Contacts of the helix formed by residues 229 - 240 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A TYR* 4.4 10.5 - - - -
257A TYR* 6.0 0.7 - - - -
263B ARG* 4.1 1.7 + - - -
290B ALA 4.6 2.1 + - - -
291B ALA* 3.9 9.3 + - - -
292B GLY* 4.3 15.3 - - - -
223G GLN* 5.8 0.3 + - - -
226G VAL* 3.4 16.5 + - - +
227G SER 3.2 5.1 - - - +
228G TRP* 1.3 76.9 - - - +
230G ILE* 1.3 62.4 + - - +
231G PRO* 3.6 8.3 - - - +
232G ALA* 3.1 30.1 + - - +
233G MSE 3.4 16.5 + - - +
249G ALA* 5.8 0.6 - - - +
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Residues in contact with ILE 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A GLU* 6.1 1.1 - - - -
2100A GOL 5.6 4.3 - - - +
227G SER 4.6 2.9 - - - +
228G TRP 3.8 4.4 + - - +
229G SER* 1.3 71.0 - - - +
231G PRO* 1.3 74.5 - - + +
233G MSE 3.1 9.4 + - + +
234G ALA* 3.1 19.1 + - - +
249G ALA* 3.8 30.7 - - + +
255G ASP* 4.9 4.7 - - + +
258G GLU* 4.8 9.9 - - + -
259G ILE* 3.7 30.7 - - + -
262G GLN* 3.4 25.1 - - - +
264G ALA* 3.5 21.9 - - + +
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Residues in contact with PRO 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A TYR* 5.3 3.1 - - + -
258A GLU* 3.4 29.2 - - - +
261A ARG* 3.7 26.7 - - - +
263B ARG* 3.6 25.9 + - + +
229G SER* 3.5 8.1 - - - +
230G ILE* 1.3 95.9 - - + +
232G ALA* 1.3 56.1 + - - +
234G ALA* 3.3 7.4 + - + +
235G HIS* 2.8 28.2 + - - +
262G GLN* 3.7 6.7 - - - +
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Residues in contact with ALA 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B ARG* 3.8 13.6 - - - +
291B ALA 4.0 11.7 - - - +
292B GLY* 4.2 8.7 - - - +
203G VAL* 4.3 11.7 - - + +
225G THR* 4.1 11.0 - - - +
226G VAL* 5.4 1.6 - - + +
229G SER* 3.1 28.7 + - - +
231G PRO* 1.3 77.0 - - - +
233G MSE 1.3 62.4 + - - +
235G HIS* 3.2 4.1 - - - +
236G VAL* 3.0 27.5 + - - +
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Residues in contact with MSE 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223G GLN* 3.8 21.1 - - - +
224G PRO* 5.2 2.2 - - + -
225G THR* 3.6 17.0 + - - +
229G SER 3.4 7.6 + - - +
230G ILE* 3.1 11.9 + - + +
232G ALA* 1.3 76.9 - - - +
234G ALA* 1.3 59.2 + - - +
236G VAL* 3.1 6.1 + - - +
237G ARG* 2.8 27.4 + - - +
244G ILE* 4.1 17.5 - - + +
245G VAL 4.6 0.7 - - - +
246G ALA* 3.6 40.2 - - + -
249G ALA* 3.6 16.4 - - + -
259G ILE* 4.1 11.7 - - + -
264G ALA* 3.3 33.0 - - + +
265G ALA* 4.5 1.6 - - - -
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Residues in contact with ALA 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G ILE 3.1 7.5 + - - +
231G PRO* 3.6 10.8 - - + +
233G MSE 1.3 77.0 - - - +
235G HIS* 1.3 62.7 + - - +
237G ARG* 3.7 3.1 - - - +
238G GLU* 3.0 43.3 + - - +
262G GLN* 4.4 11.7 - - + +
263G ARG 4.6 1.8 - - - +
264G ALA* 3.7 33.1 + - + +
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Residues in contact with HIS 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ARG* 2.9 32.6 + - - +
263B ARG* 3.0 39.6 + - + -
265B ALA 3.4 21.1 - - - -
266B ASP* 2.6 28.7 + - - -
293B LEU* 4.6 1.3 - - + -
203G VAL* 3.8 18.0 - - + +
207G ILE* 5.5 0.7 - - + -
231G PRO 2.8 15.0 + - - +
232G ALA* 3.2 12.8 - - - +
234G ALA* 1.3 77.0 - - - +
236G VAL* 1.3 63.9 + - - +
238G GLU* 3.6 6.3 + - - +
239G LYS* 3.5 16.8 + - + +
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Residues in contact with VAL 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203G VAL* 4.1 21.3 - - + +
206G ALA* 3.9 25.6 - - + -
207G ILE* 4.0 14.6 - - + -
210G CYS* 5.1 1.1 - - - -
224G PRO* 4.3 16.2 - - + -
225G THR* 3.5 24.2 - - + -
232G ALA 3.0 14.4 + - - +
233G MSE 3.1 5.4 + - - +
235G HIS* 1.3 74.9 - - - +
237G ARG* 1.3 65.5 + - - +
239G LYS* 3.0 11.8 + - - +
240G VAL* 3.0 28.2 + - + +
244G ILE* 4.7 3.4 - - + -
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Residues in contact with ARG 237 (chain G).
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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235D HIS* 3.2 28.1 + - - +
238D GLU* 5.7 3.2 + - - +
239D LYS* 2.9 55.6 + - - +
233G MSE 2.8 16.3 + - - +
234G ALA 3.3 3.7 + - - +
236G VAL* 1.3 78.6 - - - +
238G GLU* 1.3 82.1 + - - +
239G LYS 3.2 0.3 + - - -
240G VAL* 3.5 5.7 - - - +
242G ILE 5.3 1.0 - - - +
244G ILE* 3.9 23.8 - - + +
262G GLN 5.3 0.2 + - - -
263G ARG* 2.9 32.9 + - - +
264G ALA 4.2 3.6 - - - +
265G ALA* 3.7 22.0 - - - +
266G ASP* 3.5 27.9 + - - +
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Residues in contact with GLU 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D GLU* 5.0 8.7 - - - +
239D LYS* 3.1 21.7 + - + +
234G ALA* 3.0 33.0 + - - +
235G HIS* 4.1 5.5 - - - +
236G VAL 3.3 0.2 - - - -
237G ARG* 1.3 98.5 + - - +
239G LYS* 1.3 59.1 + - - +
262G GLN 5.1 3.8 - - - +
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Residues in contact with LYS 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ARG* 3.0 55.2 - - - +
238B GLU* 4.9 8.1 - - - +
240B VAL 3.2 20.6 - - - +
241B GLY* 5.0 2.9 - - - +
242B ILE 4.7 6.3 - - - -
243B PRO* 4.8 2.0 - - - +
266B ASP* 3.4 24.7 + - - -
239D LYS* 3.9 1.6 + - - -
207G ILE* 3.5 38.5 - - + +
235G HIS* 3.5 9.0 + - - +
236G VAL 3.0 3.7 + - - +
238G GLU* 1.3 81.2 - - - +
240G VAL* 1.3 64.2 + - - +
241G GLY 4.1 0.2 + - - -
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Residues in contact with VAL 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D LYS* 2.7 30.2 + - - -
207G ILE* 3.6 38.6 - - + +
210G CYS* 3.5 32.8 - - + -
236G VAL* 3.0 16.3 + - + +
237G ARG 3.5 3.2 - - - +
239G LYS* 1.3 76.7 - - - +
241G GLY* 1.3 60.5 + - - +
242G ILE 3.6 19.8 - - - +
244G ILE* 3.9 19.7 - - + -
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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