Contacts of the helix formed by residues 269 - 284 (chain A) in PDB entry 5J3V
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 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A PRO* 3.5 27.6 - - + +
230A GLU* 5.8 0.2 - - - +
232A ARG* 4.6 0.9 - - - +
267A ASP* 3.0 7.2 + - - +
268A GLN* 1.3 79.4 - - + +
270A GLU* 1.3 67.8 + - - +
271A ASN* 3.0 25.3 + - - +
272A VAL* 3.1 28.3 + - + +
273A ALA* 3.1 11.4 + - - +
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ASP 5.1 1.1 - - - -
268A GLN 3.3 5.9 + - - +
269A ASP* 1.3 72.6 + - - +
271A ASN* 1.3 65.6 + - - +
273A ALA* 3.1 7.1 + - + +
274A LEU* 3.0 23.3 + - + +
311A SER* 5.3 12.8 + - - -
313A ILE* 5.2 9.4 - - - +
314A ASP* 5.5 1.2 - - - +
374A ASN* 5.6 1.7 - - - +
375A LEU* 4.1 35.9 + - + +
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Residues in contact with ASN 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLU* 4.8 3.8 + - - -
233A LYS* 3.7 37.3 - - + +
237A ARG* 5.3 0.2 + - - -
269A ASP* 3.0 18.1 + - - +
270A GLU* 1.3 81.0 - - - +
272A VAL* 1.3 61.4 + - + +
274A LEU* 3.5 16.3 + - - +
275A GLU* 3.6 17.5 + - - +
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PRO* 3.3 32.3 - - + +
232A ARG* 4.2 21.5 - - + +
233A LYS* 4.1 17.3 - - + +
236A CYS* 4.3 11.5 - - - -
264A ARG* 4.4 4.7 - - - +
267A ASP* 3.7 24.0 - - + +
269A ASP* 3.1 26.8 + - + +
271A ASN* 1.3 74.3 - - + +
273A ALA* 1.3 64.9 + - - +
274A LEU 3.3 0.2 + - - -
275A GLU* 3.3 4.5 + - - +
276A ALA* 3.1 20.6 + - - +
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Residues in contact with ALA 273 (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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264A ARG 3.3 15.2 + - - +
265A THR* 3.4 25.1 - - - +
267A ASP 4.3 7.6 - - - +
269A ASP 3.1 11.8 + - - +
270A GLU* 3.1 15.8 + - - +
272A VAL* 1.3 78.4 - - - +
274A LEU* 1.3 56.1 + - - +
276A ALA* 3.5 1.9 + - - +
277A CYS* 3.0 27.7 + - - +
375A LEU* 3.7 16.8 - - + +
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Residues in contact with LEU 274 (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 GLU* 3.0 11.9 + - + +
271A ASN* 3.8 14.1 - - - +
272A VAL 3.2 0.2 - - - -
273A ALA* 1.3 74.7 - - - +
275A GLU* 1.3 71.5 + - + +
277A CYS* 3.0 12.6 + - - +
278A GLU* 3.2 17.2 + - - +
373A TRP* 3.8 36.8 - - + +
374A ASN* 3.3 31.9 - - - +
375A LEU* 3.9 12.9 - - + +
378A CYS* 3.7 15.7 - - + -
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Residues in contact with GLU 275 (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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233A LYS* 4.2 18.4 - - + +
236A CYS* 4.4 7.6 - - + +
237A ARG* 3.1 57.0 + - - +
240A VAL* 3.7 20.8 - - - +
271A ASN* 3.6 14.3 + - - +
272A VAL* 3.3 8.8 + - - +
274A LEU* 1.3 82.5 - - + +
276A ALA* 1.3 61.2 + - - +
278A GLU* 3.4 35.6 + - - +
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Residues in contact with ALA 276 (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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236A CYS* 4.1 5.8 - - - +
261A MET* 4.1 20.4 - - - +
264A ARG* 3.5 46.4 - - + +
265A THR* 3.9 4.0 + - - +
272A VAL 3.1 10.8 + - - +
273A ALA 3.9 1.6 - - - +
275A GLU* 1.3 76.7 - - - +
277A CYS* 1.3 61.2 + - - +
278A GLU 3.3 0.2 - - - -
279A PHE* 3.3 18.1 - - - +
280A TRP* 3.8 10.4 + - - -
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Residues in contact with CYS 277 (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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265A THR* 4.4 7.4 - - + -
273A ALA 3.0 17.7 + - - +
274A LEU* 3.0 7.1 + - - +
276A ALA* 1.3 75.6 - - - +
278A GLU* 1.3 60.3 + - - +
279A PHE 3.0 6.2 + - - -
280A TRP* 3.3 31.0 + - - +
281A LEU 3.9 2.8 + - - -
304A LEU* 4.4 5.8 - - - -
375A LEU* 3.8 11.4 - - + -
378A CYS* 3.5 23.9 - - - -
379A SER* 3.4 33.9 - - - -
382A ALA* 4.8 2.0 - - - +
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Residues in contact with GLU 278 (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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240A VAL* 4.2 12.6 - - + +
274A LEU* 3.2 16.7 + - - +
275A GLU* 3.5 35.0 - - - +
276A ALA 3.3 0.6 - - - -
277A CYS* 1.3 75.2 - - - +
279A PHE* 1.3 62.3 + - - +
280A TRP 3.2 0.4 - - - -
281A LEU* 3.4 9.8 + - + +
282A THR* 3.1 27.3 + - - -
373A TRP* 3.3 27.0 + - + +
378A CYS* 3.7 17.0 - - - -
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Residues in contact with PHE 279 (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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239A LEU* 4.1 10.5 - - + -
240A VAL* 3.7 26.1 - - + +
243A LEU* 3.7 35.8 - - + +
250A LEU* 5.8 0.7 - - + -
254A MET* 4.9 5.6 - - + -
257A ILE* 3.7 30.1 - - + -
258A VAL* 4.8 6.3 - - + -
261A MET* 3.7 34.5 - - + -
276A ALA 3.3 15.9 + - - +
277A CYS 3.0 0.4 - - - -
278A GLU* 1.3 79.8 - - - +
280A TRP* 1.3 75.6 + + + +
282A THR* 3.4 2.0 + - - -
283A LEU* 2.9 52.2 + - + +
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Residues in contact with TRP 280 (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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258A VAL* 3.5 40.2 - - + -
261A MET* 3.8 10.8 - - + -
262A LEU* 3.7 29.6 - - + -
265A THR* 3.2 20.0 + - - +
276A ALA 3.8 5.3 + - - -
277A CYS* 3.3 27.5 + - - +
278A GLU 3.2 0.4 - - - -
279A PHE* 1.3 92.4 - + - +
281A LEU* 1.3 62.6 + - - +
283A LEU* 4.0 5.2 - - + +
284A ALA* 3.0 26.7 + - - +
293A LEU* 3.9 20.2 - - + +
300A LEU* 3.5 38.5 - - + +
304A LEU* 3.9 19.7 - - + -
382A ALA* 4.2 15.6 - - + +
386A LEU* 5.2 6.4 - - + +
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Residues in contact with LEU 281 (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 CYS 3.9 0.6 + - - -
278A GLU* 3.4 13.2 + - + +
279A PHE 3.4 0.4 - - - -
280A TRP* 1.3 79.6 - - - +
282A THR* 1.3 61.6 + - - +
284A ALA* 3.5 6.8 + - - +
285A GLU* 3.4 29.9 + - - +
373A TRP* 3.8 30.7 - - + -
378A CYS* 4.1 14.1 - - - +
381A ALA* 3.5 40.6 - - + +
382A ALA* 3.6 11.4 - - + +
385A VAL* 3.7 17.4 - - + +
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Residues in contact with THR 282 (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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240A VAL* 3.3 26.0 - - - +
243A LEU* 3.7 17.5 - - + -
244A GLU* 3.6 39.7 + - + +
278A GLU* 3.1 16.2 + - - +
279A PHE 3.8 4.0 - - - -
281A LEU* 1.3 79.4 - - - +
283A LEU* 1.3 63.0 + - - +
285A GLU* 3.3 18.9 + - - +
286A GLN* 3.6 12.2 + - - +
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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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243A LEU* 3.7 17.6 - - + +
247A MET* 4.6 3.1 - - + -
254A MET* 3.7 29.2 - - + -
258A VAL* 4.8 2.2 - - + -
279A PHE* 2.9 37.7 + - + +
280A TRP* 4.0 9.0 - - + +
281A LEU 3.4 0.2 - - - -
282A THR* 1.3 72.4 - - - +
284A ALA* 1.3 57.3 + - - +
285A GLU 3.0 10.1 + - - -
286A GLN* 3.1 23.3 + - + +
288A ILE* 4.9 3.1 - - + -
289A CYS* 3.1 25.8 - - + +
292A VAL* 5.3 2.5 - - + -
293A LEU* 3.7 38.6 - - + -
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Residues in contact with ALA 284 (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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280A TRP 3.0 18.9 + - - +
281A LEU* 3.9 4.0 - - - +
282A THR 3.2 0.8 - - - -
283A LEU* 1.3 75.7 - - - +
285A GLU* 1.3 59.3 + - - +
286A GLN 3.4 1.1 - - - +
289A CYS* 3.6 14.8 - - - +
382A ALA 5.3 0.9 - - - +
385A VAL* 3.6 29.0 - - + +
386A LEU* 3.9 24.2 - - + -
389A VAL* 3.6 20.7 - - + +
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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