Contacts of the helix formed by residues 250 - 263 (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 ARG 250 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225E GLU* 6.2 0.2 - - - -
248E GLU* 3.4 42.1 + - - +
249E VAL* 1.4 75.7 - - - +
251E PRO* 1.4 72.3 - - + +
252E ASP* 3.3 33.4 + - - +
253E VAL* 3.4 19.4 + - + +
254E TYR* 3.1 26.1 + - - +
280E TYR* 2.9 10.7 + - - -
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Residues in contact with PRO 251 (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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249E VAL 4.9 0.7 - - - +
250E ARG* 1.4 86.5 - - + +
252E ASP* 1.3 67.8 + - - +
254E TYR* 3.2 7.0 + - + +
255E SER* 2.9 27.3 + - - -
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Residues in contact with ASP 252 (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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250E ARG* 3.3 38.3 + - - -
251E PRO* 1.3 79.0 - - - +
253E VAL* 1.3 73.6 + - - +
255E SER* 4.0 5.2 - - - -
256E GLY* 3.5 17.7 + - - -
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Residues in contact with VAL 253 (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* 5.3 5.2 - - + +
225E GLU* 4.3 35.2 - - + +
247E ALA* 4.8 4.5 - - + -
248E GLU 4.9 1.1 - - - +
250E ARG* 3.4 31.1 + - - +
251E PRO 3.2 1.0 - - - -
252E ASP* 1.3 86.0 + - - +
254E TYR* 1.3 66.2 + - - +
256E GLY* 4.3 0.3 - - - -
257E LEU* 3.3 21.7 + - + +
280E TYR* 3.2 30.9 - - + +
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Residues in contact with TYR 254 (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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250E ARG 3.1 17.0 + - - +
251E PRO* 3.2 8.0 + - + +
253E VAL* 1.3 76.9 - - - +
255E SER* 1.3 71.4 + - - +
257E LEU* 3.1 4.7 + - - +
258E SER* 2.9 30.8 + - - -
279E ALA 3.8 22.4 - - - -
280E TYR* 3.7 23.5 - + + -
282E PRO* 3.2 19.0 + - + +
283E ALA* 3.0 40.9 + - + +
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Residues in contact with SER 255 (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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251E PRO 2.9 18.1 + - - -
252E ASP* 4.0 5.4 - - - -
253E VAL 3.3 0.2 - - - -
254E TYR* 1.3 84.5 - - - +
256E GLY* 1.3 52.6 + - - +
258E SER* 2.9 24.1 + - - -
259E VAL* 2.9 27.4 + - - +
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Residues in contact with GLY 256 (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* 3.8 10.2 - - - +
232E GLN* 4.8 2.0 + - - -
252E ASP 3.5 11.3 + - - -
253E VAL 4.5 0.4 - - - -
255E SER* 1.3 74.8 + - - +
257E LEU* 1.3 66.6 + - - +
258E SER 3.2 0.2 + - - -
259E VAL* 3.5 9.0 + - - +
260E ALA* 3.3 22.2 + - - +
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Residues in contact with LEU 257 (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* 4.2 23.8 - - + +
227E LEU* 4.0 25.1 - - + -
228E ALA* 4.2 13.4 - - + +
231E LEU* 5.1 2.5 - - + -
245E TYR* 4.1 12.8 - - - +
253E VAL* 3.3 15.5 + - + +
254E TYR 3.1 9.8 + - - +
255E SER 3.1 1.0 - - - -
256E GLY* 1.3 77.0 - - - +
258E SER* 1.3 64.1 + - - +
260E ALA* 3.1 2.6 + - - +
261E LEU* 3.1 41.1 + - + +
280E TYR* 4.1 21.3 - - + -
283E ALA* 3.8 19.7 - - + -
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Residues in contact with SER 258 (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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254E TYR* 2.9 29.7 + - - -
255E SER* 2.9 11.1 + - - -
257E LEU* 1.3 79.3 - - - +
259E VAL* 1.3 65.6 + - - +
260E ALA 3.0 0.9 + - - -
261E LEU* 3.2 2.9 + - - +
262E SER* 3.1 26.7 + - - -
282E PRO 5.4 0.3 + - - -
283E ALA* 4.4 21.1 + - - +
286E SER* 6.0 1.7 - - - -
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Residues in contact with VAL 259 (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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232E GLN* 4.4 14.1 - - - +
255E SER* 2.9 26.9 + - - +
256E GLY* 4.0 8.1 - - - +
258E SER* 1.3 78.4 - - - +
260E ALA* 1.3 58.1 + - - +
262E SER* 3.3 8.2 + - - -
263E GLY* 2.9 23.6 + - - -
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Residues in contact with ALA 260 (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* 3.9 21.1 - - + -
231E LEU* 4.1 15.3 - - + +
232E GLN* 3.7 24.2 - - - +
256E GLY 3.3 16.7 + - - +
257E LEU 3.1 4.5 + - - +
258E SER 3.0 0.8 - - - -
259E VAL* 1.3 76.8 - - - +
261E LEU* 1.3 67.3 + - - +
262E SER 3.0 1.3 + - - -
263E GLY* 3.5 7.3 + - - +
264E CYS* 3.5 18.0 + - - -
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Residues in contact with LEU 261 (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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227E LEU* 5.3 3.4 - - + -
231E LEU* 3.5 26.2 - - + -
240E LEU* 3.9 18.8 - - + -
245E TYR* 4.8 1.1 - - + +
257E LEU* 3.1 34.1 + - + +
258E SER 3.2 0.9 + - - +
260E ALA* 1.3 78.3 - - - +
262E SER* 1.3 56.3 + - - +
264E CYS* 2.7 24.1 + - - +
267E LEU* 4.2 13.2 - - + -
270E LEU* 5.5 2.2 - - + -
283E ALA* 3.4 35.4 - - + +
284E VAL* 3.8 20.4 - - + -
286E SER* 5.1 0.9 - - - +
287E VAL* 3.1 26.9 - - + +
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Residues in contact with SER 262 (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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258E SER* 3.1 16.4 + - - -
259E VAL* 3.3 11.4 + - - -
260E ALA 3.0 0.4 - - - -
261E LEU* 1.3 77.0 - - - +
263E GLY* 1.3 60.6 + - - +
264E CYS 3.1 5.1 + - - -
265E LYS* 3.3 19.8 + - - -
286E SER* 3.0 32.5 - - - -
287E VAL* 4.6 0.7 - - - -
290E ARG* 4.0 7.3 + - - +
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Residues in contact with GLY 263 (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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235E PRO* 3.9 20.1 - - - +
259E VAL 2.9 16.8 + - - -
260E ALA* 3.7 6.3 - - - -
261E LEU 3.3 0.4 - - - -
262E SER* 1.3 75.3 + - - +
264E CYS* 1.3 59.6 + - - -
265E LYS* 3.1 21.6 + - - +
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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