact with GLU 270 (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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266B ILE* 2.9 17.3 + - + +
267B GLN* 3.6 21.5 - - - +
269B CYS* 1.3 77.2 - - - +
271B ASP* 1.3 61.7 + - - +
273B ASN* 3.1 18.0 + - - +
274B ILE 4.5 2.3 - - - +
276B ARG* 3.0 33.5 + - - +
304B SER* 4.5 5.2 + - - -
336B ALA* 5.8 4.8 - - - +
337B THR 5.5 4.5 - - - +
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Residues in contact with ASP 271 (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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267B GLN* 2.9 47.9 + - - +
268B ASP* 3.6 13.0 - - - +
269B CYS 3.3 0.2 - - - -
270B GLU* 1.3 75.4 - - - +
272B GLU* 1.3 62.0 + - + +
273B ASN* 3.2 12.6 + - - +
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Residues in contact with GLU 272 (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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230B ARG* 3.0 49.8 + - - +
231B LYS* 5.2 0.3 - - - -
234B PHE 5.6 0.5 - - - +
246B LYS* 2.9 37.2 + - - +
268B ASP* 3.1 18.6 + - - +
269B CYS 3.1 3.0 + - - +
271B ASP* 1.3 79.7 - - + +
273B ASN* 1.3 72.6 + - - +
274B ILE* 3.3 9.3 + - + +
603B GOL 3.7 3.2 + - - +
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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