Contacts of the helix formed by residues 279 - 297 (chain A) in PDB entry 2YD0
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 ALA 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A VAL* 3.8 17.7 - - + -
269A VAL* 3.5 29.7 - - + +
275A LYS 4.2 0.4 + - - -
276A ILE* 3.1 23.2 + - + +
278A GLN* 1.3 77.1 - - - +
280A ASP* 1.3 64.3 + - - +
281A TYR 3.3 2.0 + - - -
282A ALA* 3.5 7.3 + - - +
283A LEU* 3.2 21.3 + - - +
333A LEU* 4.4 7.6 - - + +
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Residues in contact with ASP 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 4.4 17.8 - - - +
276A ILE 5.3 1.5 - - - +
277A ASN* 5.0 10.3 - - - +
278A GLN 3.4 2.2 - - - -
279A ALA* 1.3 77.9 - - - +
281A TYR* 1.3 63.7 + - - +
283A LEU* 3.4 9.3 + - - +
284A ASP* 3.2 33.5 + - - +
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Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLN 4.6 1.6 + - - +
279A ALA 3.3 0.6 - - - -
280A ASP* 1.3 79.3 - - - +
282A ALA* 1.3 64.9 + - - +
284A ASP* 3.4 8.7 + - + +
285A ALA* 3.1 24.9 + - + +
334A PHE* 4.0 37.7 + + + -
344A LYS* 3.4 55.5 + - + +
347A ILE* 4.0 20.2 - - + -
348A THR* 2.6 29.0 + - - -
391A HIS* 3.6 20.2 - + - -
394A LEU* 4.5 1.6 - - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A VAL* 4.5 7.4 - - + -
278A GLN 5.2 0.2 + - - -
279A ALA* 3.5 8.3 + - - +
281A TYR* 1.3 83.2 - - - +
283A LEU* 1.3 57.5 + - - +
285A ALA* 3.6 7.3 - - - +
286A ALA* 2.9 30.7 + - - +
308A LEU* 4.9 1.0 - - + +
332A LEU* 3.4 48.5 + - + +
347A ILE* 4.1 8.1 - - + -
351A VAL* 4.7 5.0 - - + +
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Residues in contact with LEU 283 (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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257A VAL* 3.6 27.4 - - + +
258A SER* 3.6 22.9 - - - +
259A LYS* 3.9 20.2 - - + +
267A VAL* 3.6 39.7 - - + +
268A SER* 4.3 4.3 - - - -
269A VAL* 4.0 12.7 - - + +
279A ALA 3.2 17.2 + - - +
280A ASP* 3.7 10.3 - - - +
282A ALA* 1.3 73.4 - - - +
284A ASP* 1.3 68.2 + - - +
286A ALA* 3.2 4.9 + - - +
287A VAL* 3.1 27.5 + - - +
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Residues in contact with ASP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LYS* 3.3 33.0 + - - +
280A ASP* 3.2 20.1 + - - +
281A TYR* 4.0 8.7 - - + +
283A LEU* 1.3 76.3 - - - +
285A ALA* 1.3 62.9 + - - +
287A VAL* 3.3 3.0 + - - +
288A THR* 3.1 27.7 + - - +
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Residues in contact with ALA 285 (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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281A TYR* 3.1 28.1 + - + +
282A ALA* 3.6 8.5 - - - +
283A LEU 3.2 0.2 - - - -
284A ASP* 1.3 78.6 - - - +
286A ALA* 1.3 56.9 + - - +
288A THR* 3.3 2.5 + - - -
289A LEU* 2.9 43.9 + - + +
347A ILE* 5.6 0.2 - - + -
348A THR* 5.0 4.3 - - + -
351A VAL* 4.9 8.5 - - + -
391A HIS* 4.2 26.7 - - + +
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Residues in contact with ALA 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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267A VAL* 3.8 23.6 - - + -
282A ALA 2.9 16.8 + - - +
283A LEU* 3.6 5.4 - - - +
285A ALA* 1.3 75.8 - - - +
287A VAL* 1.3 63.6 + - - +
290A LEU* 3.0 27.0 + - - +
306A GLN* 6.3 0.2 - - + -
308A LEU* 3.9 22.4 - - + -
351A VAL* 3.9 3.5 - - + +
355A LEU* 3.5 17.1 - - + +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LYS* 3.8 46.9 - - + +
260A ILE 4.7 2.2 - - - +
261A THR* 4.3 17.0 - - + +
267A VAL* 4.0 22.4 - - + -
283A LEU* 3.1 13.2 + - + +
284A ASP* 3.8 7.0 - - - +
285A ALA 3.2 0.2 - - - -
286A ALA* 1.3 76.4 - - - +
288A THR* 1.3 65.7 - - - +
290A LEU* 3.8 1.2 - - - +
291A GLU* 3.0 48.8 + - - +
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Residues in contact with THR 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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284A ASP* 3.1 18.3 + - - +
285A ALA* 3.8 5.4 - - - -
287A VAL* 1.3 80.6 - - - +
289A LEU* 1.3 57.1 + - - +
291A GLU* 3.5 9.5 + - - +
292A PHE* 3.0 25.8 + - - +
390A THR* 3.8 33.0 - - + +
391A HIS* 4.9 4.9 - - + -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ALA* 2.9 23.0 + - + +
288A THR* 1.3 74.4 - - - +
290A LEU* 1.3 66.6 + - - +
292A PHE* 3.0 4.9 + - - +
293A TYR* 3.0 34.1 + - + -
348A THR* 3.9 21.5 - - + +
351A VAL* 4.1 8.3 - - + -
352A ALA* 3.7 30.5 - - + +
355A LEU* 3.9 12.1 - - + -
386A SER* 3.5 33.0 - - - +
387A VAL* 4.5 1.3 - - + -
390A THR* 3.6 26.2 - - + +
391A HIS* 4.6 2.2 - - + -
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A THR* 3.9 23.3 - - + -
265A VAL* 4.1 25.8 - - + -
267A VAL* 4.4 7.2 - - + -
286A ALA 3.0 17.9 + - - +
287A VAL 3.8 3.4 - - - +
289A LEU* 1.3 75.1 - - - +
291A GLU* 1.3 63.4 + - - +
293A TYR* 3.2 5.3 + - - +
294A GLU* 3.1 31.4 + - + +
301A TYR* 4.2 23.6 - - + -
306A GLN* 4.9 5.6 - - + -
355A LEU* 3.9 32.3 - - + +
358A GLN* 5.0 0.4 - - + -
359A TRP* 4.2 21.7 - - + -
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Residues in contact with GLU 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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261A THR* 3.5 20.4 - - - -
262A LYS* 2.9 52.0 + - + +
287A VAL* 3.0 31.0 + - - +
288A THR* 3.7 7.5 - - - +
290A LEU* 1.3 73.2 - - - +
292A PHE* 1.3 65.3 + - - +
294A GLU* 3.5 14.2 + - - +
295A ASP* 3.3 21.5 + - - +
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Residues in contact with PHE 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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288A THR 3.0 14.8 + - - +
289A LEU* 3.3 8.7 - - - +
291A GLU* 1.3 79.2 - - - +
293A TYR* 1.3 71.0 + + - +
295A ASP* 3.1 7.3 + - - +
296A TYR* 2.8 61.2 + + + +
382A MET* 4.6 2.7 - - + -
385A VAL* 4.1 9.2 - - + -
386A SER* 3.6 34.8 - - - -
389A VAL* 3.8 32.5 - - + -
390A THR* 3.8 24.5 - - + -
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Residues in contact with TYR 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 LEU* 3.0 31.3 + - + +
290A LEU* 3.2 0.8 + - - +
292A PHE* 1.3 81.5 - + - +
294A GLU* 1.3 62.1 + - - +
295A ASP 3.0 1.8 - - - -
296A TYR* 4.2 2.5 - - + -
297A PHE* 2.9 58.8 + + + +
352A ALA 2.8 22.8 + - - -
355A LEU* 3.9 11.9 - - + -
356A ALA* 3.4 25.0 - - + +
359A TRP* 3.6 30.0 - + + -
382A MET* 3.7 32.5 + - + +
386A SER* 3.2 30.9 + - - -
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Residues in contact with GLU 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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261A THR* 5.1 0.7 - - - -
262A LYS* 5.8 0.3 - - - +
263A SER* 2.5 38.2 + - - -
265A VAL* 4.4 2.9 - - - +
290A LEU* 3.1 20.7 + - - +
291A GLU* 3.7 14.8 - - - +
292A PHE 3.3 0.2 - - - -
293A TYR* 1.3 76.4 - - - +
295A ASP* 1.3 59.7 + - - +
298A SER* 3.3 20.3 + - - -
299A ILE 3.5 13.4 + - - -
300A PRO* 3.6 14.6 - - + +
301A TYR* 2.8 42.1 + - + +
359A TRP* 4.0 7.4 - - + -
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Residues in contact with ASP 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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291A GLU 3.3 8.4 + - - +
292A PHE* 3.1 10.0 + - + +
293A TYR 3.0 0.2 - - - -
294A GLU* 1.3 80.2 - - - +
296A TYR* 1.3 66.4 + - - +
298A SER* 3.3 5.9 + - - -
458A LYS* 5.1 4.3 + - - -
1948A K 2.6 48.6 - - - -
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Residues in contact with TYR 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 PHE* 2.8 47.4 + + + +
293A TYR* 4.0 4.0 - - - +
295A ASP* 1.3 78.3 - - - +
297A PHE* 1.3 75.5 + + - +
298A SER* 3.6 1.9 + - - -
382A MET* 3.8 18.3 - - + -
385A VAL* 3.9 21.7 - - + +
449A ARG* 4.4 15.7 + - - -
454A ALA 4.7 1.6 + - - -
457A PHE* 4.5 5.0 - - - -
458A LYS* 3.7 66.2 + - + +
461A ILE* 3.9 25.3 - - + +
462A VAL* 4.1 3.1 - - - +
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Residues in contact with PHE 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A TYR* 2.9 50.3 + + - +
296A TYR* 1.3 92.9 - + - +
298A SER* 1.3 70.0 + - - +
299A ILE* 3.2 10.8 + - + +
356A ALA 4.8 3.4 - - - -
359A TRP* 3.3 51.6 - + + +
360A PHE* 3.7 30.3 - + - -
382A MET* 4.0 14.1 - - + -
461A ILE* 4.5 8.1 - - + -
462A VAL* 3.5 19.7 - - - +
465A LEU* 3.7 20.9 - - + -
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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
------------------------------------------------------------
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