Contacts of the helix formed by residues 221 - 234 (chain B) in PDB entry 3G33
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 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B MET* 1.3 75.0 - - - +
222B GLY* 1.3 61.8 + - - +
223B ASP* 3.9 5.3 + - - +
224B GLU* 2.9 41.9 + - - +
225B LEU* 3.1 28.7 + - - +
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Residues in contact with GLY 222 (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 GLN* 4.2 26.6 - - - +
221B SER* 1.3 74.0 - - - +
223B ASP* 1.3 62.6 + - - +
225B LEU* 3.2 4.6 + - - +
226B THR* 2.8 38.8 + - - +
241B ARG* 5.8 0.4 - - - -
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Residues in contact with ASP 223 (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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221B SER* 3.9 5.2 + - - +
222B GLY* 1.3 78.3 - - - +
224B GLU* 1.3 62.4 + - + +
226B THR* 3.0 18.7 + - - -
227B GLU* 3.1 22.0 + - + +
241B ARG* 3.2 25.6 + - - +
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Residues in contact with GLU 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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220B MET* 4.1 15.6 + - + +
221B SER* 2.9 35.1 + - - +
222B GLY 3.3 0.2 - - - -
223B ASP* 1.3 77.9 - - + +
225B LEU* 1.3 60.4 + - - +
227B GLU* 4.2 4.8 - - - +
228B LEU* 3.3 29.1 + - + +
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Residues in contact with LEU 225 (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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168B LEU* 5.9 3.1 - - + -
209B GLY* 5.0 4.0 - - - +
212B VAL* 3.7 34.3 - - + -
213B GLN* 4.4 25.8 - - + +
216B GLY 5.3 2.0 - - - +
220B MET* 3.6 28.5 - - + +
221B SER 3.1 20.6 + - - +
222B GLY* 3.5 5.2 - - - +
223B ASP 3.1 0.4 - - - -
224B GLU* 1.3 76.3 - - - +
226B THR* 1.3 66.2 + - + +
227B GLU 3.2 0.2 - - - -
228B LEU* 3.1 5.8 + - + +
229B LEU* 3.0 46.2 + - + +
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Residues in contact with THR 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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213B GLN* 5.2 2.5 - - - +
222B GLY* 2.8 23.0 + - - +
223B ASP* 3.0 16.5 + - - -
225B LEU* 1.3 75.8 - - + +
227B GLU* 1.3 57.3 + - - +
229B LEU* 4.6 3.8 - - + -
230B ALA* 3.0 26.2 + - - +
237B VAL* 4.1 6.7 - - - +
240B LEU* 3.2 21.3 - - + +
241B ARG* 3.6 34.5 + - + +
244B GLN* 3.5 26.9 - - - +
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Residues in contact with GLU 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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223B ASP* 3.1 21.6 + - - +
224B GLU* 4.2 6.3 - - - +
226B THR* 1.3 74.1 - - - +
228B LEU* 1.3 60.8 + - - +
230B ALA* 4.1 4.8 - - - +
231B GLY* 3.1 24.1 + - - -
237B VAL* 3.8 31.8 - - + +
241B ARG* 4.9 4.0 + - - +
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Residues in contact with LEU 228 (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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167B ARG 5.1 9.9 - - - +
168B LEU* 5.7 8.3 - - + -
169B SER* 5.2 9.0 - - - +
220B MET* 3.8 28.0 - - + -
224B GLU* 3.3 18.6 + - + +
225B LEU* 3.1 10.0 + - + +
227B GLU* 1.3 77.9 - - - +
229B LEU* 1.3 63.8 + - + +
231B GLY* 3.4 7.2 + - - -
232B ILE* 3.1 24.5 + - + +
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Residues in contact with LEU 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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164B ILE* 4.9 5.8 - - + +
168B LEU* 4.0 27.8 - - + -
205B THR* 3.4 29.2 + - - +
208B ILE* 4.0 18.8 - - + +
209B GLY* 3.6 26.9 - - - -
212B VAL* 6.2 1.8 - - + -
225B LEU* 3.0 39.5 + - + +
226B THR* 4.7 2.0 - - + -
228B LEU* 1.3 74.7 - - + +
230B ALA* 1.3 63.0 + - - +
232B ILE* 3.1 26.2 + - + +
233B THR* 3.4 6.4 + - - +
240B LEU* 3.7 11.2 - - + -
244B GLN* 5.1 3.1 - - - +
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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
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226B THR 3.0 19.7 + - - +
227B GLU 4.1 3.1 - - - +
229B LEU* 1.3 76.5 - - - +
231B GLY* 1.3 57.1 + - - +
233B THR 3.4 0.3 + - - -
234B GLY* 2.8 29.5 + - - -
235B THR* 3.2 40.1 + - - +
237B VAL* 4.3 21.3 - - + +
240B LEU* 3.6 8.0 - - + +
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Residues in contact with GLY 231 (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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167B ARG* 4.7 3.3 + - - -
227B GLU 3.1 18.1 + - - -
228B LEU 3.4 2.7 + - - -
229B LEU 3.3 0.2 - - - -
230B ALA* 1.3 76.8 - - - +
232B ILE* 1.3 62.3 + - - +
234B GLY* 4.2 4.6 + - - -
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Residues in contact with ILE 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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28B LEU* 4.3 15.1 - - + +
32B LEU* 4.9 3.5 - - - +
164B ILE* 3.9 38.8 - - + +
167B ARG* 3.5 71.4 + - + +
168B LEU* 4.2 7.9 - - + -
228B LEU* 3.1 18.6 - - + +
229B LEU* 3.3 12.3 - - + +
230B ALA 3.0 0.8 - - - -
231B GLY* 1.3 78.7 - - - +
233B THR* 1.3 63.3 + - + +
234B GLY* 3.2 4.6 + - - -
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Residues in contact with THR 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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28B LEU* 5.2 3.4 - - + -
32B LEU* 3.7 30.3 - - + +
160B PHE* 4.9 7.4 - - + -
164B ILE* 4.0 26.9 - - + -
201B SER* 4.4 19.5 - - - +
205B THR* 4.0 21.5 - - - +
229B LEU 3.4 8.3 + - - +
232B ILE* 1.3 75.3 - - + +
234B GLY* 1.3 58.3 + - - +
235B THR* 3.1 35.5 + - - +
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Residues in contact with GLY 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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32B LEU* 5.6 0.2 - - - -
230B ALA 2.8 8.8 + - - -
231B GLY* 4.7 4.7 - - - -
232B ILE 3.2 4.4 + - - -
233B THR* 1.3 79.0 - - - +
235B THR* 1.3 64.4 + - - +
236B GLU* 5.4 1.9 - - - +
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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