Contacts of the helix formed by residues 229 - 240 (chain A) 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 SER 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A VAL* 3.5 15.4 + - - +
227A SER 3.2 4.1 - - - +
228A TRP* 1.3 77.1 - - - +
230A ILE* 1.3 62.4 + - - +
231A PRO* 3.5 8.7 - - - +
232A ALA* 3.0 33.4 + - - +
233A MSE 3.3 17.0 + - - +
249A ALA* 5.7 0.7 - - - +
263E ARG* 4.2 1.2 + - - -
290E ALA 4.5 2.0 + - - -
291E ALA 3.8 8.5 + - - -
292E GLY* 4.3 14.4 - - - -
254G TYR* 4.4 11.9 - - - -
257G TYR* 6.0 0.7 - - - -
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Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A SER 5.0 0.7 - - - +
228A TRP 3.7 1.8 + - - +
229A SER* 1.3 71.1 - - - +
231A PRO* 1.3 74.7 - - + +
233A MSE 3.1 10.4 + - + +
234A ALA* 3.0 18.9 + - - +
249A ALA* 4.5 17.9 - - + +
255A ASP* 4.0 6.3 - - - +
258A GLU* 3.7 27.4 - - + -
259A ILE* 3.7 24.2 - - + -
262A GLN* 3.5 25.6 - - - +
264A ALA* 3.5 21.6 - - + +
2100A GOL 3.7 22.4 - - - +
258G GLU* 6.2 0.4 - - - -
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Residues in contact with PRO 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A SER* 3.5 9.2 - - - +
230A ILE* 1.3 93.9 - - + +
232A ALA* 1.3 55.1 + - - +
234A ALA* 3.2 6.9 + - + +
235A HIS* 2.9 28.8 + - - +
262A GLN* 3.9 10.1 - - - +
263E ARG* 3.8 26.6 + - + +
257G TYR* 5.3 2.7 - - + -
258G GLU* 3.4 27.6 - - - +
261G ARG* 3.9 27.4 - - - +
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A VAL* 4.5 6.7 - - + +
225A THR* 4.1 11.7 - - - +
226A VAL* 5.3 2.0 - - + +
229A SER* 3.0 29.8 + - - +
231A PRO* 1.3 77.1 - - - +
233A MSE 1.3 62.5 + - - +
235A HIS* 3.2 4.4 - - - +
236A VAL* 3.1 26.2 + - - +
263E ARG* 3.7 14.0 - - - +
291E ALA 3.9 11.0 - - - +
292E GLY* 4.2 12.8 - - - +
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Residues in contact with MSE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLN* 3.8 23.8 - - - +
224A PRO* 5.1 3.1 - - + -
225A THR* 3.5 16.8 + - - +
229A SER 3.3 7.8 + - - +
230A ILE* 3.1 10.6 + - + +
232A ALA* 1.3 77.5 - - - +
234A ALA* 1.3 60.4 + - - +
236A VAL* 3.2 6.1 + - - +
237A ARG* 2.9 26.5 + - - +
244A ILE* 4.2 17.4 - - + +
245A VAL 4.7 0.4 - - - +
246A ALA* 3.7 37.5 - - + -
249A ALA* 3.9 16.2 - - + -
259A ILE* 3.9 10.8 - - + -
264A ALA* 3.4 34.1 - - + +
265A ALA* 4.5 1.3 - - - -
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ILE 3.0 12.5 + - - +
231A PRO* 3.6 11.4 - - + +
233A MSE 1.3 75.3 - - - +
235A HIS* 1.3 58.0 + - - +
237A ARG* 3.2 3.5 + - - +
238A GLU* 2.9 50.0 + - - +
262A GLN* 4.4 11.2 - - + +
263A ARG 4.6 0.9 - - - +
264A ALA* 3.8 27.7 + - + +
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Residues in contact with HIS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A VAL* 3.6 18.6 - - + +
207A ILE* 4.9 2.7 - - + -
231A PRO 2.9 13.7 + - - +
232A ALA* 3.2 13.5 - - - +
234A ALA* 1.3 77.2 - - - +
236A VAL* 1.3 64.1 + - - +
238A GLU* 3.5 8.4 + - - +
239A LYS* 3.5 15.4 + - - +
237E ARG* 3.2 32.3 + - - +
263E ARG* 3.0 39.8 + - - +
265E ALA 3.4 25.4 - - - -
266E ASP* 2.7 24.8 + - - -
293E LEU* 4.6 1.8 - - + -
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A VAL* 4.0 29.4 - - + +
206A ALA* 3.9 18.4 - - + +
207A ILE* 4.8 2.9 - - + -
210A CYS* 5.1 0.4 - - - -
224A PRO* 4.2 16.6 - - + -
225A THR* 3.6 23.3 - - + -
232A ALA 3.1 12.4 + - - +
233A MSE 3.7 6.1 - - - +
235A HIS* 1.3 75.5 - - - +
237A ARG* 1.3 68.1 + - - +
239A LYS* 3.0 14.6 + - - +
240A VAL* 3.0 33.0 + - + +
244A ILE* 4.6 3.4 - - + -
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Residues in contact with ARG 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A MSE 2.9 16.7 + - - +
234A ALA 3.6 3.5 + - - +
236A VAL* 1.3 78.1 - - - +
238A GLU* 1.3 84.2 + - - +
239A LYS 3.2 0.7 + - - -
240A VAL* 3.5 6.5 - - - +
242A ILE 5.3 0.8 - - - +
244A ILE* 3.9 23.1 - - + +
263A ARG* 2.8 35.7 + - - +
264A ALA* 3.8 5.5 - - - +
265A ALA* 3.7 22.4 - - - +
266A ASP* 3.5 29.3 + - - +
235F HIS* 3.2 34.1 + - - +
238F GLU* 5.9 1.2 + - - -
239F LYS* 2.9 37.5 + - - +
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ALA* 2.9 34.2 + - - +
235A HIS* 3.9 6.9 - - - +
236A VAL 3.3 0.2 - - - -
237A ARG* 1.3 99.4 + - - +
239A LYS* 1.3 58.0 + - - +
262A GLN 4.9 5.0 - - - +
237E ARG* 5.7 3.1 + - - -
238E GLU* 6.0 2.9 - - - +
238F GLU* 5.9 3.1 - - - +
239F LYS* 3.1 17.1 + - - +
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Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ILE* 3.8 42.3 - - + +
235A HIS 3.5 9.8 + - - +
236A VAL 3.0 7.5 + - - +
238A GLU* 1.3 82.3 + - - +
240A VAL* 1.3 62.7 + - - +
241A GLY 4.0 0.2 + - - -
237E ARG* 2.8 44.7 + - - +
238E GLU* 3.0 23.2 + - - +
239E LYS 3.9 1.4 + - - -
240E VAL 2.8 24.0 + - - +
241E GLY* 4.8 6.3 - - - +
242E ILE 6.0 0.4 - - - -
266E ASP* 6.2 0.2 - - - -
239F LYS* 3.9 1.7 + - - -
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ILE* 3.8 25.4 - - + +
210A CYS* 3.6 34.5 - - + -
236A VAL* 3.0 26.1 + - + +
237A ARG 3.5 3.3 - - - +
239A LYS* 1.3 78.6 - - - +
241A GLY* 1.3 59.2 + - - +
242A ILE 3.3 21.6 - - - +
244A ILE* 3.8 22.4 - - + -
239F LYS* 2.7 30.3 + - - -
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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