Contacts of the strand formed by residues 180 - 186 (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 GLN 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU 2.8 8.4 + - - +
144B ASP* 3.1 20.6 - - - +
145B ILE* 2.9 25.5 + - - +
174B ILE* 4.9 2.2 - - - -
175B GLY 3.6 16.8 - - - +
176B PRO* 3.8 21.6 - - - +
179B THR* 1.3 71.7 - - - +
181B VAL* 1.3 68.4 + - - +
196B LEU* 3.5 28.5 + - + +
197B ASN* 3.7 19.2 - - - +
199B TYR 5.5 3.0 + - - +
239B GLY 2.7 26.2 + - - +
241B ARG* 3.3 19.0 + - - +
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 3.1 13.7 - - + +
147B ILE* 4.4 6.3 - - + -
169B LEU* 3.8 35.2 - - + -
172B MET* 4.0 11.9 - - - -
174B ILE* 4.0 22.6 - - + +
179B THR* 4.4 0.9 - - + -
180B GLN* 1.3 81.4 - - - +
182B GLY* 1.3 71.5 + - - +
183B ILE* 4.2 11.9 - - + -
194B PHE* 3.3 20.5 - - + -
195B ASN 3.5 10.9 - - - +
196B LEU* 3.5 9.2 + - - +
199B TYR* 5.8 0.9 + - - +
205B VAL* 4.6 12.9 - - + +
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Residues in contact with GLY 182 (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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145B ILE 2.9 9.1 + - - +
146B VAL* 3.2 11.0 - - - -
147B ILE 2.9 24.0 + - - -
181B VAL* 1.3 74.3 - - - +
183B ILE* 1.3 68.1 + - - +
184B VAL* 5.7 0.2 - - - -
194B PHE* 3.3 14.4 - - - -
195B ASN* 4.6 0.2 - - - -
196B LEU* 3.5 16.6 - - - +
233B ALA* 6.1 1.6 - - - -
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Residues in contact with ILE 183 (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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147B ILE* 3.3 24.9 - - + +
149B LEU* 4.0 17.5 - - + -
165B LEU* 4.3 19.1 - - + -
169B LEU* 4.6 2.2 - - + -
181B VAL* 4.2 6.7 - - + -
182B GLY* 1.3 80.3 - - - +
184B VAL* 1.3 67.5 + - - +
192B HIS* 3.7 1.9 - - - -
193B GLU* 2.8 34.3 + - + -
194B PHE* 3.0 48.9 + - + +
209B ALA* 4.6 5.4 - - + -
212B ILE* 3.7 25.8 - - + -
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Residues in contact with VAL 184 (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* 4.1 18.2 - - + -
147B ILE 2.9 10.0 + - - +
148B VAL* 3.4 10.4 - - + -
149B LEU* 2.9 26.9 + - - +
183B ILE* 1.3 78.0 - - - +
185B GLN* 1.3 60.7 + - - +
190B VAL* 3.2 34.3 - - + -
191B THR 3.3 6.1 - - - +
192B HIS* 3.8 30.1 - - + +
194B PHE 5.9 0.2 - - - +
225B GLY* 4.2 14.6 - - - +
228B THR* 4.9 2.2 - - + -
229B ALA* 4.5 5.2 - - - -
233B ALA* 4.1 7.0 - - + -
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Residues in contact with GLN 185 (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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149B LEU* 3.3 17.9 - - + +
151B GLY* 3.2 21.7 - - - -
158B TRP* 3.8 8.7 - - - -
184B VAL* 1.3 74.8 - - - +
186B TYR* 1.3 63.6 + - - +
190B VAL* 3.5 0.9 - - - -
191B THR* 2.9 35.4 + - - +
193B GLU* 2.7 39.8 + - + +
212B ILE* 3.6 9.3 - - - +
213B VAL 2.8 23.2 + - - +
214B GLN* 3.6 3.5 - - - -
215B ARG* 2.9 38.8 + - + +
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Residues in contact with TYR 186 (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* 3.6 31.9 - - + -
149B LEU 2.8 23.0 + - - -
150B ASP* 3.4 25.3 - - - -
151B GLY* 2.8 27.9 + - - -
185B GLN* 1.3 77.4 - - - +
187B GLY* 1.3 62.2 + - - +
189B ASN 3.3 11.2 - - - +
190B VAL* 3.7 17.7 - - + -
215B ARG* 6.3 1.6 - - - -
216B GLY 5.2 0.4 - - - -
220B THR* 3.8 11.9 - - + -
221B MET 3.3 19.5 - - - +
222B THR* 2.8 46.4 + - + +
225B GLY* 3.9 8.3 - - - -
250B ILE* 4.5 4.0 - - + +
251B VAL 4.1 0.4 + - - -
252B THR* 3.3 23.9 + - - -
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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