Contacts of the helix formed by residues 355 - 368 (chain A) 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 GLU 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A PRO 3.3 6.8 + - - +
354A LYS* 1.3 67.4 - - - +
356A ASN* 1.3 64.9 + - - +
357A ILE 3.0 6.3 + - - -
358A LYS* 3.0 36.1 + - - +
359A LYS* 3.2 10.4 + - - +
395A ALA* 4.6 1.7 - - - +
396A GLU* 3.6 30.8 + - + +
398A LYS* 3.9 24.2 - - - +
399A THR* 2.8 29.7 + - - +
438B GLU* 5.6 5.2 - - - +
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Residues in contact with ASN 356 (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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354A LYS* 3.5 7.3 - - + +
355A GLU* 1.3 77.3 - - - +
357A ILE* 1.3 61.8 + - + +
359A LYS* 3.5 24.9 + - - +
360A GLU* 3.2 32.0 + - + +
398A LYS* 2.7 33.4 + - - +
438B GLU* 5.5 3.2 + - - -
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Residues in contact with ILE 357 (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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313A THR* 4.1 9.4 - - + -
316A GLN* 3.9 27.6 - - + +
317A THR* 4.2 21.8 - - + +
320A LEU* 3.8 15.1 - - + +
349A LEU* 3.9 22.7 - - + +
352A SER* 3.4 24.7 - - - +
354A LYS* 3.2 34.3 + - + +
355A GLU 3.0 0.6 - - - -
356A ASN* 1.3 76.0 - - + +
358A LYS* 1.3 65.3 + - - +
359A LYS 3.1 1.3 - - - -
360A GLU* 3.6 1.0 + - - -
361A ALA* 3.0 22.9 + - - +
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Residues in contact with LYS 358 (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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349A LEU 4.1 10.3 - - - +
350A LEU* 3.6 26.3 - - - +
351A SER* 4.3 3.8 - - - +
352A SER 2.7 30.6 + - - +
353A PRO* 4.6 7.8 + - - +
354A LYS 3.4 5.4 + - - +
355A GLU* 3.0 30.7 + - - +
357A ILE* 1.3 77.7 - - - +
359A LYS* 1.3 66.0 + - - +
361A ALA* 3.4 4.2 + - - +
362A CYS* 3.1 26.8 + - - -
391A LEU* 4.2 21.3 - - + +
399A THR* 4.3 11.4 - - + -
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Residues in contact with LYS 359 (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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355A GLU 3.2 6.7 + - - +
356A ASN* 3.5 33.5 + - - +
358A LYS* 1.3 79.1 - - - +
360A GLU* 1.3 67.2 + - - +
362A CYS* 2.8 27.5 + - - +
363A TRP* 2.9 10.8 + - + +
398A LYS* 3.4 44.1 - - + +
399A THR* 3.8 19.4 + - - +
402A GLU* 3.8 14.9 - - + +
442B ASN* 5.4 5.7 + - - -
493B GLU* 5.2 8.9 + - - -
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Residues in contact with GLU 360 (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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317A THR* 4.3 4.7 - - - +
320A LEU* 3.7 20.7 - - + +
321A ARG* 3.0 57.8 + - - +
356A ASN* 3.2 19.7 + - + +
358A LYS 3.6 0.2 - - - -
359A LYS* 1.3 93.1 + - - +
361A ALA* 1.3 57.1 + - - +
363A TRP* 3.4 24.8 - - + +
364A THR* 2.9 33.4 + - - -
493B GLU* 3.9 8.7 - - - +
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Residues in contact with ALA 361 (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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320A LEU* 3.9 4.4 - - + +
346A LEU* 4.1 15.5 - - + +
349A LEU* 4.1 19.5 - - + -
350A LEU* 3.5 19.5 - - + -
357A ILE 3.0 19.5 + - - +
358A LYS* 3.5 7.0 - - - +
360A GLU* 1.3 78.1 - - - +
362A CYS* 1.3 58.0 + - - +
364A THR* 3.6 2.1 - - - -
365A ILE* 3.0 35.5 + - - +
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Residues in contact with CYS 362 (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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350A LEU* 4.2 2.9 - - - -
358A LYS 3.1 19.1 + - - -
359A LYS 2.8 8.1 + - - +
361A ALA* 1.3 78.5 - - - +
363A TRP* 1.3 54.3 + - - +
365A ILE* 3.4 9.8 + - - +
366A SER* 2.8 34.3 + - - -
388A LEU* 4.0 17.0 - - + -
391A LEU* 3.9 25.1 - - - -
399A THR* 4.3 11.0 - - - -
402A GLU* 3.5 19.2 - - + +
403A ALA* 3.9 15.3 - - - +
406A ALA* 4.1 3.2 - - + +
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Residues in contact with TRP 363 (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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320A LEU 4.8 3.1 - - - -
321A ARG* 4.5 15.3 - - - -
324A GLY* 3.6 29.8 - - - -
325A ASN* 3.6 19.5 - - - -
328A THR* 4.7 3.4 - - - -
359A LYS* 2.9 4.6 + - + -
360A GLU* 3.4 39.0 - - + +
362A CYS* 1.3 74.5 - - - +
364A THR* 1.3 72.8 + - - +
366A SER* 2.7 21.2 + - - -
367A ASN* 3.2 18.9 + - - +
402A GLU* 3.4 33.6 - - + +
129D LYS* 3.3 36.6 + - - +
130D ALA 5.3 0.6 - - - -
131D ALA* 2.8 33.8 + - - +
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Residues in contact with THR 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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320A LEU* 3.8 10.2 - - - +
323A VAL* 4.3 13.9 - - + -
324A GLY* 3.5 20.6 - - - -
327A VAL* 3.7 25.6 - - + -
342A VAL* 5.3 0.2 - - + -
346A LEU* 4.0 23.6 - - + -
360A GLU 2.9 21.2 + - - -
361A ALA 3.6 4.7 - - - -
363A TRP* 1.3 80.7 - - - +
365A ILE* 1.3 65.0 + - - +
367A ASN* 2.9 16.4 + - - +
368A ILE* 3.3 15.4 + - + +
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Residues in contact with ILE 365 (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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343A LEU* 5.7 0.4 - - + -
346A LEU* 3.8 24.2 - - + -
350A LEU* 4.1 26.7 - - + -
361A ALA 3.0 17.8 + - - +
362A CYS* 3.6 4.9 - - - +
364A THR* 1.3 76.1 - - - +
366A SER* 1.3 62.0 + - - +
368A ILE* 3.0 18.6 + - - +
369A THR* 3.1 14.6 + - + +
379A VAL* 4.2 22.7 - - + -
384A LEU* 4.1 19.1 - - + -
388A LEU* 4.0 33.7 - - + -
406A ALA* 4.2 5.6 - - + -
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Residues in contact with SER 366 (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 CYS 2.8 17.0 + - - -
363A TRP* 2.7 20.8 + - - -
364A THR 3.0 0.6 + - - -
365A ILE* 1.3 74.0 - - - +
367A ASN* 1.3 59.6 + - - +
369A THR* 3.1 20.3 + - - -
370A ALA* 3.3 7.1 + - - +
402A GLU 4.3 1.1 - - - -
405A TRP* 3.9 5.2 - - - -
406A ALA* 3.3 28.5 - - - +
409A ASN* 3.3 17.2 + - - -
127D ALA 5.1 0.4 - - - +
129D LYS* 3.9 19.8 + - - -
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Residues in contact with ASN 367 (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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324A GLY 4.7 3.4 + - - -
327A VAL* 3.5 23.7 - - + +
328A THR* 4.3 8.7 + - - -
363A TRP* 3.2 31.9 + - - +
364A THR 2.9 8.6 + - - +
366A SER* 1.3 82.7 + - - +
368A ILE* 1.3 60.0 + - - +
370A ALA* 3.6 8.0 + - - +
127D ALA 4.4 1.4 - - - +
128D LYS* 2.6 41.2 + - + +
129D LYS* 2.7 49.8 + - - +
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Residues in contact with ILE 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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327A VAL* 3.8 28.7 - - + -
334A THR* 4.2 9.6 - - + -
338A ILE* 3.8 30.3 - - + -
342A VAL* 4.5 11.9 - - + -
343A LEU* 3.8 22.4 - - + -
346A LEU* 4.6 3.6 - - + -
364A THR* 3.6 21.1 - - + +
365A ILE* 3.0 9.3 + - - +
367A ASN* 1.3 77.1 - - - +
369A THR* 1.3 58.1 + - - +
370A ALA 3.0 4.9 - - - -
371A GLY* 3.3 9.6 + - - +
375A GLN* 3.8 17.8 - - + +
379A VAL* 4.0 18.6 - - + -
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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
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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