Contacts of the helix formed by residues 363 - 379 (chain A) in PDB entry 1B0K
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 TYR 363 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A SER* 1.3 74.0 - - - +
364A GLU* 1.4 56.8 + - - +
366A MET* 3.6 2.3 + - - +
367A GLY* 3.0 24.9 + - - -
396A ILE* 3.9 16.8 - - + +
399A THR* 3.6 26.7 - - + -
400A ILE* 4.2 14.4 - - + -
403A ASP* 2.6 34.4 + - - +
405A TYR* 3.0 39.6 + + - -
503A ASP* 3.9 15.3 + - + +
504A GLU 4.6 4.0 - - - +
505A LEU* 3.6 31.2 - - + -
506A PRO* 3.7 19.1 - - + +
507A ARG 4.8 1.4 + - - -
510A PHE* 4.1 20.9 - + + -
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Residues in contact with GLU 364 (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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217A PRO* 5.3 7.3 - - - +
249A SER* 2.8 30.1 + - - -
251A THR* 3.9 5.6 + - - +
252A GLY* 4.7 2.6 + - - -
362A SER* 3.2 8.5 + - - +
363A TYR* 1.4 74.9 - - - +
365A ASP* 1.3 64.9 + - - +
367A GLY* 3.2 1.5 + - - +
368A ARG* 3.0 52.6 + - + +
502A ALA* 4.5 7.4 - - - +
503A ASP 3.8 16.8 - - - +
504A GLU* 4.0 28.8 + - - +
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Residues in contact with ASP 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR 5.7 1.0 - - - +
255A THR* 4.7 4.7 + - - -
359A THR 4.6 0.9 - - - +
360A ASN* 3.1 45.7 + - - +
361A SER 3.5 0.3 + - - -
362A SER* 2.9 35.0 + - - +
364A GLU* 1.3 79.8 - - - +
366A MET* 1.3 62.1 + - + +
368A ARG* 3.7 4.6 + - - +
369A SER* 2.8 29.9 + - - -
466A PRO* 3.5 19.2 - - + +
467A GLU* 5.1 1.1 - - - +
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Residues in contact with MET 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ILE* 4.4 19.7 - - + -
356A GLY 5.0 0.4 - - - +
360A ASN 4.1 19.1 - - - +
361A SER* 4.2 8.1 - - - +
362A SER 2.9 22.2 + - - +
363A TYR 3.8 4.5 - - - +
365A ASP* 1.3 74.8 - - - +
367A GLY* 1.3 56.8 + - - +
369A SER* 3.4 5.1 - - - +
370A ALA* 2.9 28.1 + - - +
389A ILE* 3.7 24.5 - - - -
390A THR 3.9 20.9 - - - +
391A PRO* 5.0 2.9 - - - -
396A ILE* 4.5 5.8 - - + -
400A ILE* 4.0 38.4 - - + -
405A TYR* 4.4 5.1 - - + +
409A LEU* 4.5 10.2 - - + +
466A PRO* 5.6 0.7 - - + -
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Residues in contact with GLY 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A TYR 3.0 12.7 + - - -
364A GLU 3.2 2.4 + - - -
366A MET* 1.3 73.3 - - - +
368A ARG* 1.4 64.7 + - - +
370A ALA* 3.4 3.1 + - - +
371A ALA* 3.0 23.4 + - - +
405A TYR* 3.8 30.9 - - - -
502A ALA* 3.7 14.6 - - - +
503A ASP 5.9 0.2 - - - -
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Residues in contact with ARG 368 (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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213A GLY 3.4 22.8 + - - -
214A TRP 3.7 9.5 + - - -
215A THR 3.8 7.7 + - - -
216A SER* 4.0 7.3 - - - -
217A PRO* 6.1 2.2 - - - -
364A GLU* 3.0 41.5 + - + +
365A ASP* 4.1 4.0 - - - +
367A GLY* 1.4 73.9 - - - +
369A SER* 1.3 64.3 + - - +
371A ALA* 3.3 9.1 + - - +
372A VAL* 3.5 4.7 + - - +
467A GLU* 2.8 45.7 + - - +
500A PRO* 3.3 63.2 + - + +
501A ASP* 4.8 3.4 + - - +
502A ALA* 3.7 18.8 - - + +
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Residues in contact with SER 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ILE* 3.9 17.3 - - - +
365A ASP 2.8 23.5 + - - -
366A MET* 3.4 6.7 - - - -
368A ARG* 1.3 72.3 - - - +
370A ALA* 1.3 65.4 + - - +
372A VAL* 3.0 17.0 + - - +
373A ALA* 3.2 10.6 + - - +
409A LEU* 4.3 7.2 - - - -
466A PRO* 3.2 27.4 + - - +
467A GLU* 4.5 6.2 - - - +
470A THR* 3.8 17.3 + - - +
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Residues in contact with ALA 370 (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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366A MET 2.9 21.2 + - - +
367A GLY 3.4 5.6 + - - +
369A SER* 1.3 72.2 - - - +
371A ALA* 1.3 58.0 + - - +
373A ALA* 3.2 4.6 - - - +
374A LYS* 2.9 29.4 + - - +
405A TYR* 3.9 38.4 - - + +
408A VAL* 3.7 11.9 - - + +
409A LEU* 4.0 12.7 - - + +
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A GLY 3.0 14.3 + - - +
368A ARG 3.4 12.1 - - - +
369A SER 3.1 0.6 - - - -
370A ALA* 1.3 74.1 - - - +
372A VAL* 1.3 58.8 + - - +
374A LYS* 2.7 46.3 + - - +
375A GLN* 3.0 9.7 + - - +
500A PRO* 3.9 12.3 - - + -
501A ASP 3.8 21.3 - - - +
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Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A TRP* 3.6 28.0 - - + -
368A ARG 3.5 12.3 + - - +
369A SER 3.0 7.0 + - - +
371A ALA* 1.3 74.1 - - - +
373A ALA* 1.3 67.8 + - - +
375A GLN* 3.0 24.6 + - - +
376A ALA* 3.3 10.9 + - - +
467A GLU* 3.8 14.1 - - + +
470A THR* 4.3 6.1 - - + -
471A ALA* 3.9 34.8 - - + +
474A ILE* 4.5 5.2 - - + -
497A LEU* 4.3 13.7 - - + +
500A PRO* 4.0 10.1 - - + -
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A SER 3.2 9.0 + - - +
370A ALA* 3.2 12.8 - - - +
372A VAL* 1.3 79.8 - - - +
374A LYS* 1.3 56.6 + - - +
376A ALA* 3.3 5.2 + - - +
377A LEU* 3.1 27.0 + - - +
408A VAL* 3.7 14.6 - - + -
409A LEU* 4.4 5.8 - - + -
412A VAL* 3.7 26.1 - - + +
470A THR* 4.1 8.0 - - + +
474A ILE* 4.4 7.9 - - - -
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Residues in contact with LYS 374 (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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370A ALA 2.9 18.9 + - - +
371A ALA* 2.7 39.5 + - - +
373A ALA* 1.3 69.4 - - - +
375A GLN* 1.3 81.3 + - + +
377A LEU* 3.7 8.7 - - + +
378A ALA* 3.0 24.1 + - - +
408A VAL* 3.6 19.6 - - + +
498A GLU* 2.8 39.6 + - - -
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Residues in contact with GLN 375 (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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371A ALA 3.0 25.2 + - - +
372A VAL* 3.0 19.1 + - - +
374A LYS* 1.3 90.6 - - + +
376A ALA* 1.3 63.6 + - - +
378A ALA* 3.5 8.6 + - - +
379A HIS* 3.0 27.5 + - + +
495A PHE* 4.5 4.0 - - + -
496A LYS 4.6 1.0 - - - +
497A LEU* 3.5 18.5 - - + +
498A GLU* 2.7 65.0 + - - +
499A ALA 4.6 1.2 + - - -
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Residues in contact with ALA 376 (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 VAL 3.3 2.3 + - - +
373A ALA 3.5 9.6 - - - +
375A GLN* 1.3 80.9 - - - +
377A LEU* 1.4 55.5 + - - +
379A HIS* 3.0 20.8 + - - +
381A LEU* 3.1 30.0 + - + +
412A VAL* 4.6 2.0 - - + -
474A ILE* 3.7 39.3 - - + -
495A PHE* 4.3 13.7 - - + -
497A LEU* 4.9 3.1 - - + +
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Residues in contact with LEU 377 (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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373A ALA 3.1 9.0 + - - +
374A LYS* 3.7 10.3 - - + +
376A ALA* 1.4 72.7 - - - +
378A ALA* 1.3 60.9 + - - +
379A HIS 3.1 1.8 - - - -
380A GLY* 2.8 20.6 + - - -
381A LEU 3.9 17.0 + - - +
382A LYS* 4.2 5.8 - - - +
408A VAL* 3.7 40.6 - - + +
411A ASP* 3.8 39.7 - - + +
412A VAL* 3.9 6.3 - - + -
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Residues in contact with ALA 378 (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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374A LYS 3.0 17.4 + - - +
375A GLN* 3.5 9.6 - - - +
376A ALA 3.3 0.2 - - - -
377A LEU* 1.3 75.5 - - - +
379A HIS* 1.3 66.6 + - + +
380A GLY 3.3 0.6 + - - -
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Residues in contact with HIS 379 (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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375A GLN* 3.0 23.7 + - + -
376A ALA 3.0 7.1 + - - +
378A ALA* 1.3 82.1 - - + +
380A GLY* 1.4 58.5 + - - +
381A LEU* 3.6 0.9 - - + -
489A GLY* 3.6 1.5 - - - -
490A LYS* 2.9 30.1 + - - +
491A ASP* 3.3 28.9 - - - +
493A LYS* 6.2 0.7 - - + -
495A PHE* 3.6 59.1 - + + +
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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
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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