Contacts of the helix formed by residues 252 - 262 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2300C GOL 4.4 3.3 + - - +
99H MSE 3.6 41.7 - - + -
100H ARG* 3.9 19.5 - - + +
103H ASN* 3.9 7.4 - - - +
251H PHE* 1.3 74.5 - - - +
253H LEU* 1.3 64.3 - - - +
254H TYR* 3.3 9.5 + - - +
255H ASP* 2.8 37.8 + - - +
256H VAL* 3.1 26.2 + - - +
275H ILE* 3.4 7.4 - - - -
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Residues in contact with LEU 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D ALA 4.1 5.2 - - - +
289D GLU* 4.0 26.0 - - + +
290D ALA* 3.7 26.9 - - + +
99H MSE 5.2 1.0 - - - -
252H THR* 1.3 74.4 - - - +
254H TYR* 1.3 67.9 + - + +
256H VAL* 3.4 7.0 + - + +
257H TYR* 3.1 25.6 + - - +
275H ILE* 3.2 16.1 - - + +
280H PRO 5.3 0.2 - - - +
283H LYS* 3.9 35.0 - - + +
284H ALA* 4.1 6.1 - - + +
287H VAL* 3.7 26.9 - - + -
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Residues in contact with TYR 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C VAL* 4.9 7.9 - - + +
228C TRP* 3.5 51.5 - + + +
229C SER* 4.4 11.2 - - - -
2300C GOL 3.5 22.2 - - - +
289D GLU* 3.4 44.1 + - - +
290D ALA* 3.3 22.4 - - - -
292D GLY 4.8 0.2 - - - -
99H MSE 4.0 24.9 - - + +
252H THR* 3.1 2.9 - - - +
253H LEU* 1.3 87.6 - - + +
255H ASP* 1.3 63.6 + - - +
257H TYR* 3.3 7.7 + - - +
258H GLU* 3.0 27.8 + - + +
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Residues in contact with ASP 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2300C GOL 2.5 36.8 + - - -
100H ARG* 3.1 35.4 + - - -
230H ILE* 4.7 4.0 - - + +
249H ALA 3.6 16.4 - - - +
250H ALA* 3.9 1.3 - - - -
251H PHE 3.1 9.1 + - - +
252H THR* 2.8 36.5 + - - +
254H TYR* 1.3 75.9 - - - +
256H VAL* 1.3 63.9 + - - +
258H GLU* 3.2 4.1 + - - +
259H ILE* 2.9 29.3 + - - +
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Residues in contact with VAL 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250H ALA* 4.4 8.5 - - + -
252H THR 3.1 14.1 + - - +
253H LEU* 3.5 9.2 - - - +
255H ASP* 1.3 77.3 - - - +
257H TYR* 1.3 62.4 + - - +
259H ILE* 3.3 10.4 + - - +
260H CYS* 3.0 25.7 + - - -
268H ILE* 4.0 22.2 - - + -
270H ILE* 3.8 24.5 - - + -
284H ALA* 3.9 34.1 - - + +
287H VAL* 4.1 13.0 - - + -
288H ALA* 4.6 1.6 - - + +
295H ILE* 5.6 1.1 - - + -
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Residues in contact with TYR 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C SER* 5.9 0.9 - - - -
231C PRO* 5.3 2.5 - - + -
257D TYR* 3.8 26.0 - + - -
260D CYS* 3.4 33.7 + - + +
261D ARG* 3.5 7.3 + - - -
263D ARG* 4.4 8.5 + - - -
287D VAL* 4.8 4.9 - - + -
290D ALA* 3.6 31.9 - - + +
291D ALA* 3.7 23.6 - - + +
253H LEU 3.1 14.3 + - - +
254H TYR 3.6 8.3 - - - +
255H ASP 3.2 0.2 - - - -
256H VAL* 1.3 77.8 - - - +
258H GLU* 1.3 69.4 + - - +
260H CYS* 3.2 2.6 + - - +
261H ARG* 2.9 50.6 + - + +
287H VAL* 3.9 21.5 - - + -
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Residues in contact with GLU 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C PRO* 3.5 20.1 - - - +
258C GLU* 4.9 0.7 - - - +
262C GLN* 4.4 6.0 + - - -
2300C GOL 4.1 15.0 - - - +
230H ILE* 3.6 17.0 - - + -
254H TYR* 3.0 18.1 + - + +
255H ASP 3.5 7.9 - - - +
257H TYR* 1.3 85.8 - - - +
259H ILE* 1.3 63.0 + - - +
261H ARG* 2.7 46.3 + - - +
262H GLN* 3.0 44.1 + - - +
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Residues in contact with ILE 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230H ILE* 3.9 19.7 - - + -
233H MSE 5.9 1.1 - - - -
246H ALA* 4.0 11.9 - - + -
249H ALA* 3.9 11.9 - - + +
250H ALA* 3.4 37.9 - - + -
255H ASP 2.9 18.0 + - - +
256H VAL* 3.6 7.2 - - - +
258H GLU* 1.3 76.1 - - - +
260H CYS* 1.3 58.8 + - - +
263H ARG* 3.0 7.1 + - - -
264H ALA* 2.8 37.1 + - + -
265H ALA* 4.0 30.1 - - + +
268H ILE* 3.9 18.4 - - + -
293H LEU* 5.3 1.6 - - + +
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Residues in contact with CYS 260 (chain H).
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* 3.3 19.3 + - + +
256H VAL* 3.0 21.7 + - - +
257H TYR* 3.5 9.0 - - - +
259H ILE* 1.3 76.5 - - - +
261H ARG* 1.3 58.8 + - - +
263H ARG* 3.0 32.9 + - - -
268H ILE* 3.8 19.1 - - - -
287H VAL* 4.1 9.0 - - + -
288H ALA* 3.9 17.5 - - - -
291H ALA* 3.6 22.2 - - + -
293H LEU* 4.1 11.4 - - - -
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Residues in contact with ARG 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C PRO* 3.6 22.2 - - - +
261C ARG* 5.3 1.8 - - - +
262C GLN* 3.6 20.6 + - - +
257D TYR* 3.2 12.3 + - - +
261D ARG* 4.5 28.1 + - + +
257H TYR* 2.9 40.9 + - + +
258H GLU* 2.7 48.0 + - - +
260H CYS* 1.3 73.1 - - - +
262H GLN* 1.3 72.6 + - - +
263H ARG* 3.3 7.4 + - - +
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Residues in contact with GLN 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C GLU* 4.6 8.1 + - - -
261C ARG* 4.1 12.5 + - - +
230H ILE* 3.6 21.6 - - - +
231H PRO* 3.8 21.7 - - - +
234H ALA* 4.4 10.0 - - + +
238H GLU* 6.0 1.7 - - - -
258H GLU* 3.0 50.5 + - - +
259H ILE 4.2 1.6 - - - +
261H ARG* 1.3 92.7 - - + +
263H ARG* 1.3 72.7 + - - +
264H ALA* 3.0 9.1 + - + +
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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