Contacts of the strand formed by residues 246 - 252 (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 LYS 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ASP* 3.5 5.8 - - + +
234B PHE* 3.7 45.0 + - + +
241B ARG 5.5 1.8 - - - +
244B VAL* 3.5 16.3 + - + +
245B LYS* 1.3 74.0 - - - +
247B VAL* 1.3 63.5 + - - +
272B GLU* 2.9 41.5 + - - +
273B ASN 3.6 13.6 + - - +
274B ILE* 3.9 13.3 - - + +
275B GLN* 3.0 25.6 + - - +
603B GOL 3.9 31.0 + - - +
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 3.9 26.2 - - + -
144B ASP 2.9 8.6 + - - +
145B ILE* 3.2 11.2 - - + +
146B VAL 2.9 25.5 + - - +
234B PHE* 3.5 5.0 - - - -
245B LYS* 4.2 10.3 - - + +
246B LYS* 1.3 79.2 - - - +
248B MET* 1.3 64.7 + - - +
249B VAL* 4.3 9.0 - - + -
275B GLN* 3.3 21.8 - - - +
277B PHE* 3.7 33.7 - - + -
331B ILE* 4.3 11.0 - - + +
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Residues in contact with MET 248 (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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146B VAL 3.2 6.3 - - - +
148B VAL* 3.6 26.5 - - + -
226B THR* 3.6 31.2 - - - +
229B ALA* 3.8 12.6 - - + -
230B ARG 4.2 4.9 - - - +
234B PHE* 4.2 7.9 - - + -
247B VAL* 1.3 75.4 - - - +
249B VAL* 1.3 65.8 + - - +
250B ILE* 3.6 27.8 - - + -
269B CYS* 3.9 16.4 - - - -
274B ILE* 3.6 27.7 - - + +
275B GLN 2.9 7.4 + - - +
276B ARG* 3.4 4.6 - - + -
277B PHE* 2.9 27.3 + - - +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 4.2 17.5 - - + -
146B VAL 3.0 6.5 + - - -
147B ILE* 3.4 17.7 - - + +
148B VAL 2.8 32.1 + - - +
164B PHE* 4.7 4.3 - - + -
168B LEU* 5.1 3.1 - - + -
247B VAL* 4.3 5.6 - - + -
248B MET* 1.3 76.4 - - - +
250B ILE* 1.3 58.1 + - - +
251B VAL* 4.0 7.1 + - + -
277B PHE* 3.3 13.2 - - + +
279B ILE* 3.9 26.9 - - + -
327B LEU* 4.3 11.7 - - + -
331B ILE* 4.1 24.9 - - + -
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Residues in contact with ILE 250 (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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148B VAL* 3.4 15.7 - - + +
186B TYR* 4.5 7.4 - - - +
222B THR* 4.3 23.6 - - + -
226B THR* 4.1 10.5 - - + +
248B MET* 3.6 34.8 - - + -
249B VAL* 1.3 73.3 - - - +
251B VAL* 1.3 60.9 + - - +
252B THR* 4.9 6.0 - - + +
276B ARG* 4.3 12.6 - - + -
277B PHE 2.8 18.2 + - - +
278B SER* 3.3 5.8 - - - -
279B ILE* 2.7 34.1 + - - +
302B ILE* 3.5 33.4 - - + -
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 4.7 0.7 - - + -
148B VAL 2.9 6.2 + - - +
149B LEU* 4.0 22.9 - - + -
150B ASP* 2.9 30.2 + - - +
155B ILE* 6.3 1.3 - - + -
161B VAL* 5.9 3.8 - - + -
164B PHE* 4.0 17.0 - - + -
186B TYR* 4.1 1.0 + - - -
249B VAL* 4.2 10.3 - - + +
250B ILE* 1.3 77.6 - - - +
252B THR* 1.3 63.8 + - - +
279B ILE* 3.6 31.6 - - + -
281B ILE* 3.8 25.8 - - + -
320B LEU* 4.5 11.4 - - + -
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Residues in contact with THR 252 (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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150B ASP* 2.9 20.9 + - - -
155B ILE* 5.3 0.7 - - - -
186B TYR* 3.3 19.7 + - - +
220B THR* 3.8 2.3 - - - +
222B THR* 3.9 3.0 + - + +
250B ILE* 4.9 7.9 - - + -
251B VAL* 1.3 77.3 - - - +
253B ASP* 1.3 57.8 + - - +
254B GLY 3.2 14.7 + - - -
279B ILE 3.0 13.5 + - - +
280B ALA* 3.4 1.4 - - - -
281B ILE* 2.9 27.5 + - - +
295B PHE* 3.7 2.1 - - + -
299B ILE* 3.5 37.7 - - + -
302B ILE* 5.8 0.2 - - + -
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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