Contacts of the helix formed by residues 252 - 262 (chain D) in PDB entry 2PGW
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 252 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D MSE 3.7 40.4 - - + -
100D ARG* 3.9 23.6 - - + +
103D ASN* 4.0 8.5 - - - +
251D PHE* 1.3 78.0 - - - +
253D LEU* 1.3 65.4 + - - +
254D TYR* 3.4 8.0 + - - +
255D ASP* 3.0 30.5 + - - +
256D VAL* 3.0 26.3 + - - +
275D ILE* 3.5 7.6 - - - -
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Residues in contact with LEU 253 (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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99D MSE 5.2 1.3 - - - -
252D THR* 1.3 75.5 - - - +
254D TYR* 1.3 69.1 + - + +
256D VAL* 3.3 7.0 + - + +
257D TYR* 3.1 26.0 + - - +
275D ILE* 3.2 14.8 - - + +
280D PRO 5.1 0.2 - - - +
283D LYS* 3.9 36.3 - - + +
284D ALA* 3.9 7.6 - - + +
287D VAL* 3.8 24.8 - - + +
286H ALA 4.0 16.4 - - - +
289H GLU* 4.1 22.4 - - + +
290H ALA* 3.9 18.1 - - + +
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Residues in contact with TYR 254 (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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99D MSE 4.0 24.5 - - + -
252D THR* 3.1 4.9 - - - +
253D LEU* 1.3 87.2 - - + +
255D ASP* 1.3 65.9 + - - +
257D TYR* 3.3 7.0 + - - +
258D GLU* 2.9 31.0 + - + +
226E VAL* 4.9 7.2 - - + +
228E TRP* 3.4 65.6 - + + +
229E SER* 4.4 8.7 - - - -
289H GLU* 3.4 44.8 + - + +
290H ALA* 3.4 19.5 - - - -
292H GLY* 5.2 1.1 - - - -
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Residues in contact with ASP 255 (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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100D ARG* 3.0 28.9 + - - -
230D ILE* 5.1 2.6 - - + +
249D ALA 3.6 15.3 - - - +
250D ALA* 3.9 0.9 - - - -
251D PHE* 3.0 17.1 + - - +
252D THR* 3.0 40.1 + - - +
254D TYR* 1.3 75.9 - - - +
256D VAL* 1.3 65.2 + - - +
258D GLU* 3.2 7.4 + - - +
259D ILE* 3.0 29.9 + - - +
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Residues in contact with VAL 256 (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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250D ALA* 4.6 7.9 - - + -
252D THR 3.0 15.0 + - - +
253D LEU* 3.4 9.4 - - - +
254D TYR 3.2 0.2 - - - -
255D ASP* 1.3 78.1 - - - +
257D TYR* 1.3 56.9 + - - +
259D ILE* 3.3 9.7 + - - +
260D CYS* 2.9 30.0 + - - -
268D ILE* 3.8 24.2 - - + -
270D ILE* 3.9 24.0 - - + -
284D ALA* 3.9 33.9 - - + +
287D VAL* 3.9 14.4 - - + -
288D ALA* 4.5 1.3 - - + +
295D ILE* 5.6 0.7 - - + -
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Residues in contact with TYR 257 (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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253D LEU 3.1 7.1 + - - +
254D TYR 3.6 7.0 - - - +
256D VAL* 1.3 76.8 - - - +
258D GLU* 1.3 69.0 + - - +
260D CYS* 3.3 2.1 + - - +
261D ARG* 2.7 54.8 + - + +
287D VAL* 3.9 20.8 - - + +
229E SER* 6.0 0.4 - - - -
231E PRO* 5.3 3.8 - - + -
257H TYR* 3.8 27.1 - + - -
260H CYS* 3.3 13.0 + - + +
261H ARG* 3.2 31.3 + - - -
263H ARG* 4.5 4.7 + - - -
287H VAL* 4.8 5.4 - - + -
290H ALA* 3.6 38.4 - - + +
291H ALA* 3.6 22.9 - - + +
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Residues in contact with GLU 258 (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 ILE* 4.6 10.8 - - + -
254D TYR* 2.9 22.7 + - + +
255D ASP* 3.2 7.8 + - - +
257D TYR* 1.3 82.9 - - - +
259D ILE* 1.3 64.6 + - - +
261D ARG* 2.7 44.4 + - - -
262D GLN* 2.9 51.8 + - - +
231E PRO* 3.5 19.0 - - - +
258E GLU* 4.7 1.6 - - - +
262E GLN* 4.4 6.7 + - - -
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Residues in contact with ILE 259 (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 ILE* 3.6 20.6 - - + -
233D MSE 4.1 4.5 - - + -
246D ALA* 4.0 10.3 - - + -
249D ALA 4.0 8.3 - - - +
250D ALA* 3.4 39.3 - - + +
255D ASP 3.0 14.9 + - - +
256D VAL* 3.6 7.4 - - - +
258D GLU* 1.3 76.2 - - - +
260D CYS* 1.3 62.4 + - - +
263D ARG* 3.1 3.3 + - - -
264D ALA* 2.9 36.1 + - + -
265D ALA* 3.9 32.9 + - + +
268D ILE* 4.3 15.7 - - + -
293D LEU* 5.3 2.0 - - + +
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Residues in contact with CYS 260 (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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256D VAL* 2.9 26.0 + - - +
257D TYR* 3.5 6.5 - - - +
258D GLU 3.2 0.2 - - - -
259D ILE* 1.3 77.9 - - - +
261D ARG* 1.3 62.3 + - - +
263D ARG* 3.0 27.0 + - - -
268D ILE* 3.9 20.4 - - - -
287D VAL* 4.1 5.2 - - + -
288D ALA* 3.9 15.9 - - - -
291D ALA* 3.7 22.4 - - + -
293D LEU* 4.0 12.8 - - - -
257H TYR* 3.4 22.1 + - + +
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Residues in contact with ARG 261 (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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257D TYR* 2.7 48.6 + - + +
258D GLU* 2.7 42.6 + - - +
260D CYS* 1.3 74.4 - - - +
262D GLN* 1.3 71.9 + - - +
263D ARG* 3.7 3.8 + - - +
231E PRO* 3.7 20.9 - - - +
261E ARG* 4.9 2.4 - - - +
262E GLN* 3.8 17.1 + - - +
257H TYR* 3.5 10.3 + - - +
261H ARG* 4.5 26.8 + - + +
263H ARG* 6.3 1.8 - - - +
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Residues in contact with GLN 262 (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 ILE* 3.4 28.1 - - - +
231D PRO* 3.9 21.4 - - - +
234D ALA* 4.3 10.5 - - + +
238D GLU* 4.9 4.3 - - - +
258D GLU* 2.9 43.9 + - - +
259D ILE 4.4 0.2 - - - +
261D ARG* 1.3 92.3 + - + +
263D ARG* 1.3 72.7 + - - +
264D ALA* 3.0 8.9 + - + +
258E GLU* 4.4 2.4 - - - +
261E ARG* 3.9 14.9 + - - +
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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