Contacts of the helix formed by residues 285 - 306 (chain A) in PDB entry 1DJ9
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 SER 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A ALA 3.2 17.6 + - - -
282A VAL* 2.9 14.4 + - - -
284A ARG* 1.3 81.0 - - - +
286A ASP* 1.3 56.4 + - - +
287A GLU* 2.6 25.6 + - - +
288A GLY* 2.8 18.9 + - - -
289A ASP* 3.2 14.9 + - - +
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Residues in contact with ASP 286 (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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285A SER* 1.3 74.0 + - - +
287A GLU* 1.3 63.7 + - - +
289A ASP* 3.2 16.5 + - - +
290A ALA* 3.0 22.1 + - - +
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Residues in contact with GLU 287 (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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55A HIS* 3.0 29.8 + - - -
57A GLN* 4.5 5.7 + - - -
282A VAL* 4.0 8.3 - - + +
285A SER* 2.6 17.7 + - - +
286A ASP* 1.3 74.3 - - - +
288A GLY* 1.3 54.0 + - - +
290A ALA* 3.2 8.6 + - + +
291A ARG* 2.6 71.3 + - + +
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Residues in contact with GLY 288 (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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50A LEU* 5.0 2.9 - - - +
282A VAL* 3.1 21.2 + - - -
283A ILE* 3.7 6.1 - - - -
285A SER* 2.8 19.7 + - - -
287A GLU* 1.3 72.4 - - - +
289A ASP* 1.3 53.8 + - - -
291A ARG* 3.4 6.9 + - - +
292A ARG* 3.0 44.9 + - - +
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Residues in contact with ASP 289 (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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215A GLN* 4.6 5.4 + - - -
284A ARG 5.5 0.9 - - - +
285A SER 3.2 9.4 + - - +
286A ASP* 3.2 18.0 + - - +
288A GLY* 1.3 73.0 - - - +
290A ALA* 1.3 67.7 + - - +
292A ARG* 2.5 42.7 + - - +
293A GLU* 2.9 26.4 + - - +
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Residues in contact with ALA 290 (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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286A ASP 3.0 10.6 + - - +
287A GLU* 3.2 13.7 + - + +
289A ASP* 1.3 78.6 - - - +
291A ARG* 1.3 59.7 + - + +
293A GLU* 3.7 5.3 - - - +
294A LYS* 2.9 31.1 + - - +
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Residues in contact with ARG 291 (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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50A LEU* 2.7 50.5 + - + -
51A GLY* 3.7 14.8 + - - -
52A LEU* 3.8 21.2 - - - +
55A HIS* 4.1 9.1 - - - +
56A PRO* 5.9 1.6 - - - +
282A VAL* 4.5 3.8 - - - -
287A GLU* 2.6 52.2 + - + +
288A GLY* 3.6 5.8 - - - +
290A ALA* 1.3 78.2 - - + +
292A ARG* 1.3 56.9 + - - +
294A LYS* 3.5 2.6 + - - -
295A LEU* 2.9 25.8 + - - +
366A ALA* 3.5 28.9 + - + +
367A ALA* 5.2 1.8 - - - +
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Residues in contact with ARG 292 (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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50A LEU* 4.0 11.6 - - + +
210A GLY 3.4 24.4 + - - +
211A VAL 3.5 24.2 - - - +
212A ILE* 4.6 0.7 - - - +
213A GLY 4.2 9.7 + - - -
214A GLU* 5.5 0.2 - - - +
215A GLN* 3.7 6.1 - - - +
216A GLY* 3.4 27.5 - - - +
283A ILE* 2.5 28.9 + - - +
284A ARG* 4.4 0.8 - - - +
285A SER 3.9 2.0 + - - -
288A GLY* 3.0 27.6 + - - +
289A ASP* 2.5 45.6 + - - +
291A ARG* 1.3 76.9 - - - +
293A GLU* 1.3 57.3 + - - +
295A LEU* 3.4 4.2 + - - +
296A ALA* 2.9 27.9 + - - +
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Residues in contact with GLU 293 (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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289A ASP 2.9 17.0 + - - +
290A ALA* 3.7 5.6 - - - +
292A ARG* 1.3 75.7 - - - +
294A LYS* 1.3 60.7 + - - +
296A ALA* 3.1 12.7 + - - +
297A ALA* 2.7 32.7 + - - +
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Residues in contact with LYS 294 (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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290A ALA 2.9 17.1 + - - +
291A ARG* 3.9 5.8 - - - +
293A GLU* 1.3 77.2 - - - +
295A LEU* 1.3 63.3 + - - +
297A ALA* 3.0 10.8 + - + +
298A LEU* 2.8 43.3 + - + +
366A ALA* 2.9 24.8 + - + +
367A ALA* 4.3 2.2 - - - +
368A HIS 2.6 29.0 + - - +
369A GLU* 3.2 28.7 + - - +
370A MET* 6.3 1.6 - - - -
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Residues in contact with LEU 295 (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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49A TYR* 3.3 22.0 - - + +
50A LEU* 4.3 5.4 - - + -
211A VAL* 4.0 23.6 - - + +
291A ARG 2.9 19.1 + - - +
292A ARG* 3.7 5.4 - - - +
294A LYS* 1.3 75.9 - - - +
296A ALA* 1.3 59.0 + - - +
298A LEU* 3.2 6.9 + - + +
299A ILE* 2.9 52.2 + - + +
319A ALA* 3.9 19.1 - - + -
364A LEU* 3.9 31.0 - - + +
365A THR 4.0 7.4 - - - +
366A ALA* 4.3 7.9 - - + +
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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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292A ARG 2.9 14.4 + - - +
293A GLU* 3.1 19.5 + - - +
295A LEU* 1.3 75.6 - - - +
297A ALA* 1.3 61.7 + - - +
299A ILE* 3.4 12.0 + - - +
300A THR* 2.9 30.7 + - - +
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Residues in contact with ALA 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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293A GLU* 2.7 24.3 + - - +
294A LYS* 3.3 14.6 - - + +
296A ALA* 1.3 72.6 - - - +
298A LEU* 1.3 66.3 + - + +
300A THR* 3.3 9.3 - - - +
301A ARG* 3.0 22.2 + - - +
370A MET* 6.4 2.5 - - - -
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Residues in contact with LEU 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 LYS* 2.8 32.7 + - + +
295A LEU* 3.5 9.4 - - + +
297A ALA* 1.3 75.9 - - + +
299A ILE* 1.3 58.8 + - - +
301A ARG* 3.0 7.6 + - - +
302A PHE* 2.8 31.4 + - - +
364A LEU* 4.1 6.9 - - + +
365A THR 3.3 28.0 - - - +
368A HIS* 3.7 22.4 - - + +
369A GLU* 3.9 1.6 - - - -
370A MET* 3.8 32.8 - - + +
373A ILE* 3.7 28.8 - - + +
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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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211A VAL* 6.5 0.2 - - + -
295A LEU* 2.9 42.5 + - + +
296A ALA* 3.4 10.5 + - + +
298A LEU* 1.3 69.9 - - - +
300A THR* 1.3 54.4 + - - +
302A PHE* 3.1 2.8 + - - +
303A ARG* 2.8 50.0 + - - +
317A CYS* 3.5 20.9 - - - +
318A SER* 3.4 31.0 - - - +
319A ALA* 3.6 7.2 - - - +
321A GLN* 3.7 18.6 - - - +
364A LEU* 3.9 17.0 - - + +
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Residues in contact with THR 300 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A ALA* 2.9 15.3 + - - +
297A ALA* 3.3 13.4 - - - -
299A ILE* 1.3 79.1 - - - +
301A ARG* 1.3 57.3 - - - +
303A ARG* 3.8 6.0 - - - +
304A ALA* 2.8 33.1 + - + +
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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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297A ALA 3.0 10.2 + - - +
298A LEU* 3.0 14.5 + - - +
300A THR* 1.3 80.3 - - - +
302A PHE* 1.3 67.2 + - - +
304A ALA* 4.0 3.8 - - - +
305A GLY* 3.1 18.5 + - - -
370A MET* 3.2 58.1 - - - +
373A ILE* 4.3 11.4 - - + -
374A ASP* 2.9 37.9 + - - +
377A LEU* 3.9 5.6 - - + +
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Residues in contact with PHE 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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298A LEU 2.8 14.5 + - - +
299A ILE 3.6 1.1 - - - +
301A ARG* 1.3 78.6 - - - +
303A ARG* 1.3 59.8 + - - +
305A GLY* 3.0 16.8 + - - -
306A VAL* 3.1 36.9 + - + +
313A LEU* 4.9 4.9 - - + -
321A GLN* 3.9 42.4 - - + -
323A LEU* 5.5 7.9 - - + -
362A LEU* 3.9 17.3 - - + -
364A LEU* 3.6 17.7 - - + -
373A ILE* 3.8 16.7 - - + +
376A LEU* 3.9 20.9 - - + -
377A LEU* 3.8 11.7 - - + +
380A LEU* 3.9 25.4 - - + -
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Residues in contact with ARG 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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299A ILE* 2.8 32.3 + - - +
300A THR* 3.8 5.8 - - - +
302A PHE* 1.3 73.8 - - - +
304A ALA* 1.3 66.9 + - - +
305A GLY 3.2 0.2 + - - -
306A VAL* 3.3 7.7 + - - -
307A GLN* 3.6 6.4 - - - +
313A LEU* 3.6 57.6 + - + +
315A ASP* 3.4 24.4 + - - +
316A SER 2.8 45.8 + - - +
317A CYS* 4.8 11.9 - - - +
321A GLN* 3.9 10.7 + - - +
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Residues in contact with ALA 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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300A THR* 2.8 25.7 + - + +
301A ARG* 4.0 4.5 - - - +
303A ARG* 1.3 73.6 - - - +
305A GLY* 1.3 61.0 + - - +
307A GLN* 2.9 41.6 - - - +
308A ASP* 4.4 4.3 - - - +
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Residues in contact with GLY 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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301A ARG 3.1 9.6 + - - -
302A PHE 3.0 9.3 + - - -
304A ALA* 1.3 79.4 - - - +
306A VAL* 1.3 59.1 + - - +
307A GLN 3.1 1.7 + - - -
308A ASP* 3.5 20.5 + - - +
309A LEU* 4.3 0.2 - - - +
377A LEU* 3.7 23.1 - - - -
381A HIS* 3.8 17.2 + - - -
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Residues in contact with VAL 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 PHE* 3.1 38.5 + - + +
303A ARG 3.7 4.3 - - - +
304A ALA 3.2 0.4 - - - -
305A GLY* 1.3 74.1 - - - +
307A GLN* 1.3 63.5 + - - +
308A ASP 3.4 0.4 - - - -
309A LEU* 3.1 45.1 + - + +
311A PHE* 5.3 10.2 + - + +
312A THR 5.1 1.3 - - - +
313A LEU* 3.4 49.6 - - + +
323A LEU* 5.7 6.7 - - + -
377A LEU* 4.8 0.4 - - + -
380A LEU* 5.1 1.3 - - + -
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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