Contacts of the helix formed by residues 295 - 309 (chain A) in PDB entry 2JG0
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 PRO 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A ASN 4.6 1.3 - - - +
294A ARG* 1.3 86.0 - - + +
296A ALA* 1.3 66.4 + - - +
297A THR* 3.2 9.9 - - - +
298A GLU* 3.0 55.6 + - + +
299A ILE* 3.2 11.5 + - - +
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Residues in contact with ALA 296 (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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288A ALA* 3.9 21.3 - - + +
294A ARG 3.3 5.2 + - - -
295A PRO* 1.3 71.4 - - - +
297A THR* 1.3 58.9 + - + +
299A ILE* 3.1 5.8 + - - +
300A TYR* 2.8 53.6 + - + +
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Residues in contact with THR 297 (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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274A ASP* 3.6 49.1 - - - +
275A THR* 6.2 0.2 - - + -
295A PRO* 4.1 11.4 - - - +
296A ALA* 1.3 80.1 - - + +
298A GLU* 1.3 61.3 + - - +
300A TYR* 4.1 2.2 - - + -
301A ARG* 2.9 29.3 + - - +
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Residues in contact with GLU 298 (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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294A ARG* 4.4 14.7 + - - +
295A PRO* 3.0 43.0 + - + +
297A THR* 1.3 77.1 + - - +
299A ILE* 1.3 66.7 + - - +
301A ARG* 3.4 6.3 + - - +
302A ASP* 3.0 30.2 + - - +
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Residues in contact with ILE 299 (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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287A THR* 4.1 17.0 - - + +
288A ALA* 3.8 28.5 - - + +
291A ASN* 3.9 23.6 - - + +
294A ARG* 3.8 46.4 - - + +
295A PRO 3.2 8.0 + - - +
296A ALA* 3.1 7.5 + - - +
298A GLU* 1.3 77.4 - - - +
300A TYR* 1.3 57.8 + - - +
302A ASP* 3.1 3.7 + - - +
303A LEU* 2.8 47.9 + - + +
325A ASN* 4.1 5.2 - - + +
327A LEU* 4.6 5.8 - - + -
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Residues in contact with TYR 300 (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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274A ASP 3.3 26.7 - - - +
275A THR* 3.5 18.8 - - - +
276A PRO* 3.6 28.3 - - + +
284A ASP* 3.3 35.2 - - + -
285A ILE* 3.7 20.8 + - - +
288A ALA* 3.6 21.4 - - + +
296A ALA* 2.8 35.4 + - + +
297A THR* 3.8 3.1 - - + +
299A ILE* 1.3 76.9 - - - +
301A ARG* 1.3 57.4 + - - +
303A LEU* 3.7 6.7 - - + +
304A ARG* 2.9 38.1 + - - +
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Residues in contact with ARG 301 (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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270A TRP* 3.6 35.6 - - + +
271A ASP 2.9 29.1 + - - -
272A ASP* 3.2 26.1 + - - +
273A ARG 3.5 12.1 + - - +
274A ASP* 3.9 28.4 + - + +
297A THR 2.9 18.6 + - - +
298A GLU* 3.7 8.1 - - - +
300A TYR* 1.3 76.3 - - - +
302A ASP* 1.3 54.9 + - - +
304A ARG* 3.7 1.8 - - - +
305A SER* 2.7 38.0 + - - -
330A THR* 3.9 20.4 - - + +
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Residues in contact with ASP 302 (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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294A ARG* 2.8 26.8 + - - +
298A GLU* 3.0 16.2 + - - +
299A ILE 3.1 3.5 + - - +
301A ARG* 1.3 77.1 - - - +
303A LEU* 1.3 58.8 + - - +
305A SER* 4.3 1.3 - - - -
306A ALA 2.9 13.9 + - - -
327A LEU* 3.5 22.6 - - + +
328A ARG* 3.3 8.3 - - - +
329A THR* 2.9 34.2 + - - +
330A THR* 2.7 41.5 + - - +
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Residues in contact with LEU 303 (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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277A ARG* 4.6 3.3 - - - +
284A ASP* 3.5 45.8 - - + +
287A THR* 4.2 8.7 - - + +
299A ILE* 2.8 36.4 + - + +
300A TYR* 3.7 8.3 - - + +
302A ASP* 1.3 75.3 - - - +
304A ARG* 1.3 63.3 + - - +
306A ALA 3.3 1.7 + - - -
307A ALA* 3.1 19.9 + - - +
313A PHE* 3.6 35.6 - - + -
324A LEU* 4.0 21.5 - - + -
327A LEU* 3.8 21.1 - - + -
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Residues in contact with ARG 304 (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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201A TYR 4.6 4.4 + - - -
204A SER* 3.0 27.3 + - - -
205A ARG* 3.4 20.0 - - - +
271A ASP* 3.0 33.8 + - + +
273A ARG* 3.3 39.9 - - - +
275A THR* 2.7 32.9 + - - +
276A PRO 3.3 20.4 + - - -
277A ARG* 3.8 20.0 - - + +
278A PRO* 3.5 17.2 - - - +
284A ASP* 5.4 0.4 - - - +
300A TYR 2.9 17.0 + - - +
301A ARG 3.7 1.8 - - - +
303A LEU* 1.3 78.0 - - + +
305A SER* 1.3 56.6 + - - +
307A ALA* 3.1 9.3 + - - +
308A ALA 2.9 21.8 + - - -
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Residues in contact with SER 305 (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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269A TYR* 3.5 20.3 - - - +
270A TRP* 3.4 0.3 - - - -
271A ASP* 3.1 20.7 + - - +
301A ARG* 2.7 25.4 + - - +
302A ASP 3.9 3.6 - - - -
304A ARG* 1.3 73.4 - - - +
306A ALA* 1.3 62.2 + - - +
308A ALA* 3.1 12.1 + - - +
309A SER* 2.9 22.7 + - - -
329A THR* 3.7 7.2 - - - -
330A THR* 3.2 27.6 - - - +
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Residues in contact with ALA 306 (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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302A ASP 2.9 18.4 + - - +
303A LEU 3.6 5.2 - - - +
305A SER* 1.3 74.3 - - - +
307A ALA* 1.3 64.0 + - - +
309A SER* 2.6 25.5 + - - -
310A GLY 3.4 2.6 + - - -
311A TRP 3.6 6.3 + - - +
312A ASP* 3.6 3.8 + - - -
313A PHE* 3.7 23.8 - - + -
317A TRP* 3.9 14.1 - - + +
327A LEU* 3.8 4.9 - - + -
329A THR* 3.6 15.1 - - - +
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Residues in contact with ALA 307 (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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196A ASN* 3.7 11.5 + - - -
205A ARG* 3.5 13.5 - - - +
207A GLN* 4.1 4.2 + - - +
277A ARG* 4.5 4.0 - - - +
303A LEU 3.1 13.2 + - - +
304A ARG* 3.3 10.5 - - - +
306A ALA* 1.3 74.4 - - - +
308A ALA* 1.3 62.7 + - - +
310A GLY* 3.0 14.7 + - - -
312A ASP* 3.8 18.4 - - + +
1548A TTZ 3.4 31.8 + - - +
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Residues in contact with ALA 308 (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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205A ARG* 3.7 23.0 - - + +
206A SER 3.7 16.6 - - - +
207A GLN* 3.1 26.9 - - - -
208A PRO* 3.4 2.3 - - - +
241A TRP* 6.3 0.4 - - + -
269A TYR* 3.5 17.5 - - + -
270A TRP 4.6 7.0 - - - +
304A ARG 2.9 12.7 + - - +
305A SER* 3.1 14.3 + - - +
307A ALA* 1.3 75.6 - - - +
309A SER* 1.3 61.5 + - - +
310A GLY 3.1 0.6 + - - -
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Residues in contact with SER 309 (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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208A PRO* 3.2 17.3 - - - +
269A TYR* 3.3 36.4 + - - -
305A SER 2.9 9.2 + - - -
306A ALA* 2.6 21.6 + - - -
308A ALA* 1.3 76.9 - - - +
310A GLY* 1.3 56.0 + - - +
311A TRP* 3.0 24.3 + - - +
317A TRP* 3.3 28.2 + - - -
329A THR* 4.8 0.7 - - - -
336A ASP* 5.0 1.4 - - - +
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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
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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