Contacts of the helix formed by residues 239 - 250 (chain D) in PDB entry 1A4Y
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 GLY 239 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237D LYS 3.7 1.0 - - - -
238D LEU* 1.3 71.8 - - - +
240D ASP* 1.3 65.4 + - - -
241D VAL* 3.1 4.5 - - - -
243D MET* 3.1 26.3 + - - +
265D CYS 2.8 22.1 + - - -
266D GLY* 3.7 13.5 - - - -
267D ILE* 3.9 5.0 - - - +
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Residues in contact with ASP 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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239D GLY* 1.3 70.7 - - - -
241D VAL* 1.3 63.4 + - + +
243D MET* 3.7 3.7 - - - +
244D ALA* 3.1 25.3 + - - +
266D GLY 4.2 1.9 + - - +
267D ILE* 3.6 2.2 - - - -
268D THR* 2.9 43.8 + - - +
270D LYS* 3.9 9.7 - - + +
271D GLY* 2.7 37.5 + - - +
274D ASP* 4.3 5.1 - - - +
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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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212D SER* 4.4 9.6 - - - +
238D LEU 5.0 1.1 - - - +
239D GLY* 5.0 1.8 - - - -
240D ASP* 1.3 80.4 - - + +
242D GLY* 1.3 67.4 + - - +
244D ALA* 2.8 17.5 + - + +
245D GLU* 3.0 33.9 + - + +
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Residues in contact with GLY 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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212D SER* 3.5 11.5 - - - -
215D CYS* 3.5 33.2 - - - +
238D LEU* 3.0 22.8 + - - -
241D VAL* 1.3 75.6 - - - +
243D MET* 1.3 56.4 + - - +
245D GLU* 2.9 7.4 + - - +
246D LEU* 2.9 24.6 + - - +
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Residues in contact with MET 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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238D LEU* 4.9 5.0 - - + +
239D GLY 3.1 12.6 + - - +
240D ASP* 3.7 9.0 - - - +
241D VAL 3.1 0.2 - - - -
242D GLY* 1.3 75.5 - - - +
244D ALA* 1.3 59.6 + - - +
246D LEU* 3.4 15.9 + - - +
247D CYS* 2.9 44.0 + - - -
250D LEU* 6.0 0.7 - - - -
260D LEU* 5.8 0.7 - - - -
262D ILE* 3.8 26.0 - - - -
267D ILE* 3.5 34.3 - - + -
271D GLY* 3.7 15.7 - - - +
272D CYS* 5.3 0.2 - - - -
274D ASP* 5.0 0.7 - - - -
275D LEU* 3.1 51.4 - - + -
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Residues in contact with ALA 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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240D ASP 3.1 14.7 + - - +
241D VAL* 2.8 11.3 + - + +
243D MET* 1.3 76.5 - - - +
245D GLU* 1.3 60.1 + - + +
247D CYS* 4.1 2.4 - - - +
248D PRO* 3.0 24.8 - - - +
274D ASP* 3.8 24.9 + - - +
277D ARG* 5.3 1.9 + - - -
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Residues in contact with GLU 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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212D SER* 3.6 21.2 - - - +
213D ASP* 4.5 3.2 - - - +
215D CYS* 4.0 11.9 - - + -
216D ARG* 3.9 20.4 - - - +
219D CYS* 3.3 19.8 - - - +
241D VAL* 3.0 34.3 - - + +
242D GLY* 2.9 6.2 + - - +
244D ALA* 1.3 79.8 - - + +
246D LEU* 1.3 56.6 + - - +
248D PRO* 3.2 13.9 - - - +
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Residues in contact with LEU 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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215D CYS* 4.0 14.6 + - - +
218D LEU* 4.0 28.7 - - + -
219D CYS* 4.0 12.5 - - - +
222D VAL* 4.3 12.7 - - + +
231D LEU* 4.8 4.3 - - + -
233D LEU* 4.0 23.3 - - + -
238D LEU* 5.2 4.7 - - + -
242D GLY 2.9 13.7 + - - +
243D MET* 3.9 17.7 - - - +
245D GLU* 1.3 75.1 - - - +
247D CYS* 1.3 63.8 + - - +
248D PRO* 3.2 3.6 - - - -
249D GLY* 3.1 13.7 + - - -
250D LEU* 3.3 26.7 + - + +
260D LEU* 4.9 10.1 - - + -
262D ILE* 5.2 2.0 - - + -
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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 MET* 2.9 42.8 + - - +
244D ALA 4.1 2.2 - - - +
246D LEU* 1.3 73.3 - - - +
248D PRO* 1.3 65.3 - - + +
250D LEU* 3.0 13.3 + - - +
251D LEU* 2.9 32.6 + - - +
274D ASP* 3.8 32.1 - - - -
275D LEU* 3.9 5.4 - - - -
277D ARG* 3.8 19.3 - - - +
278D VAL* 3.8 9.4 - - + +
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Residues in contact with PRO 248 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219D CYS* 4.1 5.4 - - - -
244D ALA 3.0 21.5 - - - +
245D GLU* 3.2 11.4 - - - +
246D LEU 3.2 5.4 - - - -
247D CYS* 1.3 93.4 - - + +
249D GLY* 1.3 59.8 + - - +
251D LEU* 3.3 20.4 + - + +
252D HIS* 3.5 13.5 + - - +
277D ARG* 5.4 2.5 - - - +
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Residues in contact with GLY 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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219D CYS* 3.1 37.0 - - - -
222D VAL* 3.5 16.7 - - - +
223D ALA* 3.8 11.7 - - - -
246D LEU 3.1 6.5 + - - -
248D PRO* 1.3 77.4 - - - +
250D LEU* 1.3 60.9 + - - +
252D HIS* 3.3 18.6 - - - +
255D SER* 3.9 1.9 - - - -
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Residues in contact with LEU 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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222D VAL* 3.9 22.2 - - + -
231D LEU* 5.6 0.9 - - + -
243D MET* 6.0 1.1 - - - -
246D LEU* 3.3 30.7 + - + +
247D CYS* 3.0 19.8 + - - +
249D GLY* 1.3 76.9 - - - +
251D LEU* 1.3 57.7 + - - +
252D HIS 3.2 4.8 + - - +
255D SER* 4.1 5.9 + - - +
257D LEU* 4.1 29.8 - - + -
260D LEU* 4.2 23.8 - - + -
275D LEU* 4.9 3.4 - - + -
278D VAL* 4.0 23.8 - - + -
282D LYS* 2.9 26.2 - - - +
285D LEU* 6.0 1.8 - - + -
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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