Contacts of the helix formed by residues 229 - 240 (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 SER 229 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254C TYR* 4.3 13.7 - - - -
257C TYR* 6.0 0.7 - - - -
290F ALA 4.5 2.2 + - - -
291F ALA* 3.7 9.5 + - - -
292F GLY* 4.3 13.9 - - - -
223H GLN* 5.8 0.3 + - - -
225H THR* 4.7 0.2 + - - -
226H VAL* 3.4 13.1 + - - +
227H SER 3.2 3.7 - - - -
228H TRP* 1.3 77.3 - - - +
230H ILE* 1.3 64.2 + - - +
231H PRO* 3.7 8.6 - - - +
232H ALA* 3.0 32.6 + - - +
233H MSE 3.3 17.5 + - - +
249H ALA* 5.7 0.7 - - - +
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Residues in contact with ILE 230 (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 4.5 11.2 - - - +
227H SER 5.0 2.5 - - - +
228H TRP 3.8 4.4 + - - +
229H SER* 1.3 73.0 - - - +
231H PRO* 1.4 73.4 - - + +
233H MSE 3.1 8.4 + - - +
234H ALA* 3.0 19.4 + - - +
249H ALA* 4.6 21.1 - - + +
255H ASP* 4.1 5.2 - - - +
258H GLU* 3.6 27.1 - - + -
259H ILE* 3.9 24.5 - - + -
262H GLN* 3.6 23.6 - - - +
264H ALA* 3.5 23.5 - - + +
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Residues in contact with PRO 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C TYR* 5.1 5.4 - - + -
258C GLU* 3.3 28.9 - - + +
261C ARG* 3.8 17.7 - - - +
263F ARG* 4.2 24.0 + - - +
229H SER* 3.5 10.8 - - - +
230H ILE* 1.4 95.3 - - + +
232H ALA* 1.3 55.1 + - - +
234H ALA* 3.2 7.9 + - + +
235H HIS* 2.9 28.6 + - - +
262H GLN* 3.8 16.6 - - - +
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Residues in contact with ALA 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F ARG* 3.5 22.1 - - - +
291F ALA 4.0 4.9 - - - +
292F GLY* 4.2 12.6 - - - +
203H VAL* 4.4 6.4 - - + +
225H THR* 4.2 11.9 - - - +
226H VAL* 5.3 1.3 - - + -
229H SER* 3.0 30.0 + - - +
230H ILE 3.2 0.2 - - - -
231H PRO* 1.3 76.4 - - - +
233H MSE 1.3 61.3 + - - +
235H HIS* 3.2 3.6 - - - +
236H VAL* 3.1 26.5 + - - +
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Residues in contact with MSE 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223H GLN* 3.1 58.6 - - - +
224H PRO* 3.7 11.0 - - + -
225H THR* 3.6 16.7 + - - +
229H SER 3.3 8.0 + - - +
230H ILE* 3.1 12.4 + - - +
232H ALA* 1.3 75.5 - - - +
234H ALA* 1.3 60.5 + - - +
236H VAL* 3.2 5.8 + - - +
237H ARG* 2.9 27.4 + - - +
244H ILE* 3.9 11.3 - - + +
245H VAL 3.4 14.1 - - - +
246H ALA* 3.6 23.8 - - - -
249H ALA* 4.2 7.9 - - + -
259H ILE* 5.8 1.6 - - - -
264H ALA* 3.3 21.3 - - + +
265H ALA* 4.5 0.9 - - - -
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Residues in contact with ALA 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230H ILE 3.0 12.4 + - - +
231H PRO* 3.2 12.1 + - + +
233H MSE 1.3 76.0 - - - +
235H HIS* 1.3 63.1 + - - +
237H ARG* 3.6 2.3 - - - +
238H GLU* 3.0 40.8 + - - +
262H GLN* 4.4 11.9 - - + +
263H ARG 4.7 2.2 - - - +
264H ALA* 3.9 28.0 + - + +
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Residues in contact with HIS 235 (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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237F ARG* 3.2 32.8 + - - +
263F ARG* 3.0 42.2 + - + +
265F ALA 3.4 25.8 - - - -
266F ASP* 2.7 24.6 + - - -
293F LEU* 4.6 0.7 - - + -
203H VAL* 3.6 18.0 - - + +
207H ILE* 4.8 2.7 - - + -
231H PRO 2.9 13.1 + - - +
232H ALA 3.2 12.1 - - - +
234H ALA* 1.3 78.4 - - - +
236H VAL* 1.3 64.8 + - - +
238H GLU* 3.7 8.1 + - - +
239H LYS* 3.5 15.2 + - - +
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Residues in contact with VAL 236 (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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203H VAL* 4.1 21.8 - - + +
206H ALA* 3.8 24.5 - - + +
207H ILE* 4.5 4.5 - - + -
210H CYS* 5.1 0.7 - - - -
224H PRO* 4.4 14.4 - - + -
225H THR* 3.6 23.8 - - + -
232H ALA 3.1 14.5 + - - +
233H MSE 3.7 6.3 - - - +
235H HIS* 1.3 76.7 - - - +
237H ARG* 1.3 65.2 + - - +
239H LYS* 3.0 6.1 + - - -
240H VAL* 3.0 44.6 + - + +
244H ILE* 4.8 2.9 - - + -
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Residues in contact with ARG 237 (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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235E HIS* 3.2 30.3 + - - +
238E GLU* 6.0 0.8 + - - +
239E LYS* 2.9 54.0 + - + +
233H MSE 2.9 16.7 + - - +
234H ALA 3.6 3.7 + - - +
236H VAL* 1.3 77.5 - - - +
238H GLU* 1.3 85.0 + - - +
239H LYS 3.2 0.9 + - - -
240H VAL* 3.4 7.5 - - - +
242H ILE 5.3 0.6 - - - +
244H ILE* 3.9 21.7 - - + +
263H ARG* 2.8 32.3 + - - +
264H ALA 4.0 5.1 - - - +
265H ALA* 3.7 25.1 - - - +
266H ASP* 3.6 27.3 + - - +
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Residues in contact with GLU 238 (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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238E GLU* 4.6 11.4 - - - +
239E LYS* 3.1 20.6 + - + +
234H ALA* 3.0 31.2 + - - +
235H HIS* 4.1 6.6 + - - +
237H ARG* 1.3 98.9 + - - +
239H LYS* 1.3 59.6 + - - +
262H GLN 6.0 1.3 - - - -
263H ARG 5.7 0.4 - - - -
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Residues in contact with LYS 239 (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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239E LYS* 4.0 1.1 + - - -
237F ARG* 3.1 28.7 + - - +
238F GLU* 2.9 31.1 + - - +
239F LYS 3.8 2.4 + - - -
240F VAL 2.7 28.3 + - - +
241F GLY* 4.7 6.7 - - - +
242F ILE 6.4 0.2 - - - -
207H ILE* 3.7 40.8 - - + -
235H HIS 3.5 11.3 + - - +
236H VAL 3.0 7.6 + - - +
238H GLU* 1.3 82.5 + - - +
240H VAL* 1.3 63.3 + - - +
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Residues in contact with VAL 240 (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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239E LYS* 2.6 30.5 + - - -
207H ILE* 3.8 21.5 - - + +
210H CYS* 3.7 33.7 - - + -
236H VAL* 3.0 30.4 + - + +
237H ARG 3.4 3.1 - - - +
239H LYS* 1.3 78.8 - - - +
241H GLY* 1.3 59.3 + - - +
242H ILE 3.3 22.6 - - - +
244H ILE* 3.8 21.1 - - + -
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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