Contacts of the helix formed by residues 230 - 242 (chain D) 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 THR 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226D PHE* 3.1 7.8 + - - +
229D GLN* 1.3 90.3 + - - +
231D TYR* 1.3 75.5 + - + +
232D LEU 3.3 2.0 - - - -
233D PRO* 3.2 6.5 - - - +
234D CYS* 3.1 22.7 + - + +
269D LEU* 4.0 14.0 - - + +
270D SER* 6.3 0.2 - - - -
273D ALA* 3.3 34.2 - - + +
286D MET* 4.6 20.1 - - + -
289D PHE* 6.0 1.6 - - + -
290D ILE* 4.6 12.6 - - + -
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Residues in contact with TYR 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D PRO* 3.3 36.6 - - + +
148D MET* 4.9 4.8 - - + +
223D ILE* 5.0 4.5 - - + -
226D PHE* 3.4 24.5 + - + -
227D VAL* 4.2 11.9 - - + +
230D THR* 1.3 78.3 - - + +
232D LEU* 1.3 59.1 + - - +
234D CYS* 3.2 4.7 + - - +
235D ILE* 2.9 34.6 + - + +
286D MET* 3.7 22.6 - - + +
289D PHE* 3.4 39.0 - + + -
340D TYR* 3.3 30.3 + + - -
341D TRP* 3.7 34.3 - + + -
407D Y01 5.7 1.6 - - + -
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Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C MET* 3.6 31.6 - - + -
227D VAL* 3.2 20.7 + - + +
228D ILE* 4.7 3.1 - - - -
231D TYR* 1.3 75.6 - - - +
233D PRO* 1.3 64.5 - - + +
235D ILE* 3.3 4.8 + - + +
236D MET* 2.9 51.2 + - + +
406D Y01 3.6 47.8 - - + -
407D Y01 4.5 28.9 - - + -
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Residues in contact with PRO 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C THR* 6.2 2.2 - - + -
265C ASN* 6.0 3.8 - - - +
286C MET* 5.2 9.9 - - + -
289C PHE* 4.9 11.1 - - + -
227D VAL 4.3 0.7 - - - +
228D ILE 4.4 7.2 - - - +
229D GLN 3.3 24.0 - - - +
230D THR 3.2 12.3 - - - +
232D LEU* 1.3 93.7 - - + +
234D CYS* 1.3 55.9 + - - +
236D MET* 3.4 7.0 + - + +
237D THR* 2.9 34.4 + - - +
269D LEU* 3.5 26.2 - - + -
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Residues in contact with CYS 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D THR* 3.1 16.1 + - + +
231D TYR 3.3 8.3 - - - +
233D PRO* 1.3 76.2 - - - +
235D ILE* 1.3 66.4 + - - +
237D THR* 3.2 4.1 + - - -
238D VAL* 2.9 25.3 + - - +
266D MET* 5.3 0.4 - - + -
269D LEU* 3.5 12.2 - - + +
289D PHE* 3.3 28.5 - - + -
290D ILE* 6.4 1.6 - - + -
293D CYS* 2.0 52.5 - - - -
333D PHE* 5.1 2.5 - - - -
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Residues in contact with ILE 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D TYR* 2.9 22.2 + - + +
232D LEU* 3.3 8.2 + - + +
234D CYS* 1.3 76.5 - - - +
236D MET* 1.3 69.8 + - + +
238D VAL* 3.4 1.6 + - - +
239D ILE* 3.0 47.6 + - + +
289D PHE* 4.3 16.8 - - + -
333D PHE* 4.2 22.7 - - + -
337D ASN* 4.8 8.7 - - - +
341D TRP* 5.0 3.4 - - - +
407D Y01 3.1 46.0 - - + -
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Residues in contact with MET 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C MET* 4.4 10.3 - - + -
289C PHE* 3.6 34.3 - - + -
290C VAL* 5.7 6.1 - - - -
293C PHE* 3.8 35.5 - - + -
232D LEU* 2.9 37.8 + - + +
233D PRO 3.7 2.5 - - - +
235D ILE* 1.3 81.7 - - + +
237D THR* 1.3 56.6 + - - +
239D ILE* 3.4 22.4 + - + +
240D LEU* 2.9 29.7 + - - +
406D Y01 6.5 2.0 - - + -
407D Y01 6.4 0.2 - - + -
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Residues in contact with THR 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C PHE* 5.2 5.8 - - - -
233D PRO* 2.9 21.3 + - - +
234D CYS* 3.2 3.7 + - - -
236D MET* 1.3 77.3 - - - +
238D VAL* 1.3 58.0 + - - +
240D LEU* 3.3 9.8 + - + +
241D SER* 2.9 27.4 + - - -
262D THR* 3.9 19.9 - - + +
265D THR* 3.5 25.1 - - + +
266D MET* 3.7 35.5 - - + -
269D LEU* 4.8 2.4 - - - +
297D VAL* 4.9 1.3 - - + -
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Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D CYS 2.9 20.0 + - - +
235D ILE 3.9 0.4 - - - +
237D THR* 1.3 75.0 - - - +
239D ILE* 1.3 66.9 + - - +
241D SER* 2.7 23.7 + - - +
242D GLN* 3.0 22.1 + - + +
266D MET* 5.3 0.4 - - - -
293D CYS* 3.6 33.9 - - - +
296D PHE* 4.7 12.3 - - + -
297D VAL* 5.0 4.7 - - + -
333D PHE* 3.6 48.9 - - + -
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Residues in contact with ILE 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C PHE* 3.8 20.4 - - + -
297C LEU* 5.2 4.9 - - + -
235D ILE* 3.0 38.7 + - + +
236D MET* 3.8 19.1 - - + +
238D VAL* 1.3 74.4 - - + +
240D LEU* 1.3 63.5 + - - +
242D GLN* 3.3 19.6 + - - +
243D VAL* 3.2 16.1 + - + +
333D PHE* 4.9 10.3 - - + -
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ILE* 6.2 3.4 - - + -
258C VAL* 4.0 28.9 - - + -
293C PHE* 3.6 23.8 - - + -
296C LEU* 3.6 33.9 - - + -
297C LEU* 5.2 1.8 - - + -
236D MET 2.9 18.3 + - - +
237D THR* 3.6 9.9 - - + +
239D ILE* 1.3 78.9 - - - +
241D SER* 1.3 57.4 + - - +
243D VAL* 3.0 26.4 + - + +
258D PHE* 3.0 33.0 - - + -
262D THR* 4.8 10.5 - - + -
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Residues in contact with SER 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D THR 2.9 12.7 + - - -
238D VAL* 2.7 28.1 + - - +
240D LEU* 1.3 76.3 - - - +
242D GLN* 1.3 61.0 + - - +
243D VAL 3.1 1.1 + - - -
244D SER* 3.6 16.1 + - - -
245D PHE* 4.5 4.9 - - - -
258D PHE* 4.3 2.4 - - - -
262D THR* 3.7 25.5 - - - +
296D PHE* 5.4 1.4 + - - +
297D VAL* 3.6 25.8 - - - +
300D ALA* 4.5 13.7 - - - +
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Residues in contact with GLN 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D VAL* 3.0 25.7 + - + +
239D ILE* 3.7 15.4 - - + +
240D LEU 3.2 0.2 - - - -
241D SER* 1.3 78.1 - - - +
243D VAL* 1.3 62.9 + - - +
244D SER 3.2 0.7 - - - -
245D PHE* 3.2 28.8 + - + +
246D TRP* 4.4 6.8 + - - -
296D PHE* 5.7 2.0 - - - +
329D PHE* 3.2 44.1 + - + +
330D PRO* 3.2 32.8 - - + +
333D PHE* 4.0 14.1 - - - +
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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