Contacts of the helix formed by residues 321 - 335 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ALA* 3.6 17.0 - - + +
154A ARG* 3.2 29.5 + - - -
186A GLY* 3.4 25.1 + - - -
187A ALA* 3.2 21.1 + - - +
214A GLU* 4.3 1.0 - - - +
218A THR* 3.9 7.2 - - - +
301A VAL* 4.8 0.2 - - - -
303A PRO* 5.1 0.4 - - - -
320A ALA* 1.3 73.9 - - - +
322A VAL* 1.3 57.7 + - - +
323A GLY* 2.9 8.7 + - - -
324A GLY 2.8 24.4 + - - -
325A THR* 2.7 36.8 + - - -
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A GLU* 3.7 22.3 + - + +
215A ALA* 3.6 27.6 - - - +
276A LEU* 3.7 18.6 - - + +
277A GLY* 3.6 32.1 - - - +
301A VAL* 3.9 13.2 - - + +
303A PRO* 4.7 7.3 - - + +
320A ALA 3.7 0.4 + - - -
321A ASP* 1.3 76.3 + - - +
323A GLY* 1.3 57.4 + - - +
325A THR* 3.6 5.6 - - - -
326A ILE* 2.9 41.7 + - + +
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Residues in contact with GLY 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLY 5.4 0.2 - - - -
218A THR* 3.4 26.8 + - - +
220A ARG* 3.5 20.2 - - - +
321A ASP* 2.9 9.2 + - - -
322A VAL* 1.3 78.5 - - - +
324A GLY* 1.3 55.3 + - - +
326A ILE* 3.3 3.2 + - - +
327A GLU* 3.0 34.6 + - - +
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Residues in contact with GLY 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A HIS* 5.5 2.0 - - - -
186A GLY 3.8 25.1 - - - +
187A ALA 3.9 4.5 - - - -
188A ARG* 3.6 15.3 + - - +
220A ARG* 5.3 0.9 - - - +
321A ASP* 2.8 13.7 + - - -
323A GLY* 1.3 72.4 - - - +
325A THR* 1.3 56.2 + - - +
327A GLU* 3.4 9.8 + - - +
328A ALA* 2.9 28.1 + - - +
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Residues in contact with THR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ALA 4.3 0.2 + - - -
189A PRO* 3.4 34.8 - - + +
194A LEU* 4.9 1.3 - - + -
274A LEU* 6.1 0.2 - - + -
276A LEU* 4.3 5.2 - - + -
301A VAL* 3.4 34.9 - - + +
320A ALA* 3.5 2.6 - - - +
321A ASP 2.7 23.1 + - - -
322A VAL* 3.6 4.9 - - - -
323A GLY 3.2 0.2 - - - -
324A GLY* 1.3 73.5 - - - +
326A ILE* 1.3 56.7 + - - +
328A ALA* 3.0 3.1 + - - +
329A LEU* 2.8 56.8 + - + +
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Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LEU* 4.6 1.3 - - + -
215A ALA* 4.2 16.8 - - + +
218A THR* 5.5 0.2 - - - +
220A ARG* 3.9 13.9 - - + +
223A ALA* 3.9 5.7 - - + +
224A LEU* 3.4 50.7 - - + +
227A PHE* 4.7 4.8 - - + +
244A MSE 5.3 3.6 - - + -
276A LEU* 3.9 26.9 - - + -
322A VAL* 2.9 37.0 + - + +
323A GLY* 3.7 6.1 - - - +
325A THR* 1.3 74.2 - - - +
327A GLU* 1.3 64.5 + - - +
329A LEU* 3.2 9.8 + - + +
330A ALA* 3.0 21.5 + - - +
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Residues in contact with GLU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A HIS* 5.8 3.1 - - - +
188A ARG* 3.4 21.8 - - - +
220A ARG* 2.9 50.7 + - - +
223A ALA* 4.0 21.5 - - + +
323A GLY 3.0 18.0 + - - +
324A GLY* 3.4 6.9 - - - +
326A ILE* 1.3 76.6 - - - +
328A ALA* 1.3 57.1 + - - +
330A ALA* 3.0 5.4 + - + +
331A GLN* 2.9 39.0 + - + +
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG* 3.6 37.2 - - + +
189A PRO* 4.4 1.1 - - + +
194A LEU* 3.6 25.8 - - + +
324A GLY 2.9 14.9 + - - +
325A THR* 3.0 7.8 + - - +
327A GLU* 1.3 75.1 - - - +
329A LEU* 1.3 56.6 + - - +
331A GLN* 3.3 1.9 + - - +
332A ALA* 2.9 32.7 + - - +
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LEU* 3.8 21.1 - - + -
197A ALA* 5.2 8.1 - - + -
198A LEU* 3.6 28.8 - - + +
227A PHE* 3.7 35.9 - - + -
274A LEU* 4.3 16.8 - - + -
276A LEU* 4.5 9.2 - - + -
325A THR* 2.8 39.8 + - + +
326A ILE* 3.6 9.9 - - - +
328A ALA* 1.3 72.4 - - - +
330A ALA* 1.3 50.6 + - - +
332A ALA* 3.6 4.5 + - - +
333A THR* 2.8 38.8 + - - -
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ALA* 3.4 36.8 - - + +
226A ALA* 4.4 8.3 - - + +
227A PHE* 4.1 6.3 - - + +
326A ILE 3.0 10.8 + - - +
327A GLU* 3.4 7.9 - - + +
329A LEU* 1.3 76.1 - - - +
331A GLN* 1.3 58.6 + - + +
333A THR* 3.4 10.6 - - - +
334A ALA* 2.8 30.9 + - - +
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Residues in contact with GLN 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG* 3.5 32.3 + - - +
327A GLU* 2.9 22.9 + - + +
328A ALA* 3.8 4.9 - - - +
330A ALA* 1.3 74.8 - - + +
332A ALA* 1.3 65.2 + - - +
333A THR 3.2 0.7 + - - -
334A ALA* 3.4 11.9 + - - +
335A GLN* 3.4 20.1 + - - +
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Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LEU* 3.8 11.7 - - + -
195A ASP* 6.1 0.9 - - - +
198A LEU* 3.6 27.4 - - + -
328A ALA 2.9 17.5 + - - +
329A LEU 4.0 1.6 - - - +
331A GLN* 1.3 76.0 - - - +
333A THR* 1.3 58.2 + - - +
335A GLN* 3.5 14.9 + - - +
336A ASP* 3.5 17.6 + - - +
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Residues in contact with THR 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LEU* 5.0 2.2 - - - +
226A ALA* 4.0 2.9 - - + +
227A PHE* 3.8 24.6 - - + -
230A ALA* 3.4 29.0 - - + +
231A THR* 3.7 10.4 - - - +
329A LEU 2.8 20.2 + - - +
330A ALA* 3.4 6.5 - - - +
331A GLN 3.1 0.2 - - - -
332A ALA* 1.3 78.1 - - - +
334A ALA* 1.3 64.7 + - - +
335A GLN 3.2 1.3 - - - -
336A ASP* 3.5 17.0 + - - +
337A ALA* 3.8 7.1 + - - +
339A TRP* 3.6 28.8 + - - -
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Residues in contact with ALA 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ALA* 6.5 0.7 - - + -
330A ALA 2.8 17.5 + - - +
331A GLN* 3.4 7.8 + - - +
333A THR* 1.3 78.4 - - - +
335A GLN* 1.3 70.5 + - - +
336A ASP 3.2 4.4 + - - -
337A ALA* 5.1 4.5 + - - +
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Residues in contact with GLN 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A GLN 3.4 12.5 + - - +
332A ALA* 3.5 11.2 + - - +
333A THR 3.2 0.8 - - - -
334A ALA* 1.3 91.1 + - - +
336A ASP* 1.3 59.1 + - - +
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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