Contacts of the helix formed by residues 226 - 242 (chain B) in PDB entry 2AVD
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 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B TRP* 4.6 1.3 + - - -
218B LYS* 2.8 39.2 + - - -
223B PRO* 3.1 28.2 + - + +
224B LYS 3.2 1.6 + - - +
225B GLY* 1.3 73.6 - - - +
227B VAL* 1.3 62.8 + - - +
228B ALA* 3.4 10.0 + - - +
229B ALA* 3.0 26.5 + - + +
230B GLU* 3.0 27.6 + - - +
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLU* 3.8 27.4 - - + +
225B GLY* 3.1 13.3 + - - +
226B ASP* 1.3 70.5 + - - +
228B ALA* 1.3 52.9 + - - +
230B GLU* 3.3 15.0 + - - +
231B CYS* 2.8 45.2 + - - -
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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
----------------------------------------------------------
188B LYS* 4.0 14.9 - - + +
189B GLU* 4.3 16.4 + - - +
215B TRP* 3.8 29.8 - - + +
226B ASP* 3.3 6.1 + - - +
227B VAL* 1.3 78.0 - - - +
229B ALA* 1.3 57.5 + - - +
231B CYS* 3.1 5.4 + - - +
232B VAL* 2.9 32.9 + - - +
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TRP* 3.7 22.2 - - + +
218B LYS* 4.2 12.1 - - + +
219B VAL* 4.8 2.8 - - - +
222B PRO* 3.7 23.4 - - + +
226B ASP* 3.0 30.5 + - + +
228B ALA* 1.3 74.5 - - - +
230B GLU* 1.3 59.7 + - - +
232B VAL* 3.3 2.2 + - - +
233B ARG* 2.9 30.0 + - - +
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PRO* 3.9 21.9 - - + +
223B PRO 4.1 3.4 - - - +
224B LYS* 4.7 1.7 - - - -
225B GLY* 3.8 18.3 + - - -
226B ASP 3.0 27.8 + - - +
227B VAL* 3.7 16.9 + - - +
229B ALA* 1.3 74.4 - - - +
231B CYS* 1.3 59.7 + - - +
233B ARG* 3.4 15.4 + - - +
234B ASN* 2.8 41.7 + - - +
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Residues in contact with CYS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LYS 3.3 21.5 - - - +
189B GLU* 3.7 27.1 - - - -
191B CYS* 3.8 6.5 - - - -
192B SER* 4.7 2.0 + - - +
227B VAL* 2.8 32.5 + - - +
228B ALA 3.5 5.2 - - - +
230B GLU* 1.3 78.5 - - - +
232B VAL* 1.3 61.9 + - - +
234B ASN* 3.4 9.0 + - - +
235B LEU* 3.0 25.3 + - - +
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LYS* 3.6 38.8 - - + +
191B CYS* 4.6 5.2 - - - -
212B ARG 3.9 2.0 - - - +
213B VAL* 3.2 42.6 - - + +
215B TRP* 4.0 17.0 - - + -
219B VAL* 3.6 11.4 - - + -
228B ALA 2.9 21.2 + - - +
229B ALA 3.8 3.8 - - - +
231B CYS* 1.3 74.4 - - - +
233B ARG* 1.3 64.5 + - - +
235B LEU* 3.3 3.3 + - - +
236B ASN* 3.0 24.5 + - - +
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Residues in contact with ARG 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 4.3 15.7 - - + +
219B VAL* 3.9 19.4 - - - +
220B LEU 5.9 0.2 - - - -
222B PRO* 3.3 32.7 - - + +
229B ALA 2.9 17.0 + - - +
230B GLU* 3.6 17.0 + - - +
232B VAL* 1.3 77.3 - - - +
234B ASN* 1.3 96.4 + - - +
236B ASN* 3.3 4.9 + - - +
237B GLU* 3.1 35.7 + - + +
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Residues in contact with ASN 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B SER* 4.8 6.5 - - - +
230B GLU* 2.8 27.6 + - - +
231B CYS* 3.8 8.7 - - - +
233B ARG* 1.3 115.5 + - - +
235B LEU* 1.3 63.5 + - - +
237B GLU* 3.3 8.0 + - - +
238B ARG* 3.1 21.0 + - - +
241B ARG* 5.3 0.3 + - - -
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Residues in contact with LEU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B VAL* 5.6 0.7 - - + -
188B LYS* 6.1 0.2 - - - +
191B CYS* 3.7 36.6 - - + +
192B SER* 3.9 19.2 + - - +
195B TYR* 3.7 28.9 - - + -
210B VAL* 4.1 23.8 - - + -
213B VAL* 6.1 0.4 - - + -
231B CYS 3.0 17.1 + - - +
232B VAL* 3.8 4.5 - - - +
234B ASN* 1.3 72.9 - - - +
236B ASN* 1.3 63.4 + - - +
238B ARG* 3.1 9.7 + - + -
239B ILE* 2.9 51.6 + - + +
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Residues in contact with ASN 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 2.9 35.8 + - - +
61A ARG* 4.4 14.0 - - + +
213B VAL* 2.7 49.1 + - - +
219B VAL* 4.1 1.6 - - - +
232B VAL* 3.0 19.5 + - - +
233B ARG 3.6 4.9 - - - +
235B LEU* 1.3 77.6 - - - +
237B GLU* 1.3 58.1 + - - +
239B ILE* 3.9 9.9 - - - +
240B ARG* 2.9 29.3 + - - +
249B LEU* 4.9 7.3 - - + +
257B THR* 4.5 4.5 + - - -
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 4.8 2.9 + - - -
61A ARG* 2.5 42.2 + - - +
233B ARG* 3.1 29.4 + - + +
234B ASN* 3.6 9.2 - - - +
235B LEU 3.2 0.2 - - - -
236B ASN* 1.3 73.1 - - - +
238B ARG* 1.3 65.7 + - - +
240B ARG* 2.6 44.2 + - - +
241B ARG* 3.2 37.2 + - - +
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Residues in contact with ARG 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B SER* 5.7 2.9 - - - +
195B TYR* 3.8 16.6 - - - -
196B GLU* 2.8 28.0 + - - +
234B ASN 3.1 13.6 + - - +
235B LEU* 3.1 14.1 + - + +
237B GLU* 1.3 76.3 - - - +
239B ILE* 1.3 63.9 + - - +
241B ARG* 3.2 38.7 + - - +
242B ASP* 3.1 30.2 + - - +
244B ARG* 3.3 26.9 - - - +
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Residues in contact with ILE 239 (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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61A ARG 5.6 0.2 - - - +
64A ARG* 2.9 18.4 + - - -
195B TYR* 3.7 34.1 - - + +
210B VAL* 4.1 17.3 - - + -
213B VAL* 6.0 0.2 - - + -
235B LEU* 2.9 49.6 + - + +
236B ASN* 4.0 9.6 - - - +
238B ARG* 1.3 71.4 - - - +
240B ARG* 1.3 64.6 + - - +
242B ASP* 3.0 12.5 + - - +
247B ILE* 3.8 31.1 - - + +
257B THR* 4.2 20.0 - - + -
259B ALA* 4.9 0.7 - - + -
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Residues in contact with ARG 240 (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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60A SER* 3.3 26.1 + - - +
61A ARG* 2.8 73.3 + - - +
62A SER 6.1 0.2 - - - -
64A ARG* 3.2 23.6 + - - +
236B ASN 2.9 14.9 + - - +
237B GLU* 2.6 35.1 + - - +
238B ARG 3.2 0.2 - - - -
239B ILE* 1.3 76.9 - - - +
241B ARG* 1.3 62.9 + - + +
247B ILE* 4.2 3.6 - - + -
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Residues in contact with ARG 241 (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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64A ARG* 4.3 1.1 - - - -
234B ASN 5.3 0.4 + - - -
237B GLU* 3.2 18.6 + - - +
238B ARG* 3.2 48.2 + - - +
239B ILE 3.2 0.8 - - - -
240B ARG* 1.3 85.5 - - + +
242B ASP* 1.3 62.5 + - - +
243B VAL* 3.1 14.2 + - - +
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Residues in contact with ASP 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 2.9 25.4 + - - -
195B TYR* 2.7 26.8 + - - +
199B LEU* 3.8 1.2 - - - +
238B ARG* 3.1 29.1 + - - +
239B ILE* 3.0 12.4 + - - +
240B ARG 3.4 0.4 - - - -
241B ARG* 1.3 75.1 - - - +
243B VAL* 1.3 61.6 + - - +
244B ARG* 2.9 54.5 + - - +
245B VAL* 3.3 14.4 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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