Contacts of the helix formed by residues 223 - 237 (chain B) in PDB entry 1GPU
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 ASP 223 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B VAL* 4.3 11.0 - - + +
218B GLU 5.6 0.5 + - - -
219B ASN* 2.9 30.9 + - + +
220B GLY 4.6 0.8 - - - -
222B GLU* 1.3 71.7 - - - +
224B LEU* 1.3 61.0 + - - +
225B ALA* 3.5 7.1 + - - +
226B GLY* 2.5 37.8 + - - -
227B ILE* 3.0 23.7 + - - +
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PHE* 3.4 43.0 - - + -
8B ASP* 4.2 21.5 - - + -
9B LYS* 4.8 13.9 - - + -
12B VAL* 4.3 11.2 - - + -
39B PRO* 3.9 30.1 - - + +
42B HIS* 4.9 2.2 - - + -
43B VAL* 3.7 22.1 - - + +
222B GLU* 2.8 18.4 + - - +
223B ASP* 1.3 71.3 - - - +
225B ALA* 1.3 63.5 + - - +
227B ILE* 3.3 5.4 + - + +
228B ALA* 3.0 18.7 + - - +
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN* 6.1 2.7 - - - +
4B PHE* 3.9 15.3 - - + +
223B ASP* 3.3 4.4 + - - +
224B LEU* 1.3 78.3 - - - +
226B GLY* 1.3 52.8 + - - +
228B ALA* 3.2 3.3 + - - +
229B LYS* 2.8 36.5 + - - +
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Residues in contact with GLY 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B TYR 5.3 0.3 - - - +
217B VAL* 3.8 8.6 - - - +
223B ASP* 2.5 36.0 + - - -
225B ALA* 1.3 71.1 - - - +
227B ILE* 1.3 63.2 + - - +
229B LYS* 3.3 8.1 + - - +
230B ALA* 2.9 23.9 + - - +
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Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PRO* 4.1 14.1 - - + +
40B ALA* 3.8 35.7 - - + +
43B VAL* 3.8 20.2 - - + -
183B ILE* 4.8 6.7 - - + -
217B VAL* 3.9 23.5 - - + +
220B GLY* 4.2 6.3 - - - +
223B ASP 3.0 18.6 + - - +
224B LEU* 3.6 8.3 - - - +
226B GLY* 1.3 75.2 - - - +
228B ALA* 1.3 65.5 + - - +
230B ALA* 3.2 3.5 + - - +
231B ILE* 3.1 33.6 + - + +
244B ILE* 5.2 1.5 - - + +
246B MET* 3.8 17.7 - - - -
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Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 3.6 25.8 - - + -
43B VAL* 3.7 10.5 - - + +
47B GLN* 6.3 1.6 - - + -
224B LEU 3.0 13.5 + - - +
225B ALA* 3.5 8.3 - - - +
227B ILE* 1.3 78.2 - - - +
229B LYS* 1.3 57.1 + - - +
231B ILE* 3.4 5.6 + - - +
232B ALA* 3.0 28.5 + - - +
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Residues in contact with LYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ALA 2.8 21.0 + - - +
226B GLY* 3.6 7.4 - - - +
227B ILE 3.2 0.2 - - - -
228B ALA* 1.3 71.3 - - - +
230B ALA* 1.3 59.1 + - - +
232B ALA* 3.2 7.2 + - + +
233B GLN* 2.9 44.5 + - + +
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 3.3 22.0 - - + +
216B TYR 4.9 2.9 - - - +
217B VAL* 3.9 8.5 - - + -
226B GLY 2.9 16.9 + - - +
227B ILE 3.2 5.4 + - - +
229B LYS* 1.3 76.2 - - - +
231B ILE* 1.3 58.8 + - - +
233B GLN* 3.3 2.2 + - - -
234B ALA* 2.9 26.3 + - - +
244B ILE* 3.7 33.6 - - + +
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Residues in contact with ILE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.2 7.6 - - + -
44B LEU* 4.0 35.7 - - + -
47B GLN* 3.7 28.0 - - + +
152B TYR* 4.1 19.5 - - + +
181B ILE* 4.6 4.0 - - + -
183B ILE* 4.3 8.5 - - + -
227B ILE* 3.1 28.1 + - + +
228B ALA* 3.7 6.1 - - - +
230B ALA* 1.3 76.8 - - - +
232B ALA* 1.3 63.6 + - - +
234B ALA* 3.1 14.1 + - - +
235B LYS* 3.2 17.8 + - - +
244B ILE* 4.1 17.9 - - + -
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B ALA 3.0 14.2 + - - +
229B LYS* 3.2 13.0 + - + +
231B ILE* 1.3 77.1 - - - +
233B GLN* 1.3 63.9 + - - +
235B LYS* 3.2 24.2 + - - +
236B LEU* 3.5 12.6 + - - +
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Residues in contact with GLN 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B GLU* 4.1 10.0 + - - +
215B LEU* 3.7 25.8 - - + -
229B LYS* 2.9 31.4 + - + +
230B ALA* 3.5 5.8 - - - +
232B ALA* 1.3 73.8 - - - +
234B ALA* 1.3 66.9 + - - +
236B LEU* 2.9 42.5 + - - +
237B SER* 3.5 6.4 + - - -
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B GLY 4.2 6.2 - - - +
181B ILE* 3.6 27.0 - - + +
213B GLU* 3.8 4.3 - - - -
215B LEU* 3.9 0.4 - - - +
230B ALA 2.9 13.4 + - - +
231B ILE* 3.4 9.9 - - - +
233B GLN* 1.3 75.9 - - - +
235B LYS* 1.3 61.9 + - - +
237B SER* 3.0 22.9 + - - +
242B THR* 3.7 35.3 + - + -
244B ILE* 4.8 0.7 - - + -
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Residues in contact with LYS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN* 2.9 28.5 + - - -
61B ASP* 5.4 1.8 + - - -
150B TYR* 3.6 53.9 + - + +
152B TYR* 3.0 24.5 + - - -
178B GLY 5.1 1.1 - - - +
181B ILE* 4.0 5.4 - - + -
231B ILE* 3.2 17.0 + - - +
232B ALA* 3.5 13.0 - - - +
233B GLN 3.1 0.8 - - - -
234B ALA* 1.3 76.6 - - - +
236B LEU* 1.3 65.3 + - + +
237B SER 3.3 0.8 + - - -
238B LYS* 3.8 16.5 + - - +
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B ALA 3.7 14.4 - - - +
233B GLN* 2.9 36.1 + - - +
235B LYS* 1.3 81.7 - - + +
237B SER* 1.3 57.2 + - - +
238B LYS* 3.0 16.6 + - - +
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Residues in contact with SER 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLY* 3.7 4.4 - - - +
213B GLU* 2.5 39.2 + - - -
233B GLN* 3.5 1.9 + - - +
234B ALA 3.0 14.9 + - - +
235B LYS 4.4 0.4 - - - -
236B LEU* 1.3 74.4 - - - +
238B LYS* 1.3 57.6 + - - +
239B ASP* 3.1 17.8 + - - -
240B LYS* 3.1 27.6 - - - +
242B THR* 3.2 5.4 + - - -
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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