Contacts of the helix formed by residues 253 - 268 (chain E) in PDB entry 2NPP
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 TYR 253 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201E PHE* 3.6 24.0 - + - -
211E ILE* 3.5 20.4 - - + -
212E ALA* 3.6 26.2 - - + -
215E LEU* 3.7 15.3 - - + -
244E LEU* 2.9 45.9 + - + +
247E VAL* 3.6 10.6 - - - +
249E SER* 3.2 20.0 - - - -
250E LEU* 3.4 23.9 - - + +
252E VAL* 1.3 84.4 - - + +
254E HIS* 1.3 68.1 + - - +
255E PRO* 3.3 4.0 - - - -
256E GLN* 3.1 12.9 - - + +
257E LEU* 2.8 22.4 + - + -
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Residues in contact with HIS 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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245E HIS* 5.1 1.2 - - - -
250E LEU* 2.9 29.8 + - + +
251E SER* 4.8 0.2 - - - -
253E TYR* 1.3 75.7 - - - +
255E PRO* 1.3 72.9 - - + +
257E LEU* 3.0 3.8 + - - +
258E ALA* 2.8 24.4 + - + +
293E MET* 2.8 73.4 + - + +
294E PHE* 5.1 0.2 - - - -
296E ASN* 4.9 9.1 + - - -
297E GLU* 3.0 45.1 + - + +
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Residues in contact with PRO 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 SER 5.6 1.8 - - - +
252E VAL 5.0 1.8 - - - -
253E TYR* 3.3 2.5 - - - +
254E HIS* 1.3 99.2 - - + +
256E GLN* 1.3 92.5 + - - +
257E LEU 2.9 1.2 + - - -
258E ALA* 3.2 5.0 + - + +
259E TYR* 3.1 22.4 + - - +
293E MET* 5.5 0.7 - - + -
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Residues in contact with GLN 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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212E ALA* 4.0 17.6 - - + +
215E LEU* 3.9 19.2 - - + +
216E GLU* 3.7 28.8 - - + +
252E VAL 3.8 13.3 + - - -
253E TYR* 3.1 25.4 - - + +
255E PRO* 1.3 99.6 - - - +
257E LEU* 1.3 60.7 + - - +
259E TYR* 3.6 8.4 - - - +
260E CYS* 3.6 21.1 + - - -
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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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215E LEU* 3.6 15.9 - - + +
241E LEU* 3.3 38.4 - - + +
244E LEU* 4.0 26.7 - - + -
245E HIS* 3.6 37.7 - - + +
250E LEU* 4.3 4.5 - - + -
253E TYR* 2.8 20.0 + - + +
254E HIS* 3.4 9.0 - - - +
256E GLN* 1.3 74.5 - - - +
258E ALA* 1.3 69.3 + - - +
259E TYR 3.0 1.3 - - - -
260E CYS* 2.7 15.9 + - + +
261E VAL* 3.0 18.5 + - + +
297E GLU* 5.5 0.2 - - - +
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Residues in contact with ALA 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 HIS* 2.8 23.4 + - + +
255E PRO* 3.8 6.5 - - + +
257E LEU* 1.3 71.9 - - - +
259E TYR* 1.3 65.7 + - - +
261E VAL* 2.9 14.3 + - - +
262E VAL* 2.8 28.5 + - + +
297E GLU* 3.7 28.7 - - + -
300E GLU* 4.3 18.6 - - - +
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Residues in contact with TYR 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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216E GLU* 6.5 0.7 - - - -
219E GLY* 4.1 29.6 - - - -
220E SER 4.9 0.4 - - - -
223E ASN* 3.9 10.2 + - - +
255E PRO 3.1 11.2 + - - +
256E GLN* 3.6 13.9 - - - +
257E LEU 2.9 0.4 + - - -
258E ALA* 1.3 76.9 - - - +
260E CYS* 1.3 55.3 + - - +
262E VAL* 3.1 6.4 + - + +
263E GLN* 2.7 72.7 + - + +
300E GLU* 5.3 2.0 + - - -
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Residues in contact with CYS 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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215E LEU* 3.6 36.3 - - - -
218E LEU* 4.3 2.5 - - - -
219E GLY* 3.7 11.2 - - - -
222E ILE* 3.2 30.0 - - + +
241E LEU* 4.1 15.9 - - + -
256E GLN 3.7 11.4 - - - -
257E LEU 2.7 13.4 + - - +
259E TYR* 1.3 76.3 - - - +
261E VAL* 1.3 55.3 + - - +
263E GLN* 3.7 4.5 - - - +
264E PHE* 2.9 36.7 + - - +
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Residues in contact with VAL 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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237E LEU* 4.7 9.1 - - + +
241E LEU* 5.0 2.9 - - + +
242E LEU* 4.4 9.2 - - + -
245E HIS* 3.8 17.5 - - + +
257E LEU* 3.0 21.5 + - + +
258E ALA* 2.9 13.7 + - - +
260E CYS* 1.3 75.1 - - - +
262E VAL* 1.3 66.2 + - + +
264E PHE* 3.4 6.9 + - - +
265E LEU* 3.2 20.5 + - + +
275E VAL* 3.7 32.9 - - + +
297E GLU* 3.6 19.7 - - + +
301E ILE* 4.5 7.2 - - + -
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Residues in contact with VAL 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 ALA* 2.8 23.0 + - + +
259E TYR* 3.6 8.1 - - + +
261E VAL* 1.3 69.3 - - + +
263E GLN* 1.3 60.2 + - - +
264E PHE 2.9 3.8 - - - -
265E LEU* 2.6 34.3 + - + +
266E GLU* 2.9 32.9 + - + +
297E GLU* 6.1 0.4 - - + -
300E GLU* 4.2 35.2 - - + +
301E ILE* 4.6 11.7 - - + -
304E VAL* 4.3 17.3 - - + -
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Residues in contact with GLN 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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219E GLY 4.7 0.9 - - - +
222E ILE* 4.4 10.7 - - + +
223E ASN* 2.6 50.6 - - + +
259E TYR* 2.7 56.4 + - + +
260E CYS* 3.8 6.1 - - - +
262E VAL* 1.3 77.3 - - - +
264E PHE* 1.3 61.0 + - - +
266E GLU* 3.5 22.8 + - - +
267E LYS* 3.2 21.1 + - - +
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Residues in contact with PHE 264 (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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222E ILE* 3.5 28.9 - - + -
225E PHE* 4.1 14.1 - + - -
229E LEU* 3.8 23.3 - - + -
233E HIS* 3.1 32.3 - - + -
236E PHE* 3.7 26.0 - + - -
237E LEU* 3.7 33.0 - - + -
241E LEU* 3.9 11.4 - - + -
260E CYS 2.9 18.8 + - - +
261E VAL 3.4 7.2 - - - +
262E VAL 2.7 1.0 + - - -
263E GLN* 1.3 76.2 - - - +
265E LEU* 1.3 65.2 + - + +
267E LYS* 3.2 6.2 + - + +
268E ASP* 3.1 20.8 + - - +
271E LEU* 3.9 10.5 - - + +
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Residues in contact with LEU 265 (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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261E VAL 3.5 13.5 - - - +
262E VAL* 2.6 17.2 + - + +
264E PHE* 1.3 72.1 - - + +
266E GLU* 1.3 62.0 + - + +
268E ASP 2.9 29.2 - - - +
269E SER* 3.2 7.8 + - - -
271E LEU* 3.7 10.8 - - + +
272E THR* 3.3 47.1 - - + +
275E VAL* 4.3 15.5 - - + -
301E ILE* 3.2 42.0 - - + +
304E VAL* 5.3 10.3 - - + +
305E ILE* 6.2 1.8 - - - -
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Residues in contact with GLU 266 (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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262E VAL* 2.9 27.3 + - + +
263E GLN* 3.9 23.8 + - - +
265E LEU* 1.3 76.6 - - - +
267E LYS* 1.3 63.5 + - - +
269E SER 5.2 0.2 + - - -
304E VAL* 3.3 39.1 - - + +
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Residues in contact with LYS 267 (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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222E ILE* 5.4 9.2 - - + +
223E ASN* 6.3 1.1 - - - -
225E PHE* 6.0 2.7 - - + +
227E LEU 5.0 7.1 - - - +
229E LEU* 4.6 20.6 - - + -
263E GLN 3.2 13.6 + - - +
264E PHE* 3.5 11.0 - - + +
265E LEU 3.1 0.4 - - - -
266E GLU* 1.3 80.0 - - - +
268E ASP* 1.3 59.9 + - - +
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Residues in contact with ASP 268 (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 6.1 0.2 - - - +
229E LEU* 3.8 27.2 + - + +
234E LYS* 4.7 13.2 - - - -
264E PHE 3.1 11.6 + - - +
265E LEU* 2.9 14.7 - - - +
267E LYS* 1.3 78.5 - - - +
269E SER* 1.3 62.1 + - - +
270E THR* 2.5 52.8 + - - -
271E LEU* 3.8 16.8 + - + +
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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