Contacts of the helix formed by residues 280 - 293 (chain W) in PDB entry 5XTE
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 280 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7O ARG* 4.8 0.3 + - - -
276W ALA* 5.1 11.2 - - - -
277W VAL 5.6 0.2 - - - -
278W ALA* 3.1 7.4 + - - +
279W GLY* 1.3 82.5 - - - +
281W ALA* 1.3 64.4 + - - +
282W GLU* 2.9 27.4 + - - +
283W ALA* 3.2 19.2 + - - +
284W ASN* 3.4 14.6 + - - +
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Residues in contact with ALA 281 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279W GLY 3.9 1.0 + - - -
280W SER* 1.3 75.2 + - - +
282W GLU* 1.3 57.5 + - - +
284W ASN* 3.2 14.7 + - - +
285W ALA 2.9 22.2 + - - -
415W GLN 6.1 0.4 - - - +
418W SER* 6.0 1.3 - - - +
419W VAL* 4.5 7.0 - - + +
423W ASP* 3.1 19.3 - - - +
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Residues in contact with GLU 282 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276W ALA* 3.3 24.4 - - + +
280W SER* 2.9 14.9 + - - +
281W ALA* 1.3 79.6 - - - +
283W ALA* 1.3 55.9 + - - +
285W ALA* 3.0 11.1 + - + +
286W PHE* 2.9 47.3 + - + -
423W ASP* 3.9 11.1 + - - +
426W ASN* 5.5 1.5 - - + +
427W ALA* 5.2 5.1 - - + +
430W LYS* 3.2 35.6 + - - +
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Residues in contact with ALA 283 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O ARG* 2.8 38.1 + - - +
276W ALA 3.6 21.2 + - - +
277W VAL* 4.4 9.4 - - + -
278W ALA* 4.5 13.9 - - - -
279W GLY 4.6 0.2 - - - +
280W SER* 3.2 12.8 + - - +
282W GLU* 1.3 75.1 - - - +
284W ASN* 1.3 67.5 + - - +
286W PHE* 3.0 10.0 + - - +
287W SER 3.0 12.0 + - - -
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Residues in contact with ASN 284 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1O MET* 3.6 25.7 - - - +
7O ARG* 3.0 22.7 - - - +
279W GLY 5.3 1.9 - - - +
280W SER 3.4 14.0 - - - +
281W ALA* 3.2 13.4 + - - +
283W ALA* 1.3 77.7 - - - +
285W ALA* 1.3 56.6 + - - +
287W SER* 3.2 3.7 + - - -
288W VAL* 2.9 36.3 + - + +
378W LEU* 4.9 0.2 - - - +
415W GLN* 4.0 26.3 + - - +
416W ILE* 5.2 5.4 - - + +
419W VAL* 3.8 17.5 - - + -
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Residues in contact with ALA 285 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281W ALA 2.9 6.0 + - - -
282W GLU 3.0 13.0 + - - +
284W ASN* 1.3 77.9 - - - +
286W PHE* 1.3 55.8 + - - +
288W VAL* 3.9 2.4 - - - +
289W LEU* 2.9 27.5 + - - +
419W VAL* 4.5 9.6 - - + +
423W ASP* 3.4 50.7 - - + +
424W ILE* 4.2 6.1 - - - +
427W ALA* 4.1 8.2 - - + +
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Residues in contact with PHE 286 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274W GLU 4.6 2.7 - - - -
275W SER* 3.5 33.4 - - - -
276W ALA 4.1 4.7 - - - -
277W VAL* 6.0 0.4 - - + -
282W GLU* 2.9 61.2 + - + -
283W ALA* 3.0 11.6 + - - +
285W ALA* 1.3 74.1 - - - +
287W SER* 1.3 60.1 + - - +
289W LEU* 3.4 6.8 - - + +
290W GLN* 2.9 28.4 + - - +
327W ASN* 4.0 17.4 + - - +
336W PHE* 3.7 36.7 - + + -
427W ALA* 3.7 33.0 - - + -
430W LYS* 4.1 8.7 - - + -
431W PHE* 5.2 3.4 - - + -
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Residues in contact with SER 287 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1O MET* 5.1 4.0 - - - +
6O SER 5.7 0.2 - - - -
7O ARG* 2.3 43.9 + - - +
283W ALA 3.0 3.6 + - - -
284W ASN* 3.2 10.3 + - - -
286W PHE* 1.3 74.1 - - - +
288W VAL* 1.3 65.4 + - - +
290W GLN* 3.1 16.1 + - - +
291W HIS* 3.0 26.1 + - - -
327W ASN* 3.9 6.7 + - - +
378W LEU* 3.6 23.1 - - - -
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Residues in contact with VAL 288 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284W ASN* 2.9 21.7 + - + +
285W ALA* 4.1 3.8 - - - +
287W SER* 1.3 76.9 - - - +
289W LEU* 1.3 56.8 + - - +
291W HIS* 3.4 3.4 + - - +
292W VAL* 2.9 38.2 + - + +
371W VAL* 4.4 2.2 - - + -
374W ALA* 4.0 5.3 - - + +
375W LYS* 4.0 21.1 - - + +
378W LEU* 3.6 19.5 - - + -
416W ILE* 3.8 23.3 - - + -
419W VAL* 4.6 11.4 - - + -
424W ILE* 3.6 27.6 - - + -
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Residues in contact with LEU 289 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285W ALA 2.9 19.8 + - - +
286W PHE* 3.4 8.3 - - + +
287W SER 3.1 0.4 - - - -
288W VAL* 1.3 75.3 - - - +
290W GLN* 1.3 66.0 + - - +
292W VAL* 3.0 15.5 + - + +
293W LEU* 3.1 35.0 + - + +
336W PHE* 3.6 33.0 - - + -
358W VAL* 5.7 2.7 - - + -
361W ILE* 3.9 16.2 - - + -
424W ILE* 3.9 20.8 - - + +
427W ALA* 4.3 9.0 - - + +
428W ALA* 4.0 32.5 - - + +
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Residues in contact with GLN 290 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O ARG* 5.0 2.2 - - - +
8O SER* 3.9 29.9 + - - +
286W PHE 2.9 10.5 + - - +
287W SER* 3.1 23.3 - - - +
289W LEU* 1.3 77.4 - - - +
291W HIS* 1.3 79.3 + - + +
293W LEU* 3.1 5.5 + - - +
294W GLY 2.9 21.1 + - - -
295W ALA* 3.2 19.3 + - + +
325W ALA* 3.5 28.1 - - + +
326W PHE* 3.9 2.1 - - - -
327W ASN* 3.1 36.2 + - - +
336W PHE* 3.6 11.4 - - + -
378W LEU* 5.4 0.4 - - - +
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Residues in contact with HIS 291 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8O SER* 5.4 5.4 + - - -
287W SER 3.0 26.7 + - - +
288W VAL 4.0 2.9 - - - +
290W GLN* 1.3 95.9 + - + +
292W VAL* 1.3 62.5 + - - +
293W LEU 3.3 0.2 - - - -
294W GLY* 3.6 8.2 + - - +
295W ALA* 3.9 20.8 + - + +
296W GLY 5.6 1.3 - - - -
298W HIS* 5.5 5.5 + - - -
374W ALA* 3.4 31.5 - - + +
377W LYS* 4.0 35.2 + - + +
378W LEU* 3.2 33.9 - - + +
381W GLY* 6.3 1.1 - - - -
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Residues in contact with VAL 292 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288W VAL* 2.9 29.2 + - + +
289W LEU* 3.0 12.3 + - + +
291W HIS* 1.3 76.6 - - - +
293W LEU* 1.3 67.0 + - + +
294W GLY* 3.2 2.6 + - - -
306W THR 5.3 0.3 - - - +
307W SER* 4.9 2.3 - - - -
308W HIS* 3.3 35.2 + - + +
361W ILE* 4.8 7.2 - - + -
366W LEU* 4.2 20.0 - - + -
370W ASP* 4.6 6.5 - - + +
371W VAL* 4.5 17.7 - - + -
374W ALA* 3.7 15.7 - - + -
377W LYS* 5.7 1.4 + - - -
424W ILE* 4.9 6.5 - - + -
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Residues in contact with LEU 293 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289W LEU* 3.1 30.9 + - + +
290W GLN 3.1 9.8 + - - +
292W VAL* 1.3 80.2 - - + +
294W GLY* 1.3 57.6 + - - +
307W SER* 2.4 27.1 + - - -
308W HIS* 4.8 5.2 - - + +
309W LEU* 3.5 42.4 - - + +
325W ALA* 4.0 22.7 - - + -
336W PHE* 4.5 10.1 - - + -
338W ILE* 4.7 3.6 - - + -
357W GLN* 5.5 1.3 - - + -
358W VAL* 3.9 21.8 - - + -
361W ILE* 3.6 30.7 - - + -
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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