Contacts of the helix formed by residues 269 - 281 (chain A) in PDB entry 4E2I
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 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A GLN 3.9 2.3 + - - -
268A VAL* 1.3 72.2 - - - +
270A TRP* 1.3 62.0 + - - +
271A LYS* 3.7 6.9 + - - +
272A LEU* 3.3 42.2 + - - +
273A VAL* 3.3 9.2 + - - +
323A ASN* 2.6 33.5 + - - -
336A ILE* 4.6 1.4 - - - +
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Residues in contact with TRP 270 (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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268A VAL* 3.6 23.7 - - + +
269A SER* 1.3 72.1 + - - +
271A LYS* 1.3 58.2 + - - +
272A LEU 3.2 1.8 - - - -
273A VAL* 3.3 2.8 + - - +
274A THR* 2.8 38.5 + - - -
332A ASN* 5.1 8.3 - - + -
335A THR* 3.6 32.8 - - + -
336A ILE* 3.6 46.8 - - + +
339A GLN* 3.2 40.6 - - + +
328B ALA 5.8 1.8 - - - +
329B ASP* 6.2 2.9 - - - -
330B SER 5.0 5.6 - - - +
331B LYS* 3.3 64.8 - - + +
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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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269A SER* 3.5 6.2 + - - +
270A TRP* 1.3 80.5 - - - +
272A LEU* 1.3 58.7 + - + +
274A THR* 3.7 7.2 - - - -
275A GLU* 2.9 39.2 + - + +
296B GLN* 4.2 21.5 - - - +
297B TYR* 6.2 1.0 - - - -
328B ALA* 4.4 22.5 + - + +
329B ASP* 4.0 26.0 - - - +
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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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269A SER* 3.3 23.0 + - - +
270A TRP 3.2 0.4 - - - -
271A LYS* 1.3 78.6 - - + +
273A VAL* 1.3 59.9 + - - +
275A GLU* 3.1 19.7 + - - +
276A TYR* 3.0 24.3 + - - +
292A TYR* 4.1 0.4 - - - +
319A LYS* 4.9 8.5 - - + +
320A HIS* 3.2 28.7 - - - +
322A ALA* 5.8 3.1 - - + -
323A ASN* 3.5 36.1 - - + +
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A SER 3.3 9.4 - - - +
270A TRP 3.3 4.9 + - - +
272A LEU* 1.3 74.8 - - - +
274A THR* 1.3 57.6 + - - +
276A TYR* 3.4 4.5 + - - +
277A ALA* 3.0 26.0 + - - +
288A LEU* 5.1 4.4 - - + +
292A TYR* 3.5 31.0 - - + -
323A ASN* 3.2 26.2 - - - +
327A PHE* 4.7 2.2 - - + -
336A ILE* 3.6 33.7 - - + +
337A CYS* 4.2 24.2 - - - -
340A ALA* 4.4 4.0 - - + -
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Residues in contact with THR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A TRP 2.8 22.4 + - - -
271A LYS* 3.7 8.6 - - - -
273A VAL* 1.3 74.4 - - - +
275A GLU* 1.3 61.5 + - - +
277A ALA* 3.2 2.3 + - - +
278A MET* 2.9 30.1 + - + +
336A ILE 5.3 1.4 + - - -
339A GLN* 4.2 12.6 + - - -
340A ALA* 3.9 17.3 + - - +
343A THR* 3.6 40.2 + - + +
333B GLN* 5.1 7.8 + - - +
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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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271A LYS* 2.9 28.5 + - + +
272A LEU* 3.2 27.4 - - - +
274A THR* 1.3 76.3 - - - +
276A TYR* 1.3 62.1 + - - +
278A MET* 3.1 10.0 + - + +
279A GLU* 3.0 35.0 + - + +
319A LYS* 3.2 36.0 + - - -
320A HIS* 3.9 4.9 - - + -
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Residues in contact with TYR 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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272A LEU 3.0 8.9 + - - +
273A VAL* 3.4 7.8 + - + +
275A GLU* 1.3 75.9 - - - +
277A ALA* 1.3 60.4 - - - +
279A GLU* 3.2 6.9 + - - +
280A THR* 3.1 46.7 + - + +
288A LEU* 4.1 23.1 - - + -
291A MET* 3.8 22.8 - - + +
292A TYR* 3.6 20.6 - + + -
295A PHE* 3.8 20.0 - + - -
312A SER* 2.7 36.7 + - - -
316A TYR* 3.6 33.4 - + + -
320A HIS* 3.2 26.0 + + + +
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Residues in contact with ALA 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 VAL 3.0 13.5 + - - +
274A THR 3.3 9.6 - - - +
275A GLU 3.1 0.2 - - - -
276A TYR* 1.3 77.6 - - - +
278A MET* 1.3 53.0 + - + +
280A THR* 4.2 1.1 - - - -
281A LYS* 2.8 34.7 + - - -
282A CYS 3.3 3.7 + - - +
288A LEU* 3.8 19.3 - - + -
340A ALA* 3.6 24.5 - - + +
344A VAL* 3.7 20.0 - - + +
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Residues in contact with MET 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 THR* 2.9 22.1 + - + +
275A GLU* 3.1 9.4 + - + +
277A ALA* 1.3 75.7 - - + +
279A GLU* 1.3 66.6 + - - +
281A LYS* 3.6 16.9 - - - +
343A THR* 3.5 46.9 - - + +
344A VAL* 4.3 7.9 - - - -
347A LYS* 3.9 33.2 - - + +
293B LEU* 6.1 1.1 - - + -
297B TYR* 5.4 7.0 - - - +
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Residues in contact with GLU 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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275A GLU* 3.0 30.4 + - + +
276A TYR* 3.3 9.4 - - - +
277A ALA 3.1 0.2 - - - -
278A MET* 1.3 82.1 - - - +
280A THR* 1.3 62.1 + - - +
281A LYS* 3.0 15.2 + - - +
316A TYR* 3.5 44.9 + - + +
319A LYS* 5.5 6.5 - - - -
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Residues in contact with THR 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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276A TYR* 3.1 40.1 + - + +
277A ALA* 3.8 1.7 + - - -
279A GLU* 1.3 77.5 - - - +
281A LYS* 1.3 71.3 + - - +
282A CYS* 3.1 20.4 + - - +
312A SER* 3.6 32.3 - - - -
316A TYR* 4.6 7.9 - - + +
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Residues in contact with LYS 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 ALA 2.8 12.7 + - - -
278A MET* 3.6 11.4 - - - +
279A GLU 3.0 14.3 - - - +
280A THR* 1.3 79.4 - - - +
282A CYS* 1.3 64.3 + - - +
283A ASP* 3.1 11.1 + - - +
344A VAL* 3.6 13.5 - - + +
348A LYS* 3.7 18.6 + - - +
363A ASN* 5.7 3.6 - - - +
367A ASP* 3.5 30.8 + - - -
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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