Contacts of the helix formed by residues 267 - 282 (chain A) in PDB entry 4JU5
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 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A VAL 3.7 0.4 + - - -
266A SER* 1.3 79.8 + - - +
268A TYR* 1.3 65.0 + - - +
269A ASP 3.5 0.9 - - - -
270A GLY* 3.3 26.5 + - - -
271A LYS* 3.0 34.7 + - - +
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Residues in contact with TYR 268 (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 LEU* 3.4 33.8 + - + +
262A PRO 3.5 17.3 - - - -
263A LYS* 3.7 47.8 - - + +
265A VAL* 3.7 19.0 + - + +
266A SER 3.4 0.4 - - - -
267A ASP* 1.3 74.9 - - - +
269A ASP* 1.3 82.9 + - - +
271A LYS* 3.3 4.9 + - - +
272A LEU* 2.9 39.0 + - + +
290A PHE* 3.5 26.7 - - - -
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Residues in contact with ASP 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ASP 3.5 0.2 - - - -
268A TYR* 1.3 93.3 - - - +
270A GLY* 1.3 55.7 + - - +
272A LEU* 3.6 20.2 - - - +
273A SER* 2.7 33.4 + - - -
276A LYS* 5.1 7.4 + - - +
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Residues in contact with GLY 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ASP* 3.3 28.1 + - - -
268A TYR 3.3 0.6 - - - -
269A ASP* 1.3 78.1 - - - +
271A LYS* 1.3 61.8 + - - +
273A SER* 3.4 8.4 + - - -
274A ASN* 3.4 27.6 + - - +
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Residues in contact with LYS 271 (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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259A LEU* 4.5 4.1 - - + +
261A LEU* 3.8 18.8 - - + -
265A VAL* 3.9 25.8 - - + -
266A SER* 2.7 27.7 + - - +
267A ASP* 3.0 29.6 + - - +
268A TYR 3.6 3.8 - - - +
270A GLY* 1.3 73.3 - - - +
272A LEU* 1.3 64.8 + - - +
273A SER 3.2 0.4 + - - -
274A ASN* 3.5 11.7 + - - +
275A PHE* 3.5 18.0 + - - +
313A PRO* 4.5 13.2 - - + -
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Residues in contact with LEU 272 (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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237A VAL* 4.1 11.7 - - + -
261A LEU* 3.9 13.9 - - + +
268A TYR* 2.9 31.8 + - + +
269A ASP* 3.8 22.4 - - - +
271A LYS* 1.3 75.0 - - - +
273A SER* 1.3 62.0 + - - +
275A PHE* 3.4 11.5 + - + +
276A LYS* 3.2 43.6 + - - +
290A PHE* 3.9 47.3 - - + -
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Residues in contact with SER 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ASP 2.7 18.8 + - - -
270A GLY* 3.4 12.3 - - - -
271A LYS 3.2 0.2 - - - -
272A LEU* 1.3 75.1 - - - +
274A ASN* 1.3 62.4 + - - +
276A LYS* 3.2 17.7 + - - +
277A THR* 3.0 32.8 + - - -
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Residues in contact with ASN 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLY 3.4 16.9 + - - +
271A LYS* 3.8 12.4 - - - +
272A LEU 3.4 0.4 - - - -
273A SER* 1.3 78.6 - - - +
275A PHE* 1.3 57.4 + - - +
277A THR* 3.2 10.7 + - - -
278A ALA* 3.0 29.8 + - - +
337B GLU* 3.8 33.9 - - + +
339B ILE* 4.6 2.5 - - + -
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Residues in contact with PHE 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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237A VAL* 3.4 34.3 - - + -
257A ILE* 3.9 17.5 - - + -
259A LEU* 3.6 44.9 - - + -
271A LYS 3.5 5.3 + - - +
272A LEU* 3.4 12.5 + - + +
274A ASN* 1.3 77.9 - - - +
276A LYS* 1.3 56.9 + - - +
279A ALA* 3.0 26.0 + - - +
288A PHE* 3.4 37.7 - + + -
289A ILE 3.3 38.6 - - - -
290A PHE* 4.1 0.9 - - + -
315A VAL* 5.3 2.5 - - + -
339B ILE* 3.5 24.0 - - + +
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Residues in contact with LYS 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 LEU* 4.1 3.0 - - + +
237A VAL* 3.6 28.7 - - + -
269A ASP* 5.1 7.1 + - - +
272A LEU* 3.2 41.8 + - - +
273A SER* 3.2 16.8 + - - +
275A PHE* 1.3 75.2 - - - +
277A THR* 1.3 63.5 + - - +
279A ALA* 3.0 12.3 + - - +
280A GLU* 3.1 23.9 + - - +
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Residues in contact with THR 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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273A SER* 3.0 17.6 + - - -
274A ASN* 3.2 13.4 + - - -
276A LYS* 1.3 75.4 - - - +
278A ALA* 1.3 59.8 + - - +
280A GLU* 3.3 25.4 - - + +
281A SER* 3.9 6.8 + - - -
337B GLU* 5.0 8.7 - - + -
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Residues in contact with ALA 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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274A ASN 3.0 9.4 + - - +
275A PHE 4.0 0.2 - - - +
277A THR* 1.3 73.4 - - - +
279A ALA* 1.3 64.2 + - - +
280A GLU 3.1 0.9 - - - -
281A SER* 3.1 13.7 + - - -
282A PHE* 3.4 19.4 - - - -
288A PHE* 3.7 9.9 - - + -
337B GLU* 4.7 3.1 - - + +
339B ILE* 3.6 34.1 - - + -
340B THR* 3.6 26.9 - - - +
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Residues in contact with ALA 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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236A LEU* 3.5 31.7 - - + +
237A VAL* 3.9 7.2 - - + -
275A PHE 3.0 16.5 + - - +
276A LYS* 3.0 15.4 + - - +
278A ALA* 1.3 73.3 - - - +
280A GLU* 1.3 62.6 + - - +
281A SER 3.3 0.2 - - - -
282A PHE 3.5 1.7 + - - -
283A LYS* 3.3 18.7 + - - -
288A PHE* 3.6 29.6 - - + -
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Residues in contact with GLU 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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236A LEU* 3.4 22.7 - - - +
276A LYS* 3.1 17.3 + - - +
277A THR* 3.3 18.2 - - + +
278A ALA 3.1 0.2 - - - -
279A ALA* 1.3 78.9 - - - +
281A SER* 1.3 61.6 + - - +
282A PHE 3.2 1.4 + - - -
283A LYS* 3.6 13.7 + - - +
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Residues in contact with SER 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 THR 3.9 8.3 + - - -
278A ALA* 3.1 13.3 + - - -
280A GLU* 1.3 77.2 - - - +
282A PHE* 1.3 81.6 + - - +
340B THR* 4.3 13.8 + - - +
344B HIS* 6.2 0.4 - - - -
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Residues in contact with PHE 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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278A ALA 3.4 14.6 - - - -
279A ALA 3.5 4.6 + - - -
280A GLU 3.2 0.6 - - - -
281A SER* 1.3 87.9 - - - +
283A LYS* 1.3 61.9 + - - +
285A LYS* 2.8 30.7 + - + -
286A ILE* 2.8 40.5 + - + +
288A PHE* 4.0 17.5 - + + -
340B THR* 3.6 33.9 - - + -
343B CYS* 3.5 35.7 - - + -
344B HIS* 3.7 33.4 - + - -
347B LEU* 4.4 11.7 - - + -
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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