Contacts of the helix formed by residues 384 - 405 (chain A) in PDB entry 2PZI
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 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A VAL* 4.2 8.3 - - + -
328A ILE* 3.7 7.2 - - - +
382A PHE* 3.9 1.6 - - - +
383A THR* 1.3 91.2 - - + +
385A ALA* 1.3 59.2 + - - +
386A GLU* 3.6 8.0 + - - +
387A GLU* 2.9 28.0 + - - +
388A MET* 3.0 27.0 + - - +
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Residues in contact with ALA 385 (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* 3.9 25.3 - - + +
264A LEU* 4.4 2.0 - - + -
265A SER* 3.3 29.8 - - - +
268A HIS* 4.1 18.7 + - + +
324A VAL* 4.5 3.8 - - - +
328A ILE* 3.8 13.7 - - + +
384A THR* 1.3 73.6 - - - +
386A GLU* 1.3 55.8 + - - +
388A MET* 3.2 3.2 + - - +
389A SER* 2.8 29.7 + - - -
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Residues in contact with GLU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PRO* 6.4 0.4 - - + -
265A SER* 3.5 23.4 + - - +
384A THR* 3.3 8.3 + - - +
385A ALA* 1.3 75.1 - - - +
387A GLU* 1.3 64.4 + - - +
389A SER* 3.2 8.3 + - - -
390A ALA* 3.1 23.4 + - - +
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Residues in contact with GLU 387 (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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372A ARG* 2.9 29.4 + - - +
382A PHE* 3.7 6.8 - - + -
383A THR* 3.3 38.2 + - - -
384A THR* 2.9 21.5 + - - +
386A GLU* 1.3 73.6 - - - +
388A MET* 1.3 65.3 + - - +
390A ALA* 3.5 6.8 + - - +
391A GLN* 3.4 25.6 + - + +
414A ILE* 5.9 4.5 - - + -
566A PHE* 4.8 11.6 - - + -
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Residues in contact with MET 388 (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* 4.7 8.7 - - + -
328A ILE* 4.1 19.1 - - + -
331A VAL* 3.4 39.5 - - + -
332A GLY 4.4 1.6 - - - +
335A LEU* 4.6 3.4 - - + -
369A LEU* 3.8 22.8 - - + +
373A ALA* 3.7 25.8 - - + -
382A PHE* 3.7 33.6 - - + +
384A THR 3.0 14.0 + - - +
385A ALA* 3.2 8.7 + - - +
387A GLU* 1.3 76.7 - - - +
389A SER* 1.3 57.0 + - - +
391A GLN* 3.2 3.5 + - - +
392A LEU* 2.9 31.2 + - + +
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Residues in contact with SER 389 (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 LEU* 3.4 20.1 + - - +
261A LEU* 4.0 24.2 - - - +
262A PRO* 5.6 2.9 - - - +
385A ALA 2.8 17.2 + - - -
386A GLU* 3.2 11.0 + - - -
388A MET* 1.3 76.3 - - - +
390A ALA* 1.3 57.1 + - - +
392A LEU 3.2 0.2 + - - -
393A THR* 2.9 35.4 + - - -
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Residues in contact with ALA 390 (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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386A GLU 3.1 11.9 + - - +
387A GLU* 3.9 9.6 - - - +
388A MET 3.3 0.2 - - - -
389A SER* 1.3 76.9 - - - +
391A GLN* 1.3 67.6 + - - +
393A THR* 3.5 6.8 + - - -
394A GLY* 3.2 17.8 + - - -
413A THR* 3.7 30.3 - - + +
414A ILE* 6.2 0.4 - - + -
568A GLY 5.6 0.3 - - - +
569A GLU* 5.2 2.3 - - - +
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Residues in contact with GLN 391 (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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369A LEU* 3.9 15.3 - - + -
382A PHE* 3.8 20.6 - - + -
387A GLU* 3.4 15.0 + - + +
388A MET 3.2 7.7 + - - +
390A ALA* 1.3 82.5 - - - +
392A LEU* 1.3 58.0 + - - +
394A GLY 3.5 0.5 + - - -
395A VAL* 3.0 32.1 + - - +
414A ILE* 3.6 19.8 - - - +
566A PHE* 3.2 30.4 - - + +
567A PRO* 4.6 0.7 - - + -
568A GLY* 3.1 32.1 + - - +
569A GLU* 3.2 22.7 + - - -
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Residues in contact with LEU 392 (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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254A ILE* 3.6 45.5 - - + +
257A LEU* 4.6 3.8 - - + -
258A LEU* 4.0 14.6 - - + +
261A LEU* 3.9 25.1 - - + -
331A VAL* 5.2 0.2 - - + -
335A LEU* 3.9 19.7 - - + -
366A TYR* 5.0 0.9 - - + -
369A LEU* 3.9 31.8 - - + +
388A MET* 2.9 22.3 + - + +
389A SER 3.2 4.0 + - - +
391A GLN* 1.3 74.0 - - - +
393A THR* 1.3 56.0 + - - +
395A VAL* 3.4 4.0 + - + +
396A LEU* 2.8 34.3 + - - +
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Residues in contact with THR 393 (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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74A GLY 5.8 2.0 - - - +
77A LEU* 5.3 6.1 - - + -
258A LEU* 3.5 25.0 - - + +
389A SER* 2.9 19.5 + - - -
390A ALA* 3.6 7.6 - - - -
392A LEU* 1.3 72.8 - - - +
394A GLY* 1.3 59.1 - - - +
396A LEU* 3.2 3.4 + - - +
397A ARG* 2.9 63.8 + - + +
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Residues in contact with GLY 394 (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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390A ALA 3.2 11.0 + - - -
391A GLN 3.8 2.2 - - - -
392A LEU 3.4 0.2 - - - -
393A THR* 1.3 76.8 - - - +
395A VAL* 1.3 62.8 + - - +
397A ARG* 3.3 16.5 + - - +
398A GLU* 3.1 24.8 + - - +
568A GLY* 3.5 24.6 - - - +
598A THR* 5.3 0.2 - - - +
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Residues in contact with VAL 395 (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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254A ILE* 3.9 16.2 - - + -
365A SER* 3.5 32.5 - - - +
366A TYR* 3.7 33.0 - - + -
369A LEU* 4.3 11.9 - - + -
391A GLN 3.0 21.4 + - - +
392A LEU* 3.6 8.3 - - + +
394A GLY* 1.3 74.9 - - - +
396A LEU* 1.3 58.0 + - - +
398A GLU* 3.0 6.6 + - - +
399A VAL* 2.8 28.6 + - + +
567A PRO 4.1 0.2 - - - -
568A GLY* 3.8 16.1 - - - +
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Residues in contact with LEU 396 (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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74A GLY* 3.8 28.9 - - - -
77A LEU* 3.9 18.4 - - + -
78A VAL* 4.1 6.7 - - + -
251A ALA* 3.6 32.3 - - + +
254A ILE* 3.6 15.5 - - + -
255A ALA 4.5 3.6 - - - +
258A LEU* 3.9 16.2 - - + -
392A LEU 2.8 20.9 + - - +
393A THR* 3.5 6.7 - - + +
395A VAL* 1.3 72.1 - - - +
397A ARG* 1.3 59.2 + - - +
399A VAL* 3.2 4.9 + - + -
400A VAL* 2.8 52.9 + - + +
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Residues in contact with ARG 397 (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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77A LEU* 3.8 20.8 - - + +
393A THR* 2.9 42.2 + - - +
394A GLY* 3.5 14.3 - - - +
396A LEU* 1.3 76.2 - - - +
398A GLU* 1.3 57.0 + - - +
401A ALA* 3.0 32.9 + - - +
408A ARG* 3.4 37.2 - - + +
409A PRO 4.2 6.6 + - - -
410A GLY* 3.7 28.3 - - - +
411A LEU 4.5 6.9 + - - +
598A THR* 4.2 6.7 - - + -
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Residues in contact with GLU 398 (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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365A SER* 2.7 18.2 + - - +
394A GLY 3.1 15.2 + - - +
395A VAL 3.0 8.8 + - - +
397A ARG* 1.3 72.1 - - - +
399A VAL* 1.3 64.3 + - + +
401A ALA* 4.0 1.2 - - - +
402A GLN* 3.1 24.8 + - - +
567A PRO 4.5 0.9 - - - -
568A GLY 3.9 9.4 - - - +
570A LEU* 3.3 15.9 - - + +
573A LYS* 2.5 31.5 + - - -
594A THR* 4.2 4.3 - - + -
597A SER* 6.0 0.3 - - - -
598A THR* 3.5 30.3 + - + +
756A GOL 2.7 41.0 + - - +
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Residues in contact with VAL 399 (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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250A VAL* 3.5 35.0 - - + -
251A ALA* 3.8 22.9 - - + +
254A ILE* 4.4 2.2 - - + -
363A TYR* 3.7 33.9 - - + -
365A SER* 5.7 0.7 - - - +
366A TYR* 4.7 0.7 - - + -
395A VAL* 2.8 31.9 + - + +
396A LEU* 3.6 7.0 - - + +
398A GLU* 1.3 75.8 - - + +
400A VAL* 1.3 67.3 + - - +
402A GLN* 3.2 3.3 + - - +
403A ASP* 3.0 31.6 + - - +
756A GOL 5.8 1.6 - - - +
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Residues in contact with VAL 400 (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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77A LEU* 4.0 28.7 - - + +
78A VAL* 4.6 0.2 - - + -
251A ALA* 4.1 13.0 - - + -
396A LEU* 2.8 45.6 + - + +
397A ARG* 4.2 2.0 - - - +
399A VAL* 1.3 71.4 - - - +
401A ALA* 1.3 54.6 + - - +
403A ASP* 3.1 8.2 - - - +
404A THR* 2.8 47.6 + - + -
408A ARG* 3.6 34.1 - - + +
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Residues in contact with ALA 401 (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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397A ARG 3.0 20.2 + - - +
398A GLU 4.0 3.4 - - - +
400A VAL* 1.3 75.5 - - - +
402A GLN* 1.3 58.5 + - - +
405A GLY* 2.9 29.5 + - - -
406A VAL 3.2 24.8 + - - +
408A ARG* 3.7 7.1 - - + +
597A SER* 3.4 25.6 - - - +
598A THR* 3.8 13.0 - - - +
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Residues in contact with GLN 402 (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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362A THR* 3.1 31.2 + - - +
363A TYR* 3.8 18.0 + - + -
398A GLU 3.1 18.5 + - - +
399A VAL* 3.6 4.9 - - - +
400A VAL 3.2 0.2 - - - -
401A ALA* 1.3 78.5 - - - +
403A ASP* 1.3 62.4 + - - +
405A GLY* 4.0 4.3 + - - -
597A SER* 5.1 10.7 - - - +
756A GOL 3.1 23.3 + - - +
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Residues in contact with ASP 403 (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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251A ALA* 4.9 6.1 - - - +
363A TYR* 2.9 26.8 + - + +
399A VAL* 3.0 28.1 + - - +
400A VAL* 3.1 16.8 - - - +
402A GLN* 1.3 79.6 - - + +
404A THR* 1.3 64.8 + - - +
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Residues in contact with THR 404 (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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400A VAL* 2.8 41.9 + - + +
403A ASP* 1.3 79.2 - - - +
405A GLY* 1.3 62.7 + - - +
406A VAL* 3.2 18.2 + - - +
408A ARG* 3.2 22.5 + - - +
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Residues in contact with GLY 405 (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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401A ALA 2.9 14.1 + - - -
402A GLN 4.0 3.4 + - - -
403A ASP 3.7 1.4 - - - -
404A THR* 1.3 78.9 - - - +
406A VAL* 1.3 61.7 + - - +
407A PRO* 4.4 3.5 - - - +
597A SER 5.6 0.9 - - - -
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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