Contacts of the helix formed by residues 360 - 374 (chain B) in PDB entry 2XWU
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 THR 360 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309B CYS* 3.6 27.4 - - - -
313B VAL* 3.8 7.0 - - + -
340B ILE* 3.6 28.9 - - + +
343B CYS* 4.0 5.4 - - + -
344B THR* 3.0 31.5 + - - +
356B THR 4.4 1.6 - - - +
357B SER 2.6 20.5 + - - +
359B LEU* 1.3 76.9 - - - +
361B LEU* 1.3 65.7 + - - +
362B THR 3.4 0.9 - - - -
363B PHE* 3.1 20.8 + - - +
364B TRP* 3.2 9.9 - - - -
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ARG* 3.7 14.8 - - - +
344B THR* 4.6 6.7 - - + -
357B SER 4.0 10.1 - - - +
358B SER* 3.7 21.7 + - - +
359B LEU 3.6 1.8 - - - -
360B THR* 1.3 76.6 - - - +
362B THR* 1.3 66.4 + - - +
363B PHE 2.9 1.0 + - - -
364B TRP* 3.1 17.1 + - + +
365B TYR* 3.6 6.2 + - - +
397B LEU* 4.0 26.7 - - + -
423B TYR* 4.4 12.1 - - + -
426B ASP* 3.7 32.3 - - + +
427B ILE* 4.3 12.1 - - + -
430B THR* 3.6 28.7 + - + +
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Residues in contact with THR 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LYS* 4.4 13.4 + - + +
17A ARG* 3.6 45.7 - - + +
18A LYS* 3.6 19.6 - - - +
313B VAL* 5.4 0.3 - - - +
317B GLU* 3.5 18.1 + - - -
358B SER 5.1 0.8 + - - -
359B LEU 4.4 4.5 + - - -
361B LEU* 1.3 77.5 - - - +
363B PHE* 1.3 64.4 + - - +
365B TYR* 3.0 21.0 + - - +
366B THR* 3.2 13.9 + - - -
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Residues in contact with PHE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B VAL* 5.1 5.8 - - + -
316B GLY* 3.5 23.3 - - - -
317B GLU* 3.0 36.6 - - + +
320B SER* 4.6 3.8 - - - -
333B PHE* 4.4 8.5 - + - -
337B VAL* 4.0 22.4 - - + -
340B ILE* 3.7 39.9 - - + -
360B THR* 3.1 17.1 + - - +
361B LEU 2.9 1.0 + - - -
362B THR* 1.3 80.3 + - - +
364B TRP* 1.3 95.3 + + - +
366B THR* 3.0 5.2 + - - -
367B LEU* 2.9 38.9 + - + -
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Residues in contact with TRP 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B VAL* 3.5 40.4 - - + -
340B ILE* 3.8 5.8 - - + -
341B MET* 3.6 36.8 - - + -
344B THR* 3.0 35.9 + - + +
360B THR* 3.2 24.3 + - - -
361B LEU* 3.1 12.3 + - + +
363B PHE* 1.3 91.4 - + - +
365B TYR* 1.3 62.7 + - - +
367B LEU* 4.0 12.8 - - + -
368B GLN* 3.5 4.5 + - - +
389B VAL* 4.4 9.0 - - + -
390B TYR* 2.6 33.3 + + + +
393B LEU* 3.6 37.0 - - + +
430B THR* 4.1 13.7 - - + -
433B TYR* 5.6 1.9 - - - +
434B VAL* 5.6 0.7 - - + -
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Residues in contact with TYR 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B LEU 3.6 4.4 + - - +
362B THR* 3.0 13.3 + - - +
363B PHE 3.0 1.2 - - - -
364B TRP* 1.3 81.0 - - - +
366B THR* 1.3 66.8 + - - +
368B GLN* 3.4 3.8 + - + +
369B ASP* 2.3 63.4 + - + +
430B THR* 5.5 1.9 - - + +
433B TYR* 3.5 61.5 - + + -
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Residues in contact with THR 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B GLU* 3.1 42.6 + - - +
320B SER* 3.7 15.3 - - - -
362B THR 3.2 2.8 + - - -
363B PHE* 3.0 8.9 + - + -
365B TYR* 1.3 85.6 - - - +
367B LEU* 1.3 68.0 + - - +
369B ASP* 3.1 5.2 + - - +
370B ASP* 2.9 44.0 + - - +
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Residues in contact with LEU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B SER* 4.9 2.5 - - - -
324B LEU* 4.2 11.9 - - + -
333B PHE* 4.1 26.5 - - + -
337B VAL* 4.2 8.7 - - + -
363B PHE* 2.9 30.5 + - + +
364B TRP* 4.0 19.3 - - + -
366B THR* 1.3 74.9 - - - +
368B GLN* 1.3 64.2 + - - +
370B ASP* 3.2 14.2 + - - +
371B ILE* 3.2 28.7 + - + +
386B TYR* 4.0 23.3 - - + -
390B TYR* 3.4 28.9 - - + +
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Residues in contact with GLN 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B TRP 3.6 7.9 - - - +
365B TYR* 3.4 4.6 + - + +
366B THR 3.3 0.4 - - - -
367B LEU* 1.3 74.3 - - - +
369B ASP* 1.3 57.9 + - - +
371B ILE* 3.2 2.5 + - - -
372B LEU* 2.6 35.1 + - + +
390B TYR* 2.8 29.6 + - + +
433B TYR* 5.3 9.6 - - + +
437B MET* 3.2 33.0 - - + +
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Residues in contact with ASP 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B ARG* 5.6 3.1 - - - -
365B TYR* 2.3 58.4 + - + +
366B THR* 3.5 5.4 - - - +
368B GLN* 1.3 76.1 - - - +
370B ASP* 1.3 65.1 + - - +
372B LEU* 3.5 9.5 + - - +
373B SER* 2.8 28.0 + - - -
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Residues in contact with ASP 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B SER* 3.1 17.0 - - - -
321B ARG* 3.0 58.3 + - + +
324B LEU* 3.6 17.3 - - + -
366B THR* 2.9 22.5 + - - +
367B LEU 3.5 7.4 - - - +
369B ASP* 1.3 78.3 - - - +
371B ILE* 1.3 66.1 + - - +
373B SER* 3.2 20.4 + - - -
374B PHE* 3.4 15.5 + - + -
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Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B LEU* 4.6 8.1 - - + -
367B LEU* 3.2 27.0 + - + +
368B GLN 3.2 5.4 + - - +
370B ASP* 1.3 77.3 - - - +
372B LEU* 1.3 64.5 + - - +
373B SER 3.1 1.0 + - - -
374B PHE* 3.1 23.3 + - + +
379B GLN* 3.5 28.3 - - + +
382B TYR* 4.0 18.4 - - + +
383B GLN* 4.2 19.1 - - - +
386B TYR* 3.5 42.8 - - + -
390B TYR* 5.2 0.9 - - + -
437B MET* 4.3 13.9 - - + -
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B GLN* 2.6 37.1 + - + +
369B ASP* 3.9 9.6 - - - +
370B ASP 3.4 0.2 - - - -
371B ILE* 1.3 78.9 - - + +
373B SER* 1.3 61.5 + - - +
374B PHE 3.3 7.6 - - - +
379B GLN* 3.8 21.9 + - - +
383B GLN* 4.5 11.9 - - - +
436B GLU* 5.1 12.8 - - + +
437B MET* 3.4 27.6 - - + +
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Residues in contact with SER 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B ARG* 3.3 30.4 + - - -
369B ASP* 2.8 24.1 + - - -
370B ASP 3.2 11.2 + - - -
371B ILE 3.0 0.8 - - - -
372B LEU* 1.3 73.5 - - - +
374B PHE* 1.3 71.2 + - - +
375B GLU* 3.7 3.3 + - - +
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Residues in contact with PHE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B ARG* 4.5 12.1 - - + -
324B LEU* 3.6 37.2 - - + -
325B ASP* 3.7 20.4 - - - -
370B ASP* 3.5 20.2 - - + -
371B ILE* 3.1 16.1 + - - +
372B LEU 3.3 3.5 - - - +
373B SER* 1.3 86.3 - - - +
375B GLU* 1.3 60.2 + - - +
378B LYS* 3.6 24.2 - - + +
379B GLN* 2.8 37.0 + - - +
382B TYR* 3.6 35.2 - + + -
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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