Contacts of the helix formed by residues 241 - 252 (chain E) in PDB entry 6D6U
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 241 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237E THR* 2.9 39.9 + - + +
238E ILE* 4.2 7.1 + - + +
239E GLN 3.8 0.2 - - - -
240E THR* 1.3 80.1 - - + +
242E ILE* 1.3 65.4 + - + +
244E CYS* 3.3 13.7 + - + +
245E THR* 3.3 17.6 + - - +
295E ALA* 5.4 0.9 - - - +
296E MET* 3.5 52.4 + - + +
299E PHE* 4.2 24.7 - + + -
350E TYR* 3.6 18.3 + + - -
351E TRP* 3.5 39.9 - + + -
354E TYR* 6.1 2.4 - + - -
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Residues in contact with ILE 242 (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 ILE 3.5 22.7 - - - +
239E GLN* 4.8 13.5 - - - +
241E TYR* 1.3 78.3 - - + +
243E PRO* 1.3 65.4 - - + +
244E CYS 3.1 0.3 + - - -
245E THR* 3.4 4.8 + - - -
246E LEU* 2.9 36.2 + - + +
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Residues in contact with PRO 243 (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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267D THR* 4.1 10.3 - - + +
271D ILE* 3.7 35.2 - - + -
274D ARG* 4.6 7.9 - - - +
239E GLN 3.7 11.0 - - - +
240E THR* 3.1 22.2 - - + +
242E ILE* 1.3 94.4 - - + +
244E CYS* 1.3 56.6 + - - +
246E LEU* 4.0 8.0 - - + +
247E ILE* 3.0 30.7 + - - +
279E LEU* 4.2 8.4 - - + +
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Residues in contact with CYS 244 (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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240E THR 4.2 4.4 + - - +
241E TYR* 3.3 10.9 + - - +
242E ILE 3.1 1.0 - - - -
243E PRO* 1.3 77.1 - - - +
245E THR* 1.3 65.5 + - - +
247E ILE 3.2 2.1 + - - -
248E VAL* 3.0 25.8 + - - +
276E MET* 3.8 5.2 - - - +
279E LEU* 3.9 22.8 - - + +
299E PHE* 4.1 8.3 - - + -
300E VAL* 3.8 23.1 - - + -
303E CYS* 2.0 50.0 - - - -
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Residues in contact with THR 245 (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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241E TYR* 3.3 11.3 + - - +
242E ILE* 4.1 4.5 - - - -
244E CYS* 1.3 76.8 - - - +
246E LEU* 1.3 64.6 + - - +
248E VAL* 3.3 7.5 + - - +
249E VAL* 2.9 31.1 + - + +
299E PHE* 3.4 24.1 - - - -
303E CYS* 4.3 0.4 - - - -
343E PHE* 3.5 27.1 - - + -
347E ASN* 5.3 0.3 + - - -
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Residues in contact with LEU 246 (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 VAL* 4.7 6.3 - - + -
267D THR* 4.0 15.7 - - + +
294D TYR* 3.0 28.5 - - - +
298D PHE* 4.5 16.2 - - + -
242E ILE* 2.9 27.3 + - + +
243E PRO* 4.1 8.5 - - + +
245E THR* 1.3 78.3 - - - +
247E ILE* 1.3 63.2 + - + +
249E VAL* 3.4 5.0 + - + -
250E LEU* 2.9 40.3 + - + +
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Residues in contact with ILE 247 (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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264D LEU* 3.5 31.9 - - + -
267D THR* 4.1 23.1 - - + +
243E PRO 3.0 18.8 - - - +
244E CYS 3.2 1.2 + - - -
246E LEU* 1.3 78.8 - - + +
248E VAL* 1.3 65.4 + - - +
250E LEU* 3.7 6.2 - - + -
251E SER* 2.9 23.9 + - - -
272E THR* 4.5 19.7 - - + +
275E THR* 4.0 25.4 - - + -
276E MET* 3.5 25.6 - - + -
279E LEU* 5.5 2.5 - - + -
307E VAL* 4.2 1.3 - - + +
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Residues in contact with VAL 248 (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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244E CYS 3.0 15.7 + - - +
245E THR* 3.5 8.1 - - - +
247E ILE* 1.3 76.5 - - - +
249E VAL* 1.3 62.3 - - - +
251E SER* 2.7 22.0 + - - -
252E TRP* 3.7 19.2 - - + +
276E MET* 4.0 3.1 - - + -
303E CYS* 3.5 41.1 - - + +
306E PHE* 4.3 16.2 - - + -
307E VAL* 3.9 7.0 - - + -
343E PHE* 3.7 34.1 - - + -
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Residues in contact with VAL 249 (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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409D Y01 6.2 4.0 - - + -
245E THR* 2.9 33.5 + - + +
246E LEU* 4.0 6.1 - - + +
248E VAL* 1.3 75.1 - - + +
250E LEU* 1.3 60.4 - - - +
252E TRP* 3.4 39.9 + - + +
253E VAL* 4.3 3.6 + - - +
343E PHE* 4.4 13.5 - - + -
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Residues in contact with LEU 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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260D VAL* 3.6 33.7 - - + +
263D VAL* 4.2 22.7 - - + -
264D LEU* 3.7 30.1 - - + -
298D PHE* 6.5 0.4 - - + -
301D LEU* 5.4 2.5 - - + -
409D Y01 4.4 17.0 - - + -
246E LEU* 2.9 26.6 + - + +
247E ILE* 3.8 7.6 - - + +
248E VAL 3.1 0.2 - - - -
249E VAL* 1.3 75.8 - - - +
251E SER* 1.3 64.4 + - - +
252E TRP 3.1 2.7 + - - -
253E VAL* 3.2 33.4 + - + +
268E LEU* 4.8 2.1 - - - +
272E THR* 5.4 1.1 - - + -
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Residues in contact with SER 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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247E ILE 2.9 13.6 + - - -
248E VAL 2.7 19.1 + - - -
250E LEU* 1.3 76.4 - - - +
252E TRP* 1.3 69.4 + - - +
253E VAL 3.2 0.7 + - - -
254E SER* 3.3 19.9 + - - -
255E PHE* 4.7 2.1 - - - -
268E LEU* 4.3 4.7 - - - +
272E THR* 4.0 26.0 - - - +
307E VAL* 3.5 28.7 - - - +
310E ALA* 5.2 6.9 - - - +
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Residues in contact with TRP 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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248E VAL* 3.7 24.1 + - + +
249E VAL* 3.5 29.4 - - + +
250E LEU 3.1 1.2 - - - -
251E SER* 1.3 84.5 + - - +
253E VAL* 1.3 61.4 + - - +
254E SER 3.0 7.3 + - - -
255E PHE* 3.0 42.8 + + + -
256E TRP* 3.2 27.5 - + + -
306E PHE* 5.4 8.1 + + - +
310E ALA* 5.3 3.1 - - + +
339E PHE* 3.5 38.4 - + + -
340E PRO* 3.4 45.1 - - + -
343E PHE* 3.7 23.8 - + + -
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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