Contacts of the helix formed by residues 226 - 234 (chain B) in PDB entry 2P1N
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 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B PHE* 3.7 49.6 - - + +
222B VAL* 4.2 8.3 - - + -
223B PRO* 2.6 39.0 + - + +
225B GLU* 1.3 81.9 - - + +
227B LEU* 1.3 63.7 + - - +
228B ALA 3.4 1.3 - - - -
229B THR* 3.1 25.6 + - - +
230B LEU* 3.6 4.7 + - - +
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Residues in contact with LEU 227 (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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218B LEU* 4.0 27.8 - - + -
222B VAL* 4.9 4.2 - - + +
223B PRO 3.7 3.4 + - - +
224B LEU* 3.2 26.3 + - + +
226B LYS* 1.3 75.4 - - - +
228B ALA* 1.3 66.2 + - - +
230B LEU* 2.9 15.0 + - + +
231B LEU* 2.9 42.6 + - + +
240B LEU* 4.3 15.5 - - + -
242B THR* 4.4 27.1 - - + -
243B GLY 4.9 2.2 - - - +
244B GLY 6.0 0.2 - - - +
245B TYR* 4.9 2.7 - - + -
257B LEU* 3.9 23.3 - - + -
261B LEU* 5.1 3.4 - - + -
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Residues in contact with ALA 228 (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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224B LEU 4.8 1.2 + - - -
225B GLU 5.0 3.8 + - - +
226B LYS 3.3 1.0 + - - -
227B LEU* 1.3 78.8 - - - +
229B THR* 1.3 64.0 + - - +
231B LEU* 3.9 2.6 - - - +
232B GLN* 3.0 30.4 + - + +
256B GLY* 3.9 19.5 - - - +
257B LEU* 4.2 8.7 - - + +
260B ALA* 3.8 25.4 - - + -
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Residues in contact with THR 229 (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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200B PHE* 4.3 13.2 - - + -
204B GLU* 3.3 40.4 - - + +
225B GLU 5.4 1.4 + - - -
226B LYS* 3.1 18.5 + - - +
228B ALA* 1.3 77.1 - - - +
230B LEU* 1.3 67.1 + - + +
232B GLN* 3.3 7.1 + - - +
233B ARG* 3.3 20.5 + - + +
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Residues in contact with LEU 230 (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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200B PHE* 4.0 24.7 - - + -
203B LEU* 3.8 27.1 - - + +
204B GLU* 4.2 24.0 - - + -
207B VAL* 4.1 9.7 - - + +
216B LEU* 4.7 12.4 - - + +
218B LEU* 3.8 31.0 - - + -
222B VAL* 4.4 11.2 - - + -
226B LYS 3.6 2.7 + - - +
227B LEU* 2.9 13.8 + - + +
229B THR* 1.3 79.8 - - - +
231B LEU* 1.3 67.8 + - + +
233B ARG* 3.1 15.9 + - + +
234B ALA* 3.2 14.2 + - - +
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Residues in contact with LEU 231 (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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216B LEU* 5.9 1.3 - - + -
227B LEU* 2.9 41.0 + - + +
228B ALA* 3.0 4.0 + - - +
230B LEU* 1.3 77.7 - - + +
232B GLN* 1.3 67.9 + - - +
234B ALA* 2.9 22.4 + - - +
235B PRO* 3.4 5.2 - - - +
237B LEU* 3.9 24.2 - - + -
240B LEU* 3.7 25.8 - - + -
257B LEU* 5.2 0.9 - - + -
260B ALA* 4.2 22.2 - - + +
261B LEU* 3.9 34.8 - - + -
264B CYS* 4.4 11.1 - - - -
267B LEU* 6.1 0.2 - - + -
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Residues in contact with GLN 232 (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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228B ALA* 3.0 21.7 + - + +
229B THR* 3.7 6.7 - - - +
231B LEU* 1.3 78.5 - - - +
233B ARG* 1.3 65.3 + - - +
235B PRO* 3.4 14.1 - - - +
256B GLY 5.5 0.2 - - - +
259B VAL* 4.5 10.9 - - - +
260B ALA* 4.0 24.8 + - + +
263B GLY* 6.3 0.8 - - - -
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Residues in contact with ARG 233 (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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204B GLU* 2.8 38.1 + - + +
207B VAL* 3.7 20.7 - - + +
208B THR* 3.2 44.6 + - - +
229B THR* 3.3 17.1 + - - +
230B LEU* 3.1 11.5 + - - +
232B GLN* 1.3 80.1 - - - +
234B ALA* 1.3 57.1 + - - +
235B PRO* 3.3 6.0 - - - +
236B GLN* 4.5 2.3 + - - +
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Residues in contact with ALA 234 (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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207B VAL* 3.8 18.4 - - + +
213B LEU* 4.8 3.4 - - + -
216B LEU* 5.5 1.6 - - + -
230B LEU 3.2 6.8 + - - +
231B LEU 2.9 15.1 + - - +
233B ARG* 1.3 73.6 - - - +
235B PRO* 1.3 64.8 - - - +
236B GLN* 2.7 26.7 + - - +
237B LEU* 3.1 38.4 + - + +
264B CYS* 4.4 2.1 - - - -
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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