Contacts of the helix formed by residues 238 - 248 (chain D) in PDB entry 3BUW
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 VAL 238 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168D ILE* 3.9 14.1 - - + -
176D GLY 4.5 2.0 - - - +
179D PHE* 3.6 43.3 - - + +
181D ILE* 3.6 23.8 - - + -
190D TRP* 3.7 34.3 - - + +
197D LYS 4.3 2.0 - - - +
198D THR* 2.8 24.6 + - + +
237D SER* 1.3 71.9 - - - +
239D PHE* 1.3 59.8 + - - +
241D PHE* 3.5 4.0 + - - +
242D ASP* 3.0 27.5 + - - +
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Residues in contact with PHE 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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160D HIS 4.3 2.0 - - - -
163D ALA* 3.5 31.4 - - + -
164D GLU* 3.5 38.8 - - + -
167D GLY* 4.4 9.0 - - - -
168D ILE* 4.2 12.1 - - + -
179D PHE* 3.8 28.5 - + - -
230D LEU* 5.9 0.2 - - + -
237D SER* 3.3 8.5 + - - +
238D VAL* 1.3 79.4 - - - +
240D GLU* 1.3 68.6 + - + +
242D ASP* 3.1 6.7 + - - +
243D ILE* 3.0 53.0 + - + +
300D LEU* 3.8 11.2 - - + -
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Residues in contact with GLU 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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164D GLU* 3.7 14.4 - - - +
199D ILE* 5.9 0.2 - - - +
228D ILE* 3.6 25.9 - - + +
229D ASP* 3.5 3.9 - - - +
230D LEU* 3.2 16.8 + - + +
231D THR* 2.9 39.7 + - + +
233D ASN* 4.5 1.0 + - - +
235D TYR 3.2 15.7 - - - +
236D ILE* 3.4 2.2 - - + -
237D SER* 2.9 40.1 + - - +
239D PHE* 1.3 82.6 - - + +
241D PHE* 1.3 62.6 + - - +
243D ILE* 3.3 8.2 + - - +
244D PHE* 3.0 24.3 + - - +
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Residues in contact with PHE 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D ILE* 3.8 19.1 - - + -
186D ALA* 3.2 38.4 - - + -
189D PHE* 3.7 15.5 - + - -
190D TRP* 3.5 26.0 - + + -
205D PHE* 3.5 35.7 - + - -
209D LEU* 5.3 0.4 - - + -
228D ILE* 4.8 2.5 - - + -
236D ILE* 4.4 5.3 - - + +
237D SER 2.9 11.6 + - - +
238D VAL 3.5 6.3 - - - +
240D GLU* 1.3 78.9 - - - +
242D ASP* 1.3 61.2 + - - +
244D PHE* 3.4 6.3 + + + +
245D THR* 2.9 43.5 + - + +
251D TRP* 3.6 25.8 - + - -
254D LEU* 5.7 0.9 - - + -
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Residues in contact with ASP 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D PHE* 3.8 24.9 - - + -
180D ARG 4.6 1.3 - - - +
181D ILE* 3.7 9.9 - - + +
182D THR* 2.8 40.1 + - - -
183D LYS* 4.6 0.3 + - - +
238D VAL 3.0 14.7 + - - +
239D PHE* 3.3 11.7 - - - +
241D PHE* 1.3 76.3 - - - +
243D ILE* 1.3 66.5 + - - +
245D THR* 3.2 7.3 + - - -
246D ARG* 3.0 46.0 + - - +
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Residues in contact with ILE 243 (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 LEU* 3.9 27.1 - - + -
239D PHE* 3.0 48.6 + - + +
240D GLU* 3.6 9.2 - - + +
242D ASP* 1.3 80.4 - - - +
244D PHE* 1.3 62.7 + - - +
246D ARG* 3.2 4.8 + - - +
247D LEU* 2.9 43.8 + - + +
300D LEU* 3.3 30.7 - - + +
301D GLY* 3.9 19.7 - - - +
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Residues in contact with PHE 244 (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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205D PHE* 6.1 0.4 - + - -
209D LEU* 5.8 0.9 - - + -
224D LEU* 3.5 21.3 - - + -
227D THR* 3.8 15.7 - - + -
228D ILE* 3.1 46.2 - - + -
230D LEU* 5.9 1.8 - - + +
240D GLU 3.0 17.8 + - - +
241D PHE* 3.9 5.4 - + - +
243D ILE* 1.3 78.3 - - - +
245D THR* 1.3 62.1 + - + +
247D LEU* 3.3 4.3 + - + -
248D PHE* 2.9 64.4 + + + +
254D LEU* 3.9 36.8 - - + -
255D LEU* 4.5 1.1 - - + -
258D TRP* 3.8 16.6 - + + -
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Residues in contact with THR 245 (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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181D ILE* 4.4 2.8 - - - +
183D LYS* 4.0 10.3 - - - +
186D ALA* 3.6 20.0 - - + +
241D PHE* 2.9 55.3 + - + +
242D ASP* 3.2 12.1 + - - -
244D PHE* 1.3 80.8 - - + +
246D ARG* 1.3 60.8 + - - +
249D GLN* 3.2 25.3 + - - +
251D TRP* 3.8 18.8 + - + -
254D LEU* 4.2 14.6 - - + +
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Residues in contact with ARG 246 (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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182D THR* 3.3 30.9 + - + -
183D LYS* 4.4 8.5 - - + +
242D ASP* 3.0 41.1 + - - +
243D ILE* 3.7 6.4 - - - +
245D THR* 1.3 74.2 + - - +
247D LEU* 1.3 66.5 + - - +
249D GLN* 2.8 39.5 + - - +
300D LEU 3.4 23.2 + - - -
301D GLY* 3.2 22.9 - - - +
302D GLN* 4.7 15.5 - - - +
303D TRP* 5.7 0.3 - - - -
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Residues in contact with LEU 247 (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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227D THR* 6.4 0.2 - - + -
230D LEU* 6.3 0.2 - - + -
243D ILE* 2.9 30.9 + - + +
244D PHE* 3.7 4.9 - - + +
246D ARG* 1.3 79.5 - - - +
248D PHE* 1.3 73.6 + - + +
249D GLN* 3.8 2.9 + - - +
261D LEU* 4.8 4.9 - - - +
295D LEU* 3.4 41.1 - - + -
301D GLY* 3.5 26.5 - - - +
302D GLN 3.7 15.9 - - - +
303D TRP* 2.9 50.9 + - + +
324D LEU* 4.9 3.8 + - - +
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Residues in contact with PHE 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D THR* 3.8 13.5 - - + -
244D PHE* 2.9 59.7 + + + +
245D THR 3.9 2.2 - - - -
247D LEU* 1.3 91.2 - - + +
249D GLN* 1.3 61.3 + - - +
254D LEU* 3.7 27.5 - - + +
257D ASN* 2.9 24.8 + - - +
258D TRP* 3.5 38.8 - + + +
261D LEU* 4.2 15.9 - - + -
262D ALA* 4.2 12.6 - - + -
268D TYR* 5.0 2.2 - + - -
295D LEU* 5.5 0.9 - - + -
303D TRP* 3.6 31.4 - + - -
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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