Contacts of the helix formed by residues 229 - 240 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223C GLN* 5.7 0.2 + - - -
226C VAL* 3.4 17.3 + - - +
227C SER 3.2 3.6 - - - +
228C TRP* 1.3 76.4 - - - +
230C ILE* 1.3 63.5 + - - +
231C PRO* 3.8 9.3 - - - +
232C ALA* 3.1 31.9 + - - +
233C MSE 3.4 16.6 + - - +
249C ALA* 5.6 0.5 - - - +
290D ALA 4.5 1.8 + - - -
291D ALA* 3.8 10.6 + - - -
292D GLY* 4.2 15.0 - - - -
254H TYR* 4.5 11.0 - - - -
257H TYR* 5.9 0.7 - - - -
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Residues in contact with ILE 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C SER 5.0 0.9 - - - +
228C TRP 3.7 1.6 + - - -
229C SER* 1.3 70.9 - - - +
231C PRO* 1.3 75.7 - - + +
233C MSE 3.0 18.7 + - + +
234C ALA* 3.0 10.7 + - - +
249C ALA* 4.6 18.2 - - + +
255C ASP* 4.1 6.1 - - - +
258C GLU* 3.7 27.1 - - + -
259C ILE* 3.9 23.6 - - + -
262C GLN* 3.6 21.5 - - - +
264C ALA* 3.5 23.6 - - + -
2300C GOL 3.4 24.9 + - - +
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Residues in contact with PRO 231 (chain C).
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* 3.6 7.4 - - - +
230C ILE* 1.3 94.8 - - + +
232C ALA* 1.3 55.2 + - - +
234C ALA* 3.2 7.5 + - + +
235C HIS* 2.8 29.3 + - - +
262C GLN* 3.7 8.3 - - - +
263D ARG* 3.8 26.6 + - + +
257H TYR* 5.3 2.7 - - + -
258H GLU* 3.5 29.4 - - - +
261H ARG* 3.6 26.2 - - - +
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Residues in contact with ALA 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C VAL* 4.3 7.1 - - + +
225C THR* 4.2 10.5 - - - +
226C VAL* 5.3 1.6 - - + +
229C SER* 3.1 30.8 + - - +
230C ILE 3.1 0.4 - - - -
231C PRO* 1.3 77.0 - - - +
233C MSE 1.3 62.2 + - - +
235C HIS* 3.3 3.5 - - - +
236C VAL* 3.1 27.0 + - - +
263D ARG* 3.6 20.6 - - - +
291D ALA 4.0 4.9 - - - +
292D GLY* 4.2 12.8 - - - +
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Residues in contact with MSE 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C GLN* 3.9 22.2 - - - +
224C PRO* 5.1 2.2 - - + -
225C THR* 3.6 17.6 + - - +
229C SER 3.4 7.5 + - - +
230C ILE* 3.0 11.9 + - + +
232C ALA* 1.3 75.4 - - - +
234C ALA* 1.3 61.3 + - - +
236C VAL* 3.3 5.4 + - - +
237C ARG* 2.9 26.9 + - - +
244C ILE* 4.0 17.6 - - + +
245C VAL 4.7 0.2 - - - +
246C ALA* 3.8 33.7 - - + -
249C ALA* 3.7 22.4 - - + -
259C ILE* 4.1 11.2 - - + -
264C ALA* 3.4 32.5 - - + +
265C ALA* 4.5 0.9 - - - -
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Residues in contact with ALA 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ILE 3.0 9.5 + - - +
231C PRO* 3.5 11.4 - - + +
233C MSE 1.3 73.9 - - - +
235C HIS* 1.3 66.0 + - - +
237C ARG* 3.3 2.1 + - - +
238C GLU* 3.0 41.4 + - - +
262C GLN* 4.4 11.7 - - + +
263C ARG 4.7 1.3 - - - +
264C ALA* 3.7 29.3 + - + +
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Residues in contact with HIS 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C VAL* 3.6 19.7 - - + +
207C ILE* 4.9 2.7 - - + -
231C PRO 2.8 13.7 + - - +
232C ALA* 3.3 11.4 - - - +
234C ALA* 1.3 76.8 - - - +
236C VAL* 1.3 63.1 + - - +
238C GLU* 3.7 6.1 + - - +
239C LYS* 3.5 16.5 + - - +
237D ARG* 3.3 30.2 + - - +
263D ARG* 3.0 44.6 + - + +
265D ALA 3.3 25.8 - - - -
266D ASP* 2.7 24.6 + - - -
293D LEU* 4.5 2.0 - - + -
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Residues in contact with VAL 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C VAL* 4.0 28.9 - - + +
206C ALA* 4.0 17.5 - - + -
207C ILE* 4.9 3.4 - - + -
210C CYS* 5.3 1.1 - - - -
224C PRO* 4.2 16.6 - - + -
225C THR* 3.6 23.8 - - + -
232C ALA 3.1 12.8 + - - +
233C MSE 3.7 7.2 - - - +
235C HIS* 1.3 76.5 - - - +
237C ARG* 1.3 66.7 + - - +
239C LYS* 3.0 5.5 + - - +
240C VAL* 3.0 41.7 + - + +
244C ILE* 4.6 3.1 - - + -
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Residues in contact with ARG 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B HIS* 3.2 28.3 + - - +
239B LYS* 3.1 48.7 + - + +
233C MSE 2.9 18.4 + - - +
234C ALA 3.7 2.6 + - - +
236C VAL* 1.3 76.2 - - - +
238C GLU* 1.3 84.4 + - - +
239C LYS 3.2 0.9 + - - -
240C VAL* 3.4 7.8 - - - +
242C ILE 5.3 0.8 - - - +
243C PRO* 5.8 0.2 - - + -
244C ILE* 3.9 22.2 - - + +
263C ARG* 2.7 36.7 + - - +
264C ALA* 3.7 15.9 - - - +
265C ALA* 3.7 11.0 - - - +
266C ASP* 3.6 28.7 + - - +
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Residues in contact with GLU 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B GLU* 5.0 8.1 - - - +
239B LYS* 3.2 20.4 + - + +
234C ALA* 3.0 31.2 + - - +
235C HIS* 4.1 5.1 - - - +
236C VAL 3.3 0.2 - - - -
237C ARG* 1.3 98.0 + - - +
239C LYS* 1.3 60.8 + - - +
262C GLN 5.0 4.7 - - - +
238D GLU* 6.1 0.7 - - - -
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Residues in contact with LYS 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B LYS* 4.1 1.8 + - - -
207C ILE* 3.7 39.8 - - + +
235C HIS 3.5 11.3 + - - +
236C VAL 3.0 8.1 + - - +
238C GLU* 1.3 83.3 + - - +
240C VAL* 1.3 62.5 + - - +
237D ARG* 3.1 42.1 + - - +
238D GLU* 3.5 19.1 + - - +
239D LYS 4.4 2.0 + - - -
240D VAL 2.8 27.4 + - - +
241D GLY* 4.7 6.2 - - - +
242D ILE 5.6 2.2 - - - +
243D PRO* 5.9 0.4 - - + -
266D ASP* 4.9 4.5 - - - +
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B LYS* 2.7 30.9 + - - -
207C ILE* 3.7 29.6 - - + +
210C CYS* 3.6 36.1 - - + -
236C VAL* 3.0 24.9 + - + +
237C ARG 3.4 2.8 - - - +
239C LYS* 1.3 79.0 - - - +
241C GLY* 1.3 58.3 + - - +
242C ILE 3.4 20.4 - - - +
244C ILE* 4.0 16.4 - - + -
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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