Contacts of the helix formed by residues 321 - 335 (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 321 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ALA* 3.6 16.2 - - + +
154B ARG* 3.1 30.0 + - - -
186B GLY* 3.4 25.5 + - - -
187B ALA* 3.1 23.0 + - + +
214B GLU* 4.2 0.9 - - - +
218B THR* 3.9 8.4 - - - +
303B PRO* 5.0 0.4 - - - -
320B ALA* 1.3 73.9 - - - +
322B VAL* 1.3 58.1 + - - +
323B GLY* 3.1 8.0 + - - -
324B GLY 2.9 23.4 + - - -
325B THR* 2.6 37.1 + - - -
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLU* 3.8 20.7 + - + +
215B ALA* 3.7 31.0 - - + +
276B LEU* 3.7 20.6 - - + +
277B GLY* 3.5 31.0 - - - +
301B VAL* 3.9 14.6 - - + +
303B PRO* 4.6 8.2 - - + +
321B ASP* 1.3 77.9 + - - +
323B GLY* 1.3 57.9 + - - +
325B THR* 3.1 6.9 + - - -
326B ILE* 2.8 38.1 + - + +
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Residues in contact with GLY 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLY 5.4 0.2 - - - -
218B THR* 3.3 26.7 + - - +
220B ARG* 3.3 19.7 - - - +
321B ASP* 3.1 9.7 + - - -
322B VAL* 1.3 78.6 - - - +
324B GLY* 1.3 56.2 + - - +
326B ILE* 3.5 3.5 + - - +
327B GLU* 3.0 34.0 + - - +
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Residues in contact with GLY 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B HIS* 5.9 0.7 - - - -
186B GLY 4.0 15.5 - - - +
187B ALA 3.9 13.2 - - - -
188B ARG* 3.6 15.1 + - - +
220B ARG* 5.5 0.9 - - - -
321B ASP* 2.9 12.8 + - - -
322B VAL 3.3 0.2 - - - -
323B GLY* 1.3 72.4 - - - +
325B THR* 1.3 59.9 + - - +
327B GLU* 3.4 8.9 + - - +
328B ALA* 2.9 28.4 + - - +
190C ASP* 5.7 1.8 - - - -
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Residues in contact with THR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ALA 4.3 0.4 + - - -
189B PRO* 3.4 35.7 - - + +
194B LEU* 4.9 1.8 - - + -
276B LEU* 4.3 5.4 - - + -
301B VAL* 3.5 35.3 - - + +
320B ALA* 3.5 3.3 - - - +
321B ASP 2.6 22.5 + - - -
322B VAL* 3.1 4.9 + - - -
324B GLY* 1.3 73.2 - - - +
326B ILE* 1.3 59.1 + - - +
328B ALA* 3.0 3.3 + - - +
329B LEU* 2.8 47.3 + - + +
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Residues in contact with ILE 326 (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 LEU* 4.7 1.1 - - + -
215B ALA* 4.2 17.7 - - + +
218B THR* 5.4 0.4 - - - +
220B ARG* 4.0 10.1 - - + +
223B ALA* 3.9 5.3 - - + +
224B LEU* 3.4 51.4 - - + +
227B PHE* 4.7 5.0 - - + +
244B MSE 5.4 2.5 - - + -
276B LEU* 3.9 26.2 - - + -
322B VAL* 2.8 40.1 + - + +
323B GLY* 3.8 7.6 - - - +
325B THR* 1.3 69.9 - - - +
327B GLU* 1.3 64.5 + - - +
329B LEU* 3.3 10.2 + - + +
330B ALA* 3.0 21.3 + - - +
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B HIS* 5.8 1.1 - - - -
188B ARG* 3.4 22.7 - - - +
220B ARG* 2.8 50.8 + - - +
223B ALA* 4.0 20.8 - - + +
323B GLY 3.0 18.7 + - - +
324B GLY* 3.4 6.9 - - - +
325B THR 3.2 0.2 - - - -
326B ILE* 1.3 77.2 - - - +
328B ALA* 1.3 57.1 + - - +
330B ALA* 3.2 4.9 + - - +
331B GLN* 2.9 37.7 + - + +
190C ASP* 5.0 3.8 - - - +
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Residues in contact with ALA 328 (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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188B ARG* 3.7 38.1 - - + +
189B PRO* 4.5 0.7 - - + +
194B LEU* 3.7 24.9 - - + +
324B GLY 2.9 14.5 + - - +
325B THR* 3.5 7.6 - - - +
327B GLU* 1.3 72.6 - - - +
329B LEU* 1.3 61.4 + - - +
331B GLN* 3.2 2.9 + - - +
332B ALA* 2.9 31.7 + - - +
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 3.7 20.4 - - + -
197B ALA* 5.2 7.6 - - + -
198B LEU* 3.5 29.0 - - + +
227B PHE* 3.7 37.4 - - + -
274B LEU* 4.3 17.0 - - + -
276B LEU* 4.5 8.5 - - + -
325B THR* 2.8 37.3 + - + +
326B ILE* 3.7 9.2 - - - +
328B ALA* 1.3 76.1 - - - +
330B ALA* 1.3 56.5 + - - +
332B ALA* 3.5 4.9 + - - +
333B THR* 2.8 33.4 + - - -
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ALA* 3.4 36.3 - - + +
226B ALA* 4.4 8.4 - - + +
227B PHE* 4.0 6.6 - - + +
326B ILE 3.0 11.1 + - - +
327B GLU 3.5 8.1 - - - +
329B LEU* 1.3 75.2 - - - +
331B GLN* 1.3 59.2 + - + +
333B THR* 3.5 10.1 - - - +
334B ALA* 2.8 32.4 + - - +
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ARG* 3.3 34.0 + - - +
327B GLU* 2.9 21.8 + - + +
328B ALA* 3.2 7.6 + - - +
330B ALA* 1.3 75.2 - - + +
332B ALA* 1.3 64.4 + - - +
333B THR 3.3 0.2 + - - -
334B ALA* 3.5 5.6 + - - +
335B GLN* 3.4 24.8 + - - +
190C ASP* 5.9 0.2 - - - -
191C PRO* 4.2 15.5 - - - +
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 3.9 12.1 - - + -
195B ASP* 6.1 0.7 - - - +
198B LEU* 3.6 28.3 - - + -
328B ALA 2.9 16.2 + - - +
329B LEU 4.0 1.6 - - - +
331B GLN* 1.3 77.3 - - - +
333B THR* 1.3 59.3 + - - +
335B GLN* 3.5 15.2 + - - +
336B ASP* 3.6 16.0 + - - +
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Residues in contact with THR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 5.2 2.0 - - - +
226B ALA 4.0 2.9 - - - +
227B PHE* 3.7 27.2 - - + -
230B ALA* 3.4 28.8 - - + +
231B THR* 3.6 15.1 - - - +
329B LEU 2.8 20.5 + - - +
330B ALA* 3.5 6.5 - - - +
332B ALA* 1.3 78.1 - - - +
334B ALA* 1.3 64.5 + - - +
335B GLN 3.2 1.1 - - - -
336B ASP* 3.5 17.2 + - - +
337B ALA* 3.8 5.9 + - - +
339B TRP* 3.6 23.6 + - - -
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Residues in contact with ALA 334 (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* 6.5 0.9 - - + -
230B ALA* 5.7 0.4 - - - -
330B ALA 2.8 20.7 + - - +
331B GLN* 3.9 7.0 - - - +
333B THR* 1.3 75.0 - - - +
335B GLN* 1.3 71.0 + - - +
336B ASP 3.2 4.6 + - - -
337B ALA* 5.0 4.7 + - - +
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Residues in contact with GLN 335 (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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331B GLN 3.4 13.1 + - - +
332B ALA* 3.5 11.2 + - - +
333B THR 3.2 1.2 - - - -
334B ALA* 1.3 89.1 + - - +
336B ASP* 1.4 58.1 + - - +
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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