Contacts of the helix formed by residues 249 - 266 (chain E) in PDB entry 2M6I
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 ALA 249 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A LEU 4.1 5.6 - - - +
250A PRO* 3.9 15.0 - - + -
301A TYR* 2.9 38.3 + - + +
245E ASN* 2.6 36.2 - - - +
248E ALA* 1.3 84.3 - - + +
250E PRO* 1.3 58.7 - - - +
251E ALA 3.0 9.9 + - - +
252E ARG 3.5 4.5 + - - -
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Residues in contact with PRO 250 (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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248D ALA 5.2 0.7 - - - +
249D ALA* 3.9 16.4 - - + -
251D ALA* 4.4 18.4 - - + +
245E ASN* 2.8 23.1 - - + +
247E ASP 3.3 14.4 - - - +
248E ALA 3.9 0.2 - - - -
249E ALA* 1.3 88.2 - - - +
251E ALA* 1.3 64.7 + - + +
252E ARG 3.2 0.9 - - - -
253E VAL* 3.2 6.6 + - + +
254E GLY* 3.1 19.2 + - - -
301E TYR* 2.9 31.2 - - + +
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Residues in contact with ALA 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PRO* 4.4 34.3 - - + +
251A ALA* 4.9 5.6 - - + +
254A GLY* 6.4 0.7 - - - -
251D ALA* 5.0 6.9 - - + +
249E ALA 3.0 0.8 - - - -
250E PRO* 1.3 82.2 - - + +
252E ARG* 1.3 60.6 + - - +
254E GLY* 3.5 2.8 + - - -
255E LEU* 3.3 28.9 + - + +
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Residues in contact with ARG 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A VAL* 4.1 13.5 - - - +
297A ALA* 6.3 0.6 - - - +
298A LEU* 3.1 33.5 - - - +
301A TYR* 3.5 37.2 + - + -
234E ILE* 4.7 10.7 + - - +
238E SER* 3.9 20.9 + - - +
241E SER* 3.3 13.1 + - - -
245E ASN* 3.3 25.4 - - - +
249E ALA 3.5 1.6 + - - -
250E PRO 3.2 0.4 - - - -
251E ALA* 1.3 77.3 - - - +
253E VAL* 1.3 63.3 + - - +
255E LEU* 3.1 11.9 + - + +
256E GLY* 2.9 49.5 + - - -
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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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238E SER* 5.1 4.7 - - - +
242E PHE* 3.6 44.2 - - + -
245E ASN* 3.3 32.7 - - + +
250E PRO* 3.2 11.9 + - + +
252E ARG* 1.3 82.4 - - - +
254E GLY* 1.3 61.6 + - - +
256E GLY* 3.6 1.0 + - - +
257E ILE* 3.1 45.8 + - + +
297E ALA* 6.3 0.2 - - + -
301E TYR* 5.0 12.6 - - + -
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Residues in contact with GLY 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D ALA* 6.4 0.4 - - - -
255D LEU* 3.3 29.9 - - - +
250E PRO 3.1 11.8 + - - -
251E ALA* 3.5 4.9 + - - -
252E ARG 3.2 0.4 - - - -
253E VAL* 1.3 81.2 - - - +
255E LEU* 1.3 59.9 + - - +
257E ILE* 4.1 4.1 - - - +
258E THR* 2.6 31.7 + - - -
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Residues in contact with LEU 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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254A GLY* 3.4 40.6 - - - +
257A ILE* 6.0 2.2 - - + -
258A THR* 4.4 11.9 - - + +
251E ALA* 3.3 18.4 - - + +
252E ARG* 3.1 12.6 + - + +
254E GLY* 1.3 80.5 - - - +
256E GLY* 1.3 57.2 + - - +
258E THR* 3.5 4.9 + - - -
259E THR* 2.6 39.6 + - - +
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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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238E SER* 5.2 8.6 - - - -
252E ARG* 2.9 38.0 + - - +
253E VAL* 4.1 1.1 - - - -
254E GLY 3.5 0.2 - - - -
255E LEU* 1.3 77.7 - - - +
257E ILE* 1.3 61.9 + - - +
259E THR* 3.4 6.7 + - - -
260E VAL* 3.3 28.8 + - - +
293E PHE* 5.9 0.2 - - - -
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Residues in contact with ILE 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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255D LEU* 6.0 2.5 - - + -
238E SER* 5.5 5.2 - - - +
253E VAL* 3.1 38.3 + - + +
254E GLY* 4.4 5.2 - - - +
256E GLY* 1.3 77.5 - - - +
258E THR* 1.3 63.3 + - - +
260E VAL* 3.8 8.7 + - - +
261E LEU* 3.9 22.8 + - + +
293E PHE* 3.8 38.4 - - + -
294E VAL* 5.1 15.3 - - + -
297E ALA* 5.0 15.3 - - + -
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Residues in contact with THR 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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255D LEU* 4.4 13.4 - - + +
254E GLY 2.6 23.4 + - - -
255E LEU* 3.5 6.1 + - - -
256E GLY 3.3 0.2 - - - -
257E ILE* 1.3 77.6 - - - +
259E THR* 1.3 58.5 + - - +
260E VAL 3.3 0.9 - - - -
261E LEU* 4.0 5.5 - - + +
262E THR* 2.6 47.2 + - - +
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Residues in contact with THR 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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234E ILE* 5.7 8.1 - - + -
255E LEU* 2.6 24.4 + - - +
256E GLY* 3.7 9.8 - - - +
257E ILE 3.3 0.2 - - - -
258E THR* 1.3 78.2 - - - +
260E VAL* 1.3 61.9 + - + +
262E THR* 4.3 3.8 - - - -
263E LEU* 2.8 61.2 + - + +
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Residues in contact with VAL 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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231E SER* 4.9 7.0 - - - +
234E ILE* 6.5 1.1 - - + -
235E VAL* 3.2 36.3 - - + -
238E SER* 6.5 0.2 - - - -
256E GLY 3.3 16.5 + - - +
257E ILE* 4.1 7.2 - - - +
258E THR 3.3 0.2 - - - -
259E THR* 1.3 80.8 - - + +
261E LEU* 1.3 68.2 + - + +
263E LEU* 4.0 5.6 - - + +
264E THR* 2.6 36.2 + - - +
293E PHE* 5.3 11.2 - - + -
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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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263D LEU* 6.5 1.3 - - + -
257E ILE* 3.9 21.4 + - + +
258E THR* 3.8 6.8 + - + +
259E THR 3.4 0.2 - - - -
260E VAL* 1.3 91.7 - - + +
262E THR* 1.3 58.3 + - - +
264E THR* 4.1 3.4 - - - +
265E THR* 2.6 33.5 + - - +
290E CYS* 5.6 14.8 - - + -
293E PHE* 5.3 11.9 - - + -
294E VAL* 6.0 4.9 - - + -
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Residues in contact with THR 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 THR* 2.6 35.3 + - - +
259E THR* 4.1 4.7 - - - -
261E LEU* 1.3 79.3 - - - +
263E LEU* 1.3 61.5 + - + +
264E THR 3.3 0.9 - - - -
265E THR* 4.1 3.4 - - - -
266E GLN* 3.2 30.0 + - + +
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Residues in contact with LEU 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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261A LEU* 6.5 0.7 - - + -
227E LEU* 4.9 7.2 - - + +
231E SER* 5.5 15.7 - - - -
234E ILE* 5.2 14.1 - - + -
259E THR* 2.8 46.0 + - + +
260E VAL* 4.0 6.3 - - + +
261E LEU 3.4 0.2 - - - -
262E THR* 1.3 80.5 - - + +
264E THR* 1.3 57.2 + - - +
266E GLN* 4.2 11.3 + - - +
267E SER* 3.1 25.2 + - - -
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Residues in contact with THR 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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224E LEU* 4.9 7.6 - - + -
227E LEU* 5.7 3.5 - - + +
228E TYR* 4.3 23.5 - - + +
231E SER* 6.0 2.4 - - - -
260E VAL* 2.6 27.7 + - - +
261E LEU* 4.5 4.1 - - - +
263E LEU* 1.3 76.5 - - - +
265E THR* 1.3 65.1 + - - +
266E GLN 3.2 1.8 - - - -
267E SER* 3.1 19.9 + - - -
268E SER* 3.6 9.0 + - - -
286E TRP* 3.5 35.2 - - + -
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Residues in contact with THR 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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266D GLN* 4.6 18.7 + - + +
261E LEU* 2.6 25.3 + - - +
262E THR* 4.0 4.2 + - - -
264E THR* 1.3 78.1 - - - +
266E GLN* 1.3 59.6 + - - +
268E SER* 3.8 15.2 + - - -
269E GLY* 4.2 2.4 + - - -
279E TYR* 5.6 5.4 - - - +
286E TRP* 5.3 9.3 - - - -
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Residues in contact with GLN 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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265A THR* 4.6 17.6 + - + +
279A TYR* 5.0 9.3 + - - -
262E THR* 3.2 23.8 + - + +
263E LEU* 4.6 12.4 + - - +
264E THR 3.2 0.4 - - - -
265E THR* 1.3 75.4 - - - +
267E SER* 1.3 62.1 + - - +
268E SER 3.0 6.4 + - - -
269E GLY* 3.4 12.7 + - - +
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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
------------------------------------------------------------
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