Contacts of the helix formed by residues 223 - 233 (chain E) 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 PRO 223 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197E GLU* 6.1 0.4 - - - +
200E PHE* 5.6 0.9 - - + -
220E ARG 4.9 1.3 - - - +
221E ALA 3.2 11.1 - - - +
222E VAL* 1.3 97.3 - - + +
224E LEU* 1.3 55.4 + - - +
225E GLU* 4.2 14.1 - - + +
226E LYS* 2.7 52.3 + - + +
227E LEU* 3.5 4.1 + - - +
244E GLY* 4.5 4.0 - - - +
246E THR 5.7 0.9 - - - +
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Residues in contact with LEU 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E PRO* 1.3 70.4 - - - +
225E GLU* 1.3 59.9 + - - +
227E LEU* 2.9 41.2 + - + +
228E ALA 4.4 1.0 + - - -
244E GLY 3.3 25.9 + - - +
245E TYR* 3.9 37.2 - - + -
246E THR 3.5 19.8 + - - +
247E ALA* 4.3 7.9 - - + -
253E VAL* 5.3 3.3 - - + +
257E LEU* 4.2 17.1 - - + +
280E TYR* 3.9 40.2 - - + -
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Residues in contact with GLU 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E PRO* 3.0 11.2 + - + +
224E LEU* 1.3 77.7 + - - +
226E LYS* 1.3 68.8 + - + +
227E LEU 3.3 0.4 + - - -
228E ALA* 4.7 4.5 + - - +
229E THR* 5.2 3.3 + - - -
246E THR 3.8 6.4 - - - +
247E ALA* 3.7 26.6 - - - +
248E GLU* 4.7 4.2 + - - +
250E ARG* 6.2 0.2 - - - -
253E VAL* 4.3 31.0 - - + +
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Residues in contact with LYS 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E PHE* 3.7 55.7 - - + +
222E VAL* 4.1 7.4 - - + -
223E PRO* 2.7 36.9 + - + +
225E GLU* 1.3 83.1 - - + +
227E LEU* 1.3 66.6 + - - +
228E ALA 3.4 0.9 - - - -
229E THR* 3.4 24.5 - - - +
230E LEU* 3.6 4.3 + - - +
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Residues in contact with LEU 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E LEU* 4.2 22.7 - - + -
222E VAL* 5.5 3.6 - - + -
223E PRO 3.5 3.1 + - - +
224E LEU* 2.9 34.8 + - + +
225E GLU 3.3 0.2 - - - -
226E LYS* 1.3 76.9 - - - +
228E ALA* 1.3 62.5 + - - +
230E LEU* 3.0 10.9 + - + +
231E LEU* 3.0 45.0 + - + +
240E LEU* 4.5 11.2 - - + -
242E THR* 3.9 29.6 - - + -
243E GLY 5.1 2.2 - - - +
245E TYR* 4.6 2.9 - - + -
257E LEU* 4.0 22.0 - - + -
261E LEU* 5.3 2.5 - - + -
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Residues in contact with ALA 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E LEU 4.4 1.4 + - - -
225E GLU 4.7 4.4 + - - +
226E LYS 3.4 0.8 - - - -
227E LEU* 1.3 73.4 - - - +
229E THR* 1.3 66.5 + - - +
231E LEU* 2.9 6.6 + - - +
232E GLN* 2.8 32.5 + - + +
256E GLY* 3.8 30.5 - - - +
257E LEU* 4.2 9.5 - - + +
260E ALA* 3.9 13.9 - - + +
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Residues in contact with THR 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E PHE* 3.6 17.8 - - + -
204E GLU* 3.4 36.6 - - - +
225E GLU 5.2 2.5 + - - -
226E LYS* 3.4 18.8 + - - +
228E ALA* 1.3 76.2 - - - +
230E LEU* 1.3 63.8 + - - +
232E GLN* 3.5 9.2 + - - +
233E ARG* 3.2 25.1 + - - +
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Residues in contact with LEU 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E PHE* 3.3 36.3 - - + -
203E LEU* 3.5 30.7 - - + +
204E GLU* 3.9 25.6 - - + -
207E VAL* 4.2 7.4 - - + +
216E LEU* 4.4 15.7 - - + -
218E LEU* 3.8 28.5 - - + -
222E VAL* 4.7 3.4 - - + -
226E LYS 4.1 4.5 - - - +
227E LEU* 3.0 15.9 + - + +
229E THR* 1.3 75.0 - - - +
231E LEU* 1.3 65.3 + - + +
233E ARG* 3.0 18.6 + - + +
234E ALA* 3.2 14.1 + - - +
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Residues in contact with LEU 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E LEU* 6.0 2.0 - - + -
227E LEU* 3.0 28.4 + - + +
228E ALA* 2.9 9.6 + - - +
230E LEU* 1.3 77.9 - - + +
232E GLN* 1.3 55.1 + - - +
234E ALA* 3.0 26.0 + - - +
235E PRO* 3.4 7.1 - - - +
237E LEU* 4.3 17.0 - - + -
240E LEU* 4.0 30.7 - - + -
257E LEU* 5.1 1.1 - - + -
260E ALA* 4.1 19.7 - - + +
261E LEU* 3.5 46.0 - - + -
264E CYS* 4.5 13.0 - - - -
267E LEU* 5.8 0.2 - - + -
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Residues in contact with GLN 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E ALA* 2.8 27.1 + - + +
229E THR* 3.6 9.6 - - - +
230E LEU 3.3 0.2 - - - -
231E LEU* 1.3 72.2 - - - +
233E ARG* 1.3 64.2 + - + +
234E ALA 3.2 1.4 + - - -
235E PRO* 3.7 12.1 - - - +
256E GLY* 4.8 2.6 + - - -
259E VAL* 4.4 13.9 - - - +
260E ALA* 3.7 27.7 - - - +
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Residues in contact with ARG 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E GLU* 2.8 35.9 + - + +
207E VAL* 3.9 20.0 - - + +
208E THR* 3.1 44.1 + - - +
229E THR* 3.2 18.1 - - - +
230E LEU* 3.0 9.0 + - - +
232E GLN* 1.3 82.1 - - - +
234E ALA* 1.3 61.8 + - - +
235E PRO* 3.5 4.3 - - - +
236E GLN* 4.8 1.2 + - - +
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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