Contacts of the helix formed by residues 397 - 414 (chain B) in PDB entry 1BK6
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 397 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A TYR* 3.7 43.7 - + + -
439A ILE* 5.4 7.0 + - + +
441A ASP* 6.4 0.7 - - + -
396B GLU* 1.3 72.6 + - - +
398B LYS* 1.3 66.6 + - - +
399B THR 2.8 1.7 + - - -
400B LYS* 3.2 7.3 + - + +
401B LYS* 3.0 48.6 + - + +
436B LEU* 4.3 16.6 - - + -
439B ILE* 4.4 23.1 - - + -
440B ALA* 3.5 18.8 - - + -
441B ASP* 2.8 44.9 + - + -
444B ILE* 3.5 13.3 - - + +
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Residues in contact with LYS 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU 5.5 0.8 + - - -
438A GLU* 3.5 25.5 + - - -
439A ILE* 4.1 23.7 + - - +
440A ALA 4.3 13.8 + - - +
441A ASP* 5.7 5.2 - - + -
355B GLU* 3.9 25.7 - - - +
356B ASN* 2.6 37.1 + - - +
359B LYS* 3.6 30.2 - - + +
396B GLU* 4.6 8.3 - - + -
397B TYR* 1.3 80.3 - - - +
399B THR* 1.3 64.9 + - - +
401B LYS* 3.8 13.2 - - - +
402B GLU* 3.7 11.6 - - - +
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Residues in contact with THR 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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355B GLU* 2.7 31.9 + - - +
358B LYS* 4.3 8.7 - - + -
359B LYS* 3.9 32.0 - - - +
362B CYS* 4.3 12.7 - - - -
391B LEU* 4.4 7.6 - - + -
395B ALA* 3.6 23.3 - - + -
396B GLU 3.1 2.3 + - - -
397B TYR 2.8 1.2 + - - -
398B LYS* 1.3 80.7 - - - +
400B LYS* 1.3 64.5 + - - +
401B LYS 3.0 1.8 - - - -
402B GLU* 2.9 14.4 + - - +
403B ALA* 3.0 10.2 + - - +
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Residues in contact with LYS 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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391B LEU 3.5 16.8 - - - +
392B LEU* 3.5 18.1 + - + +
393B GLU 3.6 26.9 + - - -
394B VAL* 4.1 1.3 - - - +
395B ALA 3.1 20.4 - - - +
396B GLU 3.0 18.7 + - - +
397B TYR* 3.8 9.2 - - + +
399B THR* 1.3 75.4 - - - +
401B LYS* 1.3 53.8 + - - +
403B ALA* 3.0 10.8 + - - +
404B CYS* 2.7 36.7 + - - +
436B LEU* 4.4 22.8 - - + +
439B ILE* 4.0 20.5 - - + +
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Residues in contact with LYS 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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401A LYS* 4.9 1.4 - - - +
441A ASP* 4.0 27.6 + - + +
397B TYR* 3.0 39.0 + - + +
398B LYS* 3.8 13.5 - - + +
400B LYS* 1.3 76.7 - - - +
402B GLU* 1.3 66.9 + - - +
404B CYS* 3.3 13.7 - - - +
405B TRP* 3.1 23.6 - - - +
436B LEU* 5.7 0.4 - - - -
441B ASP* 3.3 27.5 + - - -
443B ARG* 6.4 0.7 - - - -
444B ILE* 3.5 31.7 - - + +
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Residues in contact with GLU 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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359B LYS* 3.7 16.4 - - + +
362B CYS* 3.5 16.7 - - + +
363B TRP* 3.4 43.5 - - + +
366B SER* 4.3 0.3 - - - -
398B LYS 3.7 13.8 - - - +
399B THR 2.9 11.0 + - - +
401B LYS* 1.3 84.0 - - - +
403B ALA* 1.3 65.2 + - - +
404B CYS 3.1 1.6 - - - -
405B TRP* 3.1 15.7 + - - +
406B ALA* 3.1 13.0 + - - +
129F LYS* 2.6 31.8 + - - +
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Residues in contact with ALA 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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362B CYS* 3.9 19.4 - - - +
388B LEU* 3.9 25.6 - - + +
391B LEU* 4.6 2.5 - - + -
392B LEU* 4.0 18.8 - - + +
399B THR 3.0 11.0 + - - +
400B LYS* 3.4 8.5 - - - +
402B GLU* 1.3 76.5 - - - +
404B CYS* 1.3 63.3 + - - +
406B ALA* 3.3 8.0 + - - +
407B ILE* 3.1 27.0 + - + +
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Residues in contact with CYS 404 (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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392B LEU* 3.6 9.8 - - + +
400B LYS 2.7 12.3 + - - +
401B LYS* 3.3 13.9 - - - +
403B ALA* 1.3 77.5 - - - +
405B TRP* 1.3 59.8 + - - +
407B ILE* 3.3 3.5 + - - +
408B SER* 2.8 31.3 + - - -
433B LEU* 5.0 8.5 - - - +
436B LEU* 3.9 19.3 - - + -
444B ILE* 4.1 9.6 - - + -
447B VAL* 4.0 17.9 - - - -
448B THR* 3.5 27.8 - - - -
451B ALA* 6.4 0.2 - - - -
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Residues in contact with TRP 405 (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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366B SER* 3.9 4.3 - - - -
401B LYS* 3.1 28.5 + - + +
402B GLU* 3.1 8.3 + - - +
404B CYS* 1.3 78.1 - - - +
406B ALA* 1.3 54.9 - - - +
408B SER* 2.9 5.3 + - - -
409B ASN* 2.7 65.5 + - - +
443B ARG* 3.7 33.7 - - + -
444B ILE* 3.5 18.2 - - + +
447B VAL* 3.6 33.2 - - + -
127F ALA* 5.1 8.7 - - + -
129F LYS* 3.3 50.6 - - + +
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Residues in contact with ALA 406 (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 CYS 4.2 4.9 - - - +
365B ILE* 4.2 4.5 - - + -
366B SER* 3.4 30.6 - - - +
369B THR* 3.1 18.5 + - + +
388B LEU* 3.9 24.7 - - + -
402B GLU 3.1 9.1 + - - +
403B ALA* 3.4 10.5 - - - +
405B TRP* 1.3 80.1 - - - +
407B ILE* 1.3 62.0 + - - +
410B ALA* 3.1 13.9 + - - +
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Residues in contact with ILE 407 (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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385B ILE* 5.5 9.6 - - + -
388B LEU* 4.3 17.5 - - + -
389B VAL* 4.1 30.1 - - + +
392B LEU* 3.9 28.5 - - + -
403B ALA 3.1 16.8 + - - +
404B CYS* 3.8 3.4 - - - +
406B ALA* 1.3 74.3 - - - +
408B SER* 1.3 64.3 + - - +
410B ALA* 3.2 8.9 + - - +
411B SER* 3.1 20.9 + - - -
424B LEU* 4.1 12.4 - - + +
429B CYS* 4.3 25.4 - - + -
433B LEU* 4.7 15.3 - - + -
451B ALA* 5.6 0.9 - - + -
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Residues in contact with SER 408 (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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404B CYS* 2.8 23.9 + - - -
405B TRP 3.4 1.6 - - - -
407B ILE* 1.3 71.6 - - - +
409B ASN* 1.3 66.8 + - - +
411B SER* 2.4 26.5 + - - -
412B SER* 3.5 6.4 + - - -
433B LEU* 6.1 0.6 - - - +
447B VAL* 2.9 44.4 + - - +
450B ASP* 4.6 4.3 - - - +
451B ALA* 3.7 16.0 + - - +
454B ASN* 4.7 1.2 + - - -
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Residues in contact with ASN 409 (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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366B SER* 3.3 24.9 + - - -
369B THR* 3.3 32.0 - - - +
370B ALA* 4.2 3.1 - - - +
376B ILE* 4.1 1.4 - - - +
405B TRP* 2.7 51.7 + - - +
408B SER* 1.3 73.1 + - - +
410B ALA* 1.3 60.8 + - - +
412B SER* 3.2 24.6 + - - -
413B GLY 4.0 1.6 + - - -
447B VAL* 5.9 0.2 - - - +
127F ALA* 3.6 30.9 + - + +
129F LYS* 5.6 0.8 - - - +
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Residues in contact with ALA 410 (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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369B THR* 4.1 9.8 + - + -
376B ILE* 3.9 22.7 - - + +
380B ILE* 6.2 0.9 - - + -
385B ILE* 5.2 8.3 - - + -
406B ALA 3.1 13.9 + - - +
407B ILE* 3.2 13.5 - - - +
408B SER 3.0 0.6 - - - -
409B ASN* 1.3 77.7 - - - +
411B SER* 1.3 62.7 + - - +
412B SER 3.0 1.4 + - - -
413B GLY* 3.2 12.1 + - - -
420B ILE* 3.7 15.1 - - + +
424B LEU* 4.1 18.4 - - + -
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Residues in contact with SER 411 (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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407B ILE* 3.1 10.1 + - - -
408B SER* 2.4 30.4 + - - -
410B ALA* 1.3 76.6 - - - +
412B SER* 1.3 62.3 + - - +
414B GLY* 3.0 11.1 + - - -
415B LEU 4.5 0.2 + - - -
421B ILE* 3.3 30.0 - - - +
424B LEU* 4.0 8.0 - - - +
451B ALA* 3.6 15.0 - - - -
454B ASN* 3.4 29.8 + - - +
455B ILE* 4.9 3.8 - - - -
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Residues in contact with SER 412 (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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376B ILE* 5.5 0.4 - - - -
408B SER 3.9 5.9 + - - -
409B ASN* 3.2 18.5 + - - -
410B ALA 3.0 0.8 - - - -
411B SER* 1.3 75.7 + - - +
413B GLY* 1.3 54.3 + - - +
414B GLY 2.5 17.4 + - - -
415B LEU* 3.1 17.8 + - - +
454B ASN* 4.4 12.4 + - - +
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Residues in contact with GLY 413 (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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373B THR* 4.9 8.4 - - - +
376B ILE* 3.8 21.0 - - - +
410B ALA 3.2 9.8 + - - -
412B SER* 1.3 75.7 - - - +
414B GLY* 1.3 57.1 + - - +
415B LEU 3.4 1.1 - - - -
416B GLN* 3.8 6.7 + - - +
417B ARG* 3.2 20.3 + - - +
420B ILE* 3.3 20.5 - - - +
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Residues in contact with GLY 414 (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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410B ALA 4.1 0.2 + - - -
411B SER 3.0 13.1 + - - -
412B SER 2.5 11.9 + - - -
413B GLY* 1.3 73.8 - - - +
415B LEU* 1.3 64.2 + - - +
416B GLN 3.2 0.7 - - - -
417B ARG 3.7 5.6 - - - -
418B PRO* 3.4 22.9 - - - +
420B ILE* 4.7 2.0 - - - -
421B ILE* 3.6 24.5 - - - +
458B MET* 5.7 2.6 - - - +
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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