Contacts of the helix formed by residues 240 - 251 (chain D) in PDB entry 4OBZ
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 PRO 240 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239D GLY* 1.3 83.4 - - - +
241D VAL* 1.3 57.1 + - - +
242D ASP* 3.3 2.5 - - + +
243D GLU* 3.1 26.5 + - + +
244D VAL* 2.8 31.5 + - - +
309D MET 3.9 2.0 - - - +
310D ASP* 3.3 17.7 - - - +
317D PRO* 4.7 19.1 - - + -
318D LEU 4.7 4.9 - - - +
319D TRP* 3.4 31.6 - - + +
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Residues in contact with VAL 241 (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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239D GLY 3.4 1.2 + - - -
240D PRO* 1.3 69.3 - - - +
242D ASP* 1.4 60.5 + - - +
244D VAL* 3.9 1.2 - - - +
245D ARG* 3.0 57.4 + - - +
261D TYR* 4.9 4.2 + - - +
308D GLY* 3.8 15.3 - - - +
309D MET* 3.7 18.4 - - - +
310D ASP* 3.3 33.0 + - + +
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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
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240D PRO* 3.3 2.3 - - + +
241D VAL* 1.4 78.0 - - - +
243D GLU* 1.3 65.7 + - + +
245D ARG* 3.2 34.5 + - - +
246D GLU* 3.1 31.1 + - - +
310D ASP* 5.2 0.8 + - - -
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Residues in contact with GLU 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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221D LEU* 3.1 35.0 - - + +
222D CYS* 3.0 28.4 + - - -
223D LYS* 5.5 4.7 + - - -
226D CYS* 4.1 6.8 - - - -
240D PRO* 3.1 25.0 + - + +
242D ASP* 1.3 75.9 - - + +
244D VAL* 1.3 62.4 + - - +
246D GLU* 3.3 15.3 + - - +
247D LEU* 3.2 11.4 + - - +
319D TRP* 3.6 34.1 + - + -
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Residues in contact with VAL 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D GLY* 3.6 18.4 - - - +
240D PRO 2.8 22.6 + - - +
241D VAL 4.1 1.1 - - - +
243D GLU* 1.3 68.2 - - - +
245D ARG* 1.3 57.4 + - - +
247D LEU* 3.3 7.1 - - + +
248D GLN* 2.8 54.9 + - - +
261D TYR* 4.4 4.5 - - + -
306D PHE* 4.1 14.8 - - + +
307D MET 3.5 20.6 - - - +
308D GLY* 3.5 26.0 - - - +
319D TRP* 4.4 13.2 - - + -
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Residues in contact with ARG 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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241D VAL* 3.0 40.4 + - - +
242D ASP* 3.2 38.4 + - - +
244D VAL* 1.3 73.6 - - - +
246D GLU* 1.4 62.7 + - - +
248D GLN* 3.4 3.3 + - - +
249D LYS* 3.2 42.9 + - + +
261D TYR* 4.0 26.8 + - + +
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Residues in contact with GLU 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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219D LEU* 4.0 21.7 - - + +
221D LEU* 3.9 16.6 - - + +
223D LYS* 4.4 14.4 + - - -
242D ASP* 3.1 22.7 + - - +
243D GLU* 3.4 19.2 - - - +
245D ARG* 1.4 75.5 - - + +
247D LEU* 1.4 61.7 + - - +
249D LYS* 3.1 14.7 + - + +
250D ALA* 3.1 21.8 + - - +
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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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213D VAL* 4.9 3.1 - - + -
215D VAL* 4.7 4.0 - - + -
219D LEU* 4.0 11.4 - - - +
221D LEU* 3.7 23.3 - - + -
243D GLU 3.2 9.1 + - - +
244D VAL* 3.3 13.9 - - - +
246D GLU* 1.4 78.4 - - - +
248D GLN* 1.3 59.6 + - - +
250D ALA* 3.3 6.1 - - - +
251D ILE* 3.2 37.9 + - + +
274D ILE* 3.8 27.1 - - + -
306D PHE* 3.7 47.3 - - + -
319D TRP* 4.8 7.2 - - + -
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Residues in contact with GLN 248 (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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244D VAL* 2.8 46.5 + - - +
245D ARG 3.4 3.3 + - - +
246D GLU 3.3 0.2 - - - -
247D LEU* 1.3 76.2 - - - +
249D LYS* 1.3 64.2 + - - +
251D ILE* 3.3 11.3 + - + -
252D GLY 3.2 4.0 + - - -
253D ALA* 3.0 57.8 + - + +
261D TYR* 3.2 35.3 - - + +
304D SER* 2.7 26.8 + - - -
306D PHE* 3.0 19.5 - - - +
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Residues in contact with LYS 249 (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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245D ARG* 3.2 29.9 + - + +
246D GLU* 3.1 14.6 + - + +
248D GLN* 1.3 76.9 - - - +
250D ALA* 1.3 61.0 + - - +
251D ILE 3.4 0.5 + - - -
252D GLY* 3.4 9.4 + - - -
253D ALA 5.0 2.5 - - - -
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Residues in contact with ALA 250 (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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215D VAL* 5.1 5.8 - - + -
217D SER* 4.8 10.8 + - - +
219D LEU* 3.8 28.3 - - + -
246D GLU 3.1 11.4 + - - +
247D LEU* 3.3 11.9 - - - +
248D GLN 3.2 0.2 - - - -
249D LYS* 1.3 76.9 - - - +
251D ILE* 1.4 61.7 + - + +
252D GLY 3.5 0.6 + - - -
272D PRO* 4.7 6.9 - - - +
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Residues in contact with ILE 251 (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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215D VAL* 4.4 10.3 - - + -
247D LEU* 3.2 28.1 + - + +
248D GLN* 3.3 19.0 + - + +
250D ALA* 1.4 79.1 - - - +
252D GLY* 1.3 61.1 + - - +
253D ALA* 3.4 2.4 + - + -
263D ILE* 3.9 31.0 - - + +
267D LYS* 5.8 2.4 - - - +
271D LEU* 3.1 30.0 - - + +
272D PRO* 3.7 28.3 - - + -
274D ILE* 4.7 1.1 - - + -
290D TYR* 3.9 24.5 - - + +
304D SER* 4.1 11.7 - - - +
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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
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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