Contacts of the helix formed by residues 384 - 405 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B VAL* 4.3 6.3 - - + -
328B ILE* 4.0 7.6 - - - +
382B PHE* 4.1 1.4 - - - +
383B THR* 1.3 92.6 - - + +
385B ALA* 1.3 63.8 + - - +
386B GLU* 3.4 9.2 + - - +
387B GLU* 2.9 26.5 + - + +
388B MET* 3.1 21.3 + - - +
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Residues in contact with ALA 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 4.1 29.8 - - + +
264B LEU* 4.4 2.2 - - + -
265B SER* 3.4 19.2 + - - +
268B HIS* 4.1 25.0 + - + +
324B VAL* 4.6 2.8 - - - +
328B ILE* 4.3 10.6 - - + +
384B THR* 1.3 74.1 - - - +
386B GLU* 1.3 57.7 + - - +
388B MET* 3.4 8.6 + - - +
389B SER* 2.9 27.3 + - - -
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B SER* 3.6 18.4 + - - +
384B THR* 3.1 8.8 + - - +
385B ALA* 1.3 76.4 - - - +
387B GLU* 1.3 64.5 + - - +
388B MET 3.1 1.3 - - - -
389B SER* 3.2 11.2 + - - -
390B ALA* 3.1 22.5 + - - +
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ARG* 3.2 22.2 + - - +
382B PHE* 3.0 16.4 - - + +
383B THR* 2.9 39.0 + - - -
384B THR* 2.9 24.1 + - + +
386B GLU* 1.3 76.7 - - - +
388B MET* 1.3 62.0 + - - +
390B ALA* 3.4 6.4 + - - +
391B GLN* 3.4 23.0 + - + +
566B PHE* 4.9 16.4 - - + -
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Residues in contact with MET 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 4.7 9.0 - - + -
328B ILE* 4.2 15.9 - - + -
331B VAL* 3.5 39.9 - - + -
332B GLY 4.3 2.2 - - - +
335B LEU* 4.5 4.7 - - + -
369B LEU* 4.0 20.2 - - + -
373B ALA* 3.8 25.4 - - + -
382B PHE* 3.7 35.2 - - + +
384B THR 3.1 11.1 + - - +
385B ALA* 3.5 10.8 - - - +
386B GLU 3.1 0.4 - - - -
387B GLU* 1.3 74.7 - - - +
389B SER* 1.3 62.0 + - - +
391B GLN* 3.0 3.3 + - - +
392B LEU* 2.8 37.3 + - + +
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Residues in contact with SER 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 3.6 20.6 + - - +
261B LEU* 4.0 22.6 - - - +
262B PRO* 5.2 4.0 - - - +
385B ALA 2.9 14.7 + - - -
386B GLU* 3.3 18.6 - - - -
388B MET* 1.3 76.2 - - - +
390B ALA* 1.3 58.1 + - - +
392B LEU 3.2 0.9 + - - -
393B THR* 2.9 33.6 + - - -
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Residues in contact with ALA 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLU 3.1 9.6 + - - +
387B GLU* 3.7 10.1 - - - +
388B MET 3.3 0.2 - - - -
389B SER* 1.3 77.3 - - - +
391B GLN* 1.3 69.5 + - - +
393B THR* 3.3 8.2 + - - -
394B GLY* 3.1 18.4 + - - -
413B THR* 3.5 32.1 - - + +
414B ILE* 6.3 0.4 - - + -
568B GLY 5.0 0.9 - - - +
569B GLU* 5.2 2.1 - - - +
753B GOL 5.5 2.3 + - - -
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Residues in contact with GLN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LEU* 3.9 7.4 - - + -
382B PHE* 3.9 27.1 - - + -
387B GLU* 3.4 13.3 + - + +
388B MET 3.0 7.2 + - - +
390B ALA* 1.3 82.7 - - - +
392B LEU* 1.3 59.1 + - - +
394B GLY 3.4 1.2 + - - -
395B VAL* 3.0 32.7 + - - +
414B ILE* 3.7 18.4 - - - +
566B PHE* 3.0 31.4 - - + +
567B PRO* 4.5 1.1 - - + -
568B GLY* 2.9 34.7 + - - +
569B GLU* 3.0 25.0 + - - +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 3.7 40.3 - - + +
257B LEU* 4.7 7.2 - - + -
258B LEU* 4.1 13.7 - - + -
261B LEU* 3.8 26.0 - - + -
331B VAL* 5.0 0.7 - - + -
335B LEU* 4.1 20.9 - - + -
366B TYR* 5.3 0.7 - - + -
369B LEU* 3.6 30.1 - - + -
388B MET* 2.8 24.7 + - + +
389B SER 3.6 4.5 - - - +
391B GLN* 1.3 78.1 - - - +
393B THR* 1.3 58.4 + - - +
395B VAL* 3.9 2.0 - - + -
396B LEU* 2.9 28.1 + - - +
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Residues in contact with THR 393 (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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74B GLY 5.8 2.0 - - - +
77B LEU* 5.2 7.2 - - + -
258B LEU* 3.5 19.5 - - + +
389B SER* 2.9 15.7 + - - -
390B ALA* 3.6 10.2 - - - -
391B GLN 3.3 0.2 - - - -
392B LEU* 1.3 73.9 - - - +
394B GLY* 1.3 64.5 + - - +
396B LEU* 3.3 5.9 + - + +
397B ARG* 3.0 59.6 + - + +
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Residues in contact with GLY 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ALA 3.1 12.2 + - - -
391B GLN 3.4 1.9 + - - -
393B THR* 1.3 74.5 - - - +
395B VAL* 1.3 62.3 + - - +
397B ARG* 3.3 4.8 + - - +
398B GLU* 3.1 26.9 + - - +
568B GLY* 3.2 27.8 - - - -
753B GOL 3.8 18.0 + - - -
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Residues in contact with VAL 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 3.9 19.3 - - + -
365B SER* 3.6 36.8 - - - +
366B TYR* 3.7 23.3 - - + +
369B LEU* 3.7 19.5 - - + -
391B GLN 3.0 20.7 + - - +
392B LEU* 3.9 4.7 - - - +
394B GLY* 1.3 72.7 - - - +
396B LEU* 1.3 66.7 + - - +
398B GLU* 3.0 5.2 + - - +
399B VAL* 2.9 29.5 + - + +
567B PRO 4.2 0.4 - - - -
568B GLY* 3.9 13.5 - - - +
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Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLY* 3.6 22.9 - - - +
77B LEU* 3.8 20.9 - - + -
78B VAL* 4.1 2.7 - - + -
251B ALA* 3.7 29.6 - - - +
254B ILE* 3.8 15.4 - - + +
255B ALA* 4.5 4.7 - - + -
258B LEU* 3.5 24.2 - - + -
392B LEU 2.9 19.5 + - - +
393B THR* 3.3 6.7 + - - +
395B VAL* 1.3 75.2 - - - +
397B ARG* 1.3 58.1 + - - +
399B VAL* 3.1 6.4 + - + +
400B VAL* 2.8 49.6 + - + +
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Residues in contact with ARG 397 (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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77B LEU* 4.0 18.0 - - + +
390B ALA 5.9 0.2 + - - -
393B THR* 3.0 38.9 + - - +
394B GLY 3.5 6.5 - - - +
395B VAL 3.2 0.2 - - - -
396B LEU* 1.3 76.5 - - - +
398B GLU* 1.3 57.3 + - - +
400B VAL* 4.8 0.2 - - - -
401B ALA* 2.8 35.0 + - - +
408B ARG* 3.4 39.7 - - + +
409B PRO 4.2 6.9 + - - -
410B GLY* 3.8 19.4 - - - +
411B LEU 4.4 5.1 + - - +
598B THR* 4.2 9.0 - - + -
753B GOL 2.4 46.0 + - - -
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Residues in contact with GLU 398 (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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363B TYR* 5.3 0.8 - - - -
365B SER* 2.9 30.2 + - - +
394B GLY 3.1 16.3 + - - +
395B VAL 3.0 7.6 + - - +
397B ARG* 1.3 75.5 - - - +
399B VAL* 1.3 61.1 + - + +
401B ALA* 4.5 0.6 - - - +
402B GLN* 3.3 23.7 + - - +
567B PRO 4.3 1.6 - - - +
568B GLY 4.4 5.2 - - - +
569B GLU 4.2 0.9 - - - +
570B LEU* 3.3 16.1 - - - +
573B LYS* 2.7 31.8 + - - -
594B THR* 3.8 16.5 - - + +
597B SER* 6.1 0.2 - - - -
598B THR* 3.6 29.9 + - + +
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Residues in contact with VAL 399 (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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250B VAL* 4.1 14.1 - - + -
251B ALA* 3.6 37.2 - - + +
254B ILE* 4.2 1.3 - - + -
363B TYR* 3.7 37.2 - - + -
365B SER* 5.4 1.3 - - - +
395B VAL* 2.9 39.2 + - + +
396B LEU* 3.5 12.8 - - + +
398B GLU* 1.3 72.5 - - + +
400B VAL* 1.3 59.3 + - - +
402B GLN* 3.2 2.9 + - - +
403B ASP* 2.8 41.4 + - - +
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Residues in contact with VAL 400 (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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77B LEU* 4.0 24.5 - - + +
78B VAL* 4.2 6.1 - - + -
251B ALA* 4.1 13.5 - - + -
396B LEU* 2.8 38.2 + - + +
397B ARG* 4.1 2.0 - - - +
399B VAL* 1.3 75.1 - - - +
401B ALA* 1.3 60.5 + - - +
403B ASP* 3.3 7.1 + - - +
404B THR* 2.8 35.2 + - + +
408B ARG* 3.5 41.3 - - + +
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Residues in contact with ALA 401 (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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397B ARG 2.8 22.1 + - - +
398B GLU 4.5 0.2 - - - +
400B VAL* 1.3 73.0 - - - +
402B GLN* 1.3 56.5 + - - +
405B GLY* 2.9 29.6 + - - -
406B VAL 3.2 20.7 + - - +
407B PRO* 4.0 0.9 - - + -
408B ARG* 3.9 8.2 - - + +
597B SER* 3.3 30.7 - - - +
598B THR* 3.8 16.8 - - - +
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Residues in contact with GLN 402 (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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362B THR* 3.2 36.2 + - - +
363B TYR* 3.6 22.4 - - - -
398B GLU 3.3 18.1 + - - +
399B VAL* 3.2 5.6 + - - +
401B ALA* 1.3 75.9 - - - +
403B ASP* 1.3 66.1 + - - +
404B THR 3.0 3.1 + - - -
405B GLY* 3.9 4.2 + - - -
593B GLN* 5.8 1.6 + - - -
594B THR* 5.4 4.0 + - - +
597B SER* 5.1 9.3 - - - +
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Residues in contact with ASP 403 (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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249B PRO* 6.2 0.3 - - - +
251B ALA* 4.0 21.5 + - - +
363B TYR* 2.7 31.8 + - - -
399B VAL* 2.8 24.8 + - - +
400B VAL* 3.3 6.7 + - + +
402B GLN* 1.3 74.1 + - - +
404B THR* 1.3 60.9 + - - +
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Residues in contact with THR 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B VAL* 2.8 26.1 + - - +
403B ASP* 1.3 83.1 - - - +
405B GLY* 1.3 61.6 + - - +
406B VAL* 3.2 34.8 + - + +
408B ARG* 3.0 32.8 + - - +
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Residues in contact with GLY 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ALA 2.9 12.6 + - - -
402B GLN 3.9 3.5 + - - -
403B ASP 3.8 1.0 - - - -
404B THR* 1.3 76.7 - - - +
406B VAL* 1.3 61.5 + - - +
407B PRO* 4.1 5.2 - - - +
597B SER 5.7 1.1 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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