Contacts of the helix formed by residues 220 - 232 (chain B) in PDB entry 2AG1
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 ARG 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B ALA 4.7 4.8 + - - -
185B HIS* 4.4 33.1 + - - +
186B GLY 5.3 0.8 - - - +
215B ALA 4.3 0.2 + - - -
218B THR* 2.9 36.6 + - - +
219B ALA* 1.3 70.6 + - - +
221B LYS* 1.3 58.6 + - - +
222B THR 3.5 2.0 - - - -
223B ALA* 4.0 12.1 - - + -
224B LEU* 3.0 29.1 + - - +
244B MSE 3.7 8.0 - - - +
323B GLY* 3.3 37.9 + - - +
324B GLY* 5.2 0.6 - - - +
326B ILE* 4.0 9.3 - - + +
327B GLU* 2.8 46.0 + - - +
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Residues in contact with LYS 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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219B ALA* 2.7 27.6 + - - +
220B ARG* 1.3 70.8 - - - +
222B THR* 1.3 70.5 + - + +
224B LEU* 3.7 3.5 - - - +
225B SER* 3.0 26.6 + - - -
243B SER 5.7 4.0 - - - -
244B MSE 4.0 30.7 - - + +
247B GLY* 6.5 1.3 - - - -
248B LEU* 5.5 0.2 - - - +
410B GLY 5.6 3.2 + - - -
440B ARG* 4.9 12.9 - - - +
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Residues in contact with THR 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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220B ARG 3.5 0.2 - - - -
221B LYS* 1.3 81.0 - - + +
223B ALA* 1.3 63.4 + - - +
225B SER* 3.6 7.2 + - - -
226B ALA* 3.2 23.4 + - - +
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Residues in contact with ALA 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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220B ARG* 3.5 10.1 + - + +
221B LYS 3.3 0.2 - - - -
222B THR* 1.3 78.2 + - - +
224B LEU* 1.3 65.7 + - - +
226B ALA* 3.1 2.7 + - - -
227B PHE* 2.9 20.6 + - - +
326B ILE* 3.9 15.0 - - + -
327B GLU* 4.0 37.9 - - + +
330B ALA* 3.4 18.5 - - + +
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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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209B ILE* 5.7 1.6 - - + -
211B LEU* 4.0 28.0 - - + -
220B ARG 3.0 19.3 + - - +
221B LYS* 3.7 4.9 - - - +
223B ALA* 1.3 74.4 - - - +
225B SER* 1.3 58.3 + - - +
227B PHE* 3.1 11.5 + - + +
228B VAL* 2.8 50.2 + - + +
235B VAL* 5.1 3.1 - - + -
244B MSE 3.5 35.7 - - + +
248B LEU* 4.0 16.4 - - + -
276B LEU* 5.5 2.2 - - + -
326B ILE* 3.4 31.2 - - + +
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Residues in contact with SER 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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221B LYS 3.0 18.5 + - - -
222B THR* 3.6 7.8 + - - -
224B LEU* 1.3 76.8 - - - +
226B ALA* 1.3 57.9 + - - +
228B VAL* 4.1 0.7 - - - +
229B ALA* 2.9 30.0 + - - +
247B GLY 4.4 13.5 - - - -
248B LEU* 3.7 24.0 - - - -
249B PRO* 5.3 5.4 - - - +
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Residues in contact with ALA 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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222B THR 3.2 17.6 + - - +
223B ALA* 3.1 6.3 + - - +
225B SER* 1.3 77.1 + - - +
227B PHE* 1.3 58.1 + - - +
229B ALA* 3.9 5.4 - - - +
230B ALA* 3.1 28.6 + - - +
330B ALA* 4.4 11.2 - - + +
333B THR* 4.0 3.7 - - + +
334B ALA* 6.5 0.7 - - + -
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Residues in contact with PHE 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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198B LEU* 4.4 4.3 - - + -
201B LEU* 3.8 24.0 - - + -
209B ILE* 3.7 26.7 - - + -
223B ALA 2.9 12.8 + - - +
224B LEU* 3.1 16.6 + - + +
226B ALA* 1.3 74.5 - - - +
228B VAL* 1.3 65.4 + - + +
230B ALA* 3.4 1.4 + - - +
231B THR* 2.9 46.2 + - + +
274B LEU* 4.1 7.4 - - + -
276B LEU* 5.4 3.4 - - + -
326B ILE* 4.7 4.7 - - + +
329B LEU* 3.7 57.7 - - + -
330B ALA* 4.0 11.4 - - - +
333B THR* 3.7 16.4 - - + -
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Residues in contact with VAL 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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209B ILE* 4.7 3.8 - - + -
224B LEU* 2.8 39.9 + - + +
225B SER 4.1 3.1 - - - +
227B PHE* 1.3 77.7 - - + +
229B ALA* 1.3 59.0 + - - +
231B THR* 3.9 4.7 - - - -
232B GLY* 2.7 31.9 + - - -
233B VAL 3.8 11.7 - - - +
235B VAL* 3.6 21.5 - - + -
248B LEU* 4.0 16.8 - - + -
249B PRO* 4.7 2.0 - - + -
252B MSE 3.4 34.5 - - + +
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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
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225B SER 2.9 20.9 + - - +
226B ALA* 3.9 6.7 - - - +
227B PHE 3.3 0.2 - - - -
228B VAL* 1.3 76.9 - - - +
230B ALA* 1.3 60.0 + - - +
232B GLY* 4.1 3.1 + - - -
249B PRO* 5.5 5.6 - - + +
252B MSE 3.9 16.4 - - + +
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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 ALA 3.1 10.7 + - - +
227B PHE 3.9 0.2 - - - +
228B VAL 3.2 0.4 - - - -
229B ALA* 1.3 77.1 - - - +
231B THR* 1.3 61.1 + - - +
333B THR* 3.4 46.9 - - + +
334B ALA* 5.7 0.4 - - - -
337B ALA* 5.6 3.4 - - - +
339B TRP* 3.5 24.7 - - + +
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Residues in contact with THR 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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201B LEU* 4.3 2.0 - - + -
209B ILE* 5.2 0.2 - - - +
227B PHE* 2.9 38.1 + - + +
228B VAL* 3.6 4.0 + - - -
230B ALA* 1.3 77.0 - - - +
232B GLY* 1.3 65.1 + - - +
233B VAL* 3.3 30.4 + - - +
333B THR* 3.6 20.9 - - - +
339B TRP* 3.7 34.4 - - + +
340B PRO 4.2 7.4 - - - +
341B ASP 4.8 0.3 - - - +
342B ARG* 3.9 14.4 + - - +
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Residues in contact with GLY 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 VAL 2.7 20.4 + - - -
229B ALA 4.1 2.7 + - - -
230B ALA 3.6 1.2 - - - -
231B THR* 1.3 74.1 - - - +
233B VAL* 1.3 57.5 + - - +
234B PRO* 3.8 0.2 - - - +
252B MSE 4.2 17.9 - - - -
341B ASP 4.9 4.7 - - - -
342B ARG* 3.4 14.8 - - - +
346B CYS* 3.3 25.5 - - - -
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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