Contacts of the helix formed by residues 190 - 203 (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 ASP 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B ARG 3.7 0.8 + - - -
189B PRO* 1.3 72.4 - - - +
191B PRO* 1.3 74.1 - - - +
192B ALA* 2.7 38.8 + - - +
193B ASP* 3.0 26.1 + - - +
194B LEU* 3.1 10.4 + - - +
185C HIS* 3.3 42.4 + - + +
186C GLY 4.2 11.6 + - - +
188C ARG* 3.2 23.7 + - - +
220C ARG* 5.8 0.2 + - - -
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Residues in contact with PRO 191 (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 PRO 3.6 4.2 - - - +
190B ASP* 1.3 88.0 - - - +
192B ALA* 1.3 55.4 + - - +
194B LEU* 3.5 9.2 + - + +
195B ASP* 2.9 40.1 + - - +
188C ARG* 3.3 37.9 - - - +
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Residues in contact with ALA 192 (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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190B ASP* 2.7 21.2 + - - +
191B PRO* 1.3 73.8 - - - +
193B ASP* 1.3 55.7 + - - +
195B ASP* 3.6 9.8 + - - +
196B GLN* 3.1 28.0 + - - +
185C HIS* 4.5 15.0 - - + +
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Residues in contact with ASP 193 (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 PRO* 4.5 4.3 - - + -
190B ASP* 3.0 19.0 + - - +
192B ALA* 1.3 75.4 - - - +
194B LEU* 1.3 59.9 + - - +
196B GLN* 3.3 11.5 + - - +
197B ALA* 2.8 30.1 + - - +
316B LEU* 3.7 14.0 - - + +
318B ILE* 3.8 26.9 - - + +
183C SER* 2.6 36.1 + - - -
185C HIS* 3.7 20.8 + - - +
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Residues in contact with LEU 194 (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 PRO* 3.9 31.0 - - + +
190B ASP 3.1 8.0 + - - +
191B PRO* 3.6 12.1 - - + +
193B ASP* 1.3 77.3 - - - +
195B ASP* 1.3 65.0 + - - +
197B ALA* 3.1 7.4 + - + +
198B LEU* 2.8 31.3 + - + +
318B ILE* 5.4 1.6 - - + -
325B THR* 4.9 1.3 - - + -
328B ALA* 3.7 39.0 - - + +
329B LEU* 3.7 28.5 - - + -
332B ALA* 3.9 16.4 - - + -
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Residues in contact with ASP 195 (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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191B PRO* 2.9 29.4 + - - +
192B ALA* 3.6 9.0 - - - +
194B LEU* 1.3 74.6 - - - +
196B GLN* 1.3 53.6 + - - +
198B LEU* 3.1 10.7 + - - +
199B ALA* 2.7 36.5 + - - +
332B ALA* 6.1 0.7 - - - +
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Residues in contact with GLN 196 (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 ALA 3.1 13.6 + - - +
193B ASP* 3.6 10.0 + - - +
194B LEU 3.3 0.2 - - - -
195B ASP* 1.3 78.7 - - - +
197B ALA* 1.3 58.1 + - - +
199B ALA* 3.3 7.4 + - + +
200B LEU* 3.0 48.3 + - + +
315B ALA 4.7 6.6 - - - +
316B LEU* 3.4 32.3 - - + +
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Residues in contact with ALA 197 (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 2.8 20.1 + - - +
194B LEU* 3.4 9.4 - - + +
196B GLN* 1.3 74.0 - - - +
198B LEU* 1.3 61.8 + - + +
200B LEU* 3.3 3.6 + - - +
201B LEU* 2.9 28.5 + - - +
274B LEU* 5.6 3.6 - - + -
299B ILE* 3.7 28.5 - - + +
316B LEU* 3.8 14.3 - - + +
318B ILE* 4.8 3.8 - - + -
329B LEU* 5.2 6.7 - - + -
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Residues in contact with LEU 198 (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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194B LEU* 2.8 31.5 + - + +
195B ASP* 3.5 10.1 - - - +
197B ALA* 1.3 70.6 - - - +
199B ALA* 1.3 61.7 + - - +
201B LEU* 3.2 9.4 + - + +
202B ARG* 2.8 37.2 + - - +
227B PHE* 4.4 13.0 - - + -
329B LEU* 3.5 27.6 - - + +
332B ALA* 3.6 33.2 - - + -
333B THR* 5.2 1.8 - - - +
336B ASP* 5.0 4.3 - - - +
339B TRP* 3.7 26.9 - - + -
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Residues in contact with ALA 199 (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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195B ASP 2.7 21.5 + - - +
196B GLN* 3.7 9.4 - - + +
198B LEU* 1.3 71.6 - - - +
200B LEU* 1.3 64.1 + - + +
202B ARG* 3.2 13.2 + - - +
203B LYS* 3.1 34.3 + - + +
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Residues in contact with LEU 200 (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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196B GLN* 3.0 40.7 + - + +
197B ALA* 3.7 4.7 - - - +
198B LEU 3.3 0.2 - - - -
199B ALA* 1.3 78.2 - - + +
201B LEU* 1.3 60.9 + - - +
203B LYS* 3.5 27.2 + - + +
204B ALA* 3.3 16.5 + - - +
272B LEU* 3.2 25.6 - - + +
297B GLN* 3.5 35.8 + - + +
299B ILE* 4.2 18.6 - - + -
315B ALA* 4.9 12.6 - - + -
316B LEU* 4.9 4.3 - - + -
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Residues in contact with LEU 201 (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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197B ALA 2.9 18.4 + - - +
198B LEU* 3.5 10.1 - - + +
200B LEU* 1.3 76.8 - - - +
202B ARG* 1.3 57.5 + - - +
203B LYS 3.6 0.2 + - - -
204B ALA* 3.7 5.1 + - - +
207B PRO* 3.9 15.7 - - + -
208B VAL 5.4 0.2 - - - +
209B ILE* 5.7 0.2 - - + -
227B PHE* 3.8 30.7 - - + -
231B THR* 4.3 5.6 - - + -
233B VAL* 4.2 20.4 - - + -
272B LEU* 3.7 27.5 - - + +
274B LEU* 5.0 14.6 - - + -
299B ILE* 5.4 1.3 - - + -
339B TRP* 4.0 20.8 - - + -
342B ARG* 3.1 22.0 + - - -
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Residues in contact with ARG 202 (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* 2.8 21.1 + - - +
199B ALA* 3.2 9.1 + - - +
201B LEU* 1.3 79.2 - - - +
203B LYS* 1.3 62.7 + - + +
204B ALA 3.3 0.6 - - - +
336B ASP* 3.0 38.4 + - - -
338B ALA* 3.1 28.8 + - - +
339B TRP* 3.6 31.0 - - + -
340B PRO* 3.7 18.1 - - + +
342B ARG* 3.5 12.5 + - - +
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Residues in contact with LYS 203 (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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199B ALA* 3.1 24.2 + - + +
200B LEU* 3.6 33.7 - - + +
201B LEU 3.4 0.2 - - - -
202B ARG* 1.3 79.2 - - + +
204B ALA* 1.3 62.8 + - - +
205B GLU* 4.0 5.5 + - - +
271B ASP* 4.8 0.2 - - - +
297B GLN* 6.3 0.2 - - - +
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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