Contacts of the helix formed by residues 211 - 225 (chain B) in PDB entry 3GA5
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 ASN 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B ASP* 5.3 0.6 + - - -
183B TRP* 3.2 41.8 + - + +
209B ALA* 3.1 8.9 - - - +
210B ASN* 1.3 80.7 - - - +
212B ASP* 1.3 58.5 + - - +
213B ALA* 3.6 10.9 - - - +
214B MET* 2.9 27.9 + - - +
215B ALA* 3.1 19.1 + - - +
235B VAL 3.2 20.9 - - - +
236B ASP* 3.7 1.3 + - - +
401B RGG 2.9 31.1 + - - +
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Residues in contact with ASP 212 (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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211B ASN* 1.3 71.4 - - - +
213B ALA* 1.3 56.5 + - - +
215B ALA* 3.0 5.8 + - - +
216B MET* 2.6 41.7 + - - +
234B GLY* 3.5 3.8 - - - -
235B VAL 2.9 23.3 + - - +
236B ASP* 3.5 0.8 + - + +
237B ALA* 2.7 26.2 + - - -
238B LEU* 2.9 29.8 + - + -
241B ALA* 3.1 22.2 - - + +
250B MET* 3.8 2.4 - - - +
253B THR* 2.7 24.2 + - - -
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Residues in contact with ALA 213 (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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15B ASN* 3.6 26.0 - - + +
183B TRP 3.2 22.7 - - - +
185B THR* 2.7 34.2 + - - +
211B ASN* 3.4 8.9 + - - +
212B ASP* 1.3 78.6 - - - +
214B MET* 1.3 62.4 + - - +
216B MET* 3.3 9.6 + - - +
217B GLY 3.2 13.9 + - - -
236B ASP* 5.2 0.2 + - - -
238B LEU* 4.3 3.0 - - + +
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Residues in contact with MET 214 (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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146B LEU* 3.2 31.3 - - + +
147B LYS 3.4 28.9 - - - +
148B GLY* 3.5 8.1 - - - +
181B ALA* 3.5 15.0 - - - -
183B TRP* 3.4 32.3 - - + -
184B ASP 3.6 9.0 - - - +
188B ALA* 3.3 20.9 - - + +
209B ALA* 4.2 8.5 - - + -
210B ASN* 3.6 13.9 - - + +
211B ASN* 2.9 27.1 + - - +
213B ALA* 1.3 72.3 - - - +
215B ALA* 1.3 67.6 + - - +
217B GLY 3.1 1.9 + - - -
218B ALA* 3.0 21.3 + - - +
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Residues in contact with ALA 215 (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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209B ALA* 3.6 12.4 - - + +
211B ASN 3.1 15.0 + - - +
212B ASP* 3.0 8.6 + - - +
214B MET* 1.3 77.2 - - - +
216B MET* 1.3 57.6 + - - +
218B ALA* 3.1 5.7 + - - +
219B VAL* 2.9 32.7 + - - +
232B VAL* 3.7 16.3 - - + +
234B GLY* 4.2 2.7 - - - -
250B MET* 3.6 30.7 - - + -
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Residues in contact with MET 216 (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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15B ASN* 4.3 16.6 - - - +
185B THR* 4.2 13.9 - - + +
212B ASP* 2.6 32.9 + - - +
213B ALA* 3.5 9.4 - - - +
214B MET 3.2 0.2 - - - -
215B ALA* 1.3 72.0 - - - +
217B GLY* 1.3 61.5 + - - +
219B VAL* 3.3 9.0 + - - +
220B GLU* 3.1 25.2 + - - +
238B LEU* 4.1 12.6 - - - -
240B GLU* 3.7 35.4 - - + +
241B ALA* 4.7 6.3 - - - -
244B LEU* 3.8 24.6 - - + +
250B MET* 5.0 1.8 - - - -
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Residues in contact with GLY 217 (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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185B THR* 3.6 31.3 - - - +
189B LYS* 3.3 22.3 - - - -
213B ALA 3.2 4.8 + - - -
214B MET 3.1 6.9 + - - -
216B MET* 1.3 75.8 - - - +
218B ALA* 1.3 64.6 + - - +
220B GLU* 3.2 6.9 + - - +
221B ALA 3.1 16.8 + - - -
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Residues in contact with ALA 218 (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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146B LEU* 3.9 19.1 - - + -
188B ALA 4.5 0.2 - - - -
189B LYS 4.4 1.0 - - - +
192B MET* 3.8 21.5 - - + +
207B VAL* 4.0 16.2 - - + -
214B MET 3.0 12.7 + - - +
215B ALA* 3.1 11.2 + - - +
217B GLY* 1.3 77.2 - - - +
219B VAL* 1.3 57.0 + - - +
221B ALA* 3.2 2.9 + - - +
222B LEU* 2.9 35.6 + - - +
232B VAL* 4.4 5.6 - - + -
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Residues in contact with VAL 219 (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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215B ALA 2.9 18.2 + - - +
216B MET* 3.5 9.9 - - - +
218B ALA* 1.3 76.4 - - - +
220B GLU* 1.3 63.2 + - + +
222B LEU* 3.4 8.4 + - + +
223B LYS* 3.0 49.5 + - - +
232B VAL* 4.2 8.1 - - + -
244B LEU* 4.2 17.0 - - + -
249B ALA* 3.6 34.5 - - + +
250B MET* 3.9 16.4 - - + -
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Residues in contact with GLU 220 (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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185B THR* 3.8 23.4 - - - +
186B ALA* 6.1 0.2 - - - -
189B LYS* 3.6 37.9 + - + +
216B MET 3.1 14.6 + - - +
217B GLY* 3.2 9.1 + - - +
219B VAL* 1.3 78.4 - - + +
221B ALA* 1.3 61.9 + - - +
223B LYS* 3.4 6.4 + - - +
224B ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 221 (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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189B LYS* 3.6 17.9 - - + +
192B MET* 3.7 11.7 - - + -
193B ASP* 3.5 35.7 - - + +
196B LEU* 3.8 2.7 - - + -
217B GLY 3.1 7.2 + - - +
218B ALA 3.6 6.3 - - - +
220B GLU* 1.3 72.9 - - - +
222B LEU* 1.3 66.8 + - - +
224B ALA* 3.2 7.4 + - - +
225B HIS* 3.0 29.1 + - - -
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Residues in contact with LEU 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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192B MET* 4.4 7.0 - - + -
196B LEU* 3.7 27.8 - - + +
207B VAL* 4.6 8.5 - - + -
218B ALA* 2.9 21.9 + - + +
219B VAL* 3.7 6.5 - - + +
221B ALA* 1.3 76.1 - - - +
223B LYS* 1.3 62.2 + - - +
225B HIS 3.1 2.3 + - - -
226B ASN 2.9 4.2 + - - -
227B LYS* 2.9 57.1 + - + +
228B SER* 4.1 6.5 - - - +
230B ILE* 4.0 21.3 - - + +
232B VAL* 3.3 33.2 - - + -
249B ALA 5.7 0.4 - - - +
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Residues in contact with LYS 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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219B VAL* 3.0 36.6 + - + +
220B GLU* 3.8 6.7 - - - +
222B LEU* 1.3 74.7 - - - +
224B ALA* 1.3 63.7 + - - +
226B ASN* 3.1 13.4 + - - +
228B SER* 3.8 24.1 + - - +
244B LEU* 5.4 4.0 - - - -
249B ALA* 3.9 22.8 - - - +
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Residues in contact with ALA 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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189B LYS* 5.5 6.5 - - - +
193B ASP* 5.8 3.6 - - - +
220B GLU 3.1 14.0 + - - +
221B ALA* 3.2 13.0 + - - +
223B LYS* 1.3 77.6 - - - +
225B HIS* 1.3 64.9 + - + +
226B ASN* 3.6 1.4 + - - +
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Residues in contact with HIS 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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193B ASP* 2.7 29.8 + - - -
196B LEU* 3.6 40.2 + - + -
197B SER* 3.0 24.6 + - - -
221B ALA 3.0 26.4 + - - +
222B LEU 3.1 3.5 + - - +
224B ALA* 1.3 82.1 - - + +
226B ASN* 1.3 70.4 + - - +
227B LYS* 3.2 14.6 + - + +
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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