Contacts of the helix formed by residues 240 - 250 (chain D) in PDB entry 2P82
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 240 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D EDO 3.4 29.0 + - - -
231D LEU* 3.4 52.3 - - + -
232D GLY* 5.4 0.4 - - - -
236D ILE* 5.0 3.4 - - + -
237D ASN* 3.0 25.1 + - + +
239D VAL* 1.3 93.4 - - + +
241D VAL* 1.3 59.9 + - - +
242D ASP 3.4 1.6 - - - -
243D ALA* 3.4 7.7 + - + +
244D PHE* 2.9 30.8 + - - +
346D LEU* 3.5 33.6 - - + +
347D ARG 3.6 13.6 + - - -
348D MET* 3.9 19.6 - - + +
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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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236D ILE* 4.8 2.7 - - + -
237D ASN 4.5 2.2 - - - +
238D PRO* 3.3 30.7 + - + +
239D VAL 3.4 0.4 - - - -
240D TYR* 1.3 77.9 - - - +
242D ASP* 1.3 70.3 + - - +
244D PHE* 3.3 6.5 + - - +
245D LYS* 3.0 48.1 + - - +
273D ASP* 4.6 6.5 - - + +
311D ILE* 3.9 23.7 - - + +
312D LEU* 3.9 20.2 - - + -
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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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238D PRO 4.8 1.0 + - - -
239D VAL 4.9 2.6 + - - +
240D TYR 3.4 0.4 - - - -
241D VAL* 1.3 83.5 - - - +
243D ALA* 1.3 58.3 + - - +
245D LYS* 3.2 17.5 + - - +
246D GLU* 2.9 35.6 + - + +
343D LYS* 5.9 2.5 - - - +
344D GLU* 3.8 17.3 - - - +
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Residues in contact with ALA 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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239D VAL 5.3 1.3 + - - +
240D TYR* 3.4 11.2 + - + +
241D VAL 3.4 0.4 - - - -
242D ASP* 1.3 74.0 - - - +
244D PHE* 1.3 67.4 + - - +
246D GLU* 3.1 17.3 + - - +
247D CYS* 3.2 17.5 + - - -
340D GLU 4.6 2.5 - - - +
341D ILE* 3.5 23.6 - - + +
344D GLU* 4.3 21.7 + - + +
346D LEU 6.1 0.2 - - - +
348D MET* 3.8 22.2 - - + +
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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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231D LEU* 4.0 20.6 - - + -
236D ILE* 4.2 13.2 - - + -
240D TYR 2.9 20.7 + - - +
241D VAL* 3.5 5.8 - - - +
243D ALA* 1.3 75.2 - - - +
245D LYS* 1.3 62.2 - - + +
247D CYS* 3.2 16.5 + - - +
248D PHE* 3.3 29.0 - + - -
256D ALA* 4.0 13.9 - - + -
267D PHE* 5.8 0.2 - - + -
275D LEU* 4.2 18.4 - - + -
311D ILE* 4.1 17.7 - - + -
314D LEU* 4.0 20.2 - - + -
318D VAL* 4.3 15.3 - - + -
320D LEU* 3.8 27.6 - - + -
348D MET* 3.6 11.5 - - - -
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Residues in contact with LYS 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 26.8 + - + +
242D ASP* 3.4 16.4 + - - +
244D PHE* 1.3 76.2 - - - +
246D GLU* 1.3 62.0 + - - +
248D PHE* 3.1 18.3 + - - +
249D LYS* 3.5 6.7 - - - +
270D PHE* 3.5 46.4 - - + -
272D GLY* 3.1 26.4 + - - -
273D ASP* 2.8 26.9 + - - -
275D LEU* 5.6 0.7 - - + -
311D ILE* 3.6 25.4 - - + -
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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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242D ASP* 2.9 24.5 + - + +
243D ALA* 3.1 12.3 + - - +
245D LYS* 1.3 75.4 - - - +
247D CYS* 1.3 62.9 + - - +
249D LYS* 3.1 46.6 + - - +
250D MET* 3.4 15.2 - - + +
340D GLU* 3.7 51.0 - - + +
341D ILE* 4.4 3.8 - - + -
343D LYS* 5.0 6.0 + - - +
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Residues in contact with CYS 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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243D ALA 3.2 9.6 + - - -
244D PHE 3.2 9.2 + - - +
246D GLU* 1.3 75.8 - - - +
248D PHE* 1.3 62.0 + - + +
249D LYS 3.2 1.0 + - - -
250D MET* 3.3 21.1 + - - +
253D SER* 3.1 23.3 - - - +
255D GLY 6.0 1.3 - - - +
320D LEU* 3.7 28.5 - - + -
322D PHE* 3.9 18.5 - - + -
341D ILE* 4.1 7.9 - - - -
348D MET* 3.3 34.3 - - - -
349D PHE* 4.3 2.0 - - - -
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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
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30D TRP* 4.2 7.8 - - + +
32D LEU 3.9 2.0 + - - -
33D GLY* 2.8 27.9 + - - +
244D PHE* 3.3 52.5 - + - -
245D LYS* 3.1 15.0 + - - +
247D CYS* 1.3 77.6 - - + +
249D LYS* 1.3 58.1 + - - +
250D MET 3.4 0.4 - - - -
253D SER* 3.6 6.1 - - - -
255D GLY* 3.5 29.6 - - - -
256D ALA* 4.3 4.3 - - + -
267D PHE* 3.5 26.7 - - + -
268D ILE 3.7 5.6 - - - +
269D GLY* 3.5 28.5 - - - -
270D PHE* 4.0 17.0 - + + -
275D LEU* 3.9 21.1 - - + -
320D LEU* 6.0 0.2 - - + -
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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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30D TRP* 3.4 65.1 - - + +
33D GLY* 3.9 3.7 - - - +
245D LYS* 3.5 14.6 - - - +
246D GLU* 3.1 44.2 + - - +
248D PHE* 1.3 77.1 - - - +
250D MET* 1.3 65.1 + - + +
251D PRO* 3.6 4.5 - - - +
270D PHE* 4.1 13.9 - - + -
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Residues in contact with MET 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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33D GLY* 3.3 7.6 - - - -
246D GLU 3.4 19.1 - - - +
247D CYS* 3.3 12.9 + - - +
249D LYS* 1.3 77.2 - - - +
251D PRO* 1.3 71.9 - - + +
252D GLN* 3.5 13.7 - - - +
253D SER* 3.0 21.4 + - - +
322D PHE* 4.0 9.9 - - + -
333D TRP* 3.9 27.6 - - - -
336D LEU* 4.0 36.8 - - + +
337D VAL* 4.2 4.3 - - + -
340D GLU* 4.5 7.6 - - + -
341D ILE* 4.0 31.6 - - + -
349D PHE* 5.8 0.2 - - + -
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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