Contacts of the strand formed by residues 274 - 281 (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 ILE 274 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ARG* 3.8 32.8 - - + -
234B PHE* 3.8 26.0 - - + -
246B LYS* 3.6 20.2 - - + +
248B MET* 3.6 42.8 - - + +
269B CYS* 3.0 22.1 + - + +
270B GLU* 4.5 2.1 + - - +
272B GLU* 3.8 13.5 - - + +
273B ASN* 1.3 79.9 - - - +
275B GLN* 1.3 61.1 + - - +
276B ARG* 2.9 33.0 + - + -
304B SER* 4.1 0.3 + - - -
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Residues in contact with GLN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LYS* 2.6 34.0 + - + -
246B LYS 3.0 12.7 + - - +
247B VAL* 3.3 10.5 - - + +
248B MET 2.9 25.3 + - - +
273B ASN 3.5 3.4 + - - +
274B ILE* 1.3 70.1 - - - +
276B ARG* 1.3 60.8 + - - +
277B PHE* 3.7 19.4 - - + -
304B SER* 3.5 7.9 - - - +
310B HIS* 2.8 33.5 + - + +
334B LEU* 2.9 26.9 + - - +
336B ALA* 3.7 18.8 - - + +
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Residues in contact with ARG 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 5.4 0.7 - - - -
248B MET* 3.4 10.1 - - + -
250B ILE* 4.3 12.1 - - + -
266B ILE* 3.6 33.4 + - - +
269B CYS* 3.9 19.7 - - - +
270B GLU* 3.0 42.8 + - - +
274B ILE* 2.9 39.1 + - + +
275B GLN* 1.3 76.7 - - - +
277B PHE* 1.3 62.0 + - - +
302B ILE* 2.8 32.7 + - - +
303B ALA* 3.5 5.9 + - - -
304B SER* 2.9 47.7 + - - +
310B HIS* 3.4 12.2 - - - +
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Residues in contact with PHE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL* 3.7 30.1 - - + -
248B MET 2.9 8.7 + - - +
249B VAL* 3.3 9.4 - - + -
250B ILE* 2.8 27.5 + - - +
275B GLN* 3.7 20.4 - - + -
276B ARG* 1.3 74.3 - - - +
278B SER* 1.3 60.7 + - - +
279B ILE* 5.7 0.7 - - + -
309B LYS 3.9 9.4 - - - -
310B HIS* 3.2 38.8 - + - +
312B PHE* 4.1 4.0 - + + -
327B LEU* 3.9 25.1 - - + -
330B ARG* 3.6 44.4 - - + -
331B ILE* 3.9 14.8 - - + -
334B LEU* 4.2 2.2 - - + -
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Residues in contact with SER 278 (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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250B ILE* 3.3 10.3 - - - -
276B ARG 4.1 1.2 + - - -
277B PHE* 1.3 75.0 - - - +
279B ILE* 1.3 64.7 + - - +
280B ALA 4.2 0.4 - - - -
299B ILE* 2.9 36.2 + - - -
302B ILE* 4.3 17.5 - - - -
303B ALA* 3.5 14.1 - - - +
310B HIS 3.0 5.9 + - - +
311B PHE* 3.3 9.0 - - - -
312B PHE* 2.9 24.8 + - - -
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Residues in contact with ILE 279 (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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164B PHE* 3.7 29.4 - - + -
249B VAL* 3.9 14.6 - - + -
250B ILE 2.7 10.7 + - - +
251B VAL* 3.8 18.4 - - + -
252B THR* 3.0 29.3 + - - +
277B PHE* 5.3 0.4 - - + -
278B SER* 1.3 79.6 - - - +
280B ALA* 1.3 60.0 + - - +
281B ILE* 4.3 8.7 - - + -
299B ILE* 4.1 2.7 - - - -
312B PHE* 3.4 12.3 - - + +
314B VAL* 3.6 28.5 - - + -
320B LEU* 3.7 14.4 - - + -
323B ILE* 3.8 17.5 - - + -
327B LEU* 4.1 6.5 - - + -
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Residues in contact with ALA 280 (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 3.4 4.9 - - - -
279B ILE* 1.3 71.4 - - - +
281B ILE* 1.3 60.3 + - - +
282B LEU* 3.4 14.0 - - + +
295B PHE* 3.8 19.5 - - + -
296B VAL* 5.1 2.2 - - + -
299B ILE* 3.9 12.2 - - + +
311B PHE* 3.6 26.5 - - + -
312B PHE 2.9 6.9 + - - -
314B VAL* 2.8 29.6 + - - +
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Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ILE* 5.3 7.2 - - + -
161B VAL* 5.3 4.9 - - + -
251B VAL* 3.8 24.2 - - + -
252B THR 2.9 17.4 + - - +
253B ASP* 3.3 32.9 - - + +
279B ILE* 4.3 12.6 - - + -
280B ALA* 1.3 73.3 - - - +
282B LEU* 1.3 61.9 + - - +
283B GLY 3.3 10.8 - - - +
284B SER 5.0 0.2 + - - -
295B PHE* 3.4 6.6 - - - -
314B VAL* 3.4 11.0 - - + +
316B ASP 4.0 4.5 - - - -
317B GLU* 3.8 40.4 - - + +
320B LEU* 3.9 21.3 - - + -
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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
------------------------------------------------------------
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