Contacts of the helix formed by residues 355 - 368 (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 GLU 355 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A GLU* 5.7 5.2 - - - +
353B PRO 3.4 5.9 + - - +
354B LYS* 1.3 68.3 - - - +
356B ASN* 1.3 66.3 + - - +
357B ILE 3.0 2.6 + - - -
358B LYS* 3.2 32.4 + - - +
359B LYS* 3.2 11.8 + - - +
395B ALA* 4.6 2.0 - - - +
396B GLU* 3.5 31.1 + - + +
398B LYS* 3.9 24.9 - - - +
399B THR* 2.7 30.5 + - - +
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Residues in contact with ASN 356 (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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438A GLU* 5.8 1.2 + - - -
354B LYS* 3.6 7.7 - - + +
355B GLU* 1.3 76.4 - - - +
357B ILE* 1.3 62.2 + - + +
359B LYS* 3.4 25.8 + - - +
360B GLU* 3.2 32.1 + - + +
398B LYS* 2.6 31.9 + - - +
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Residues in contact with ILE 357 (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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313B THR* 4.1 9.0 - - + -
316B GLN* 4.0 26.2 - - + +
317B THR* 4.1 22.9 - - + +
320B LEU* 3.9 15.4 - - + +
349B LEU* 3.9 23.3 - - + +
352B SER* 3.4 23.6 - - - +
354B LYS* 3.2 35.1 + - + +
355B GLU 3.0 1.0 - - - -
356B ASN* 1.3 78.1 - - + +
358B LYS* 1.3 65.6 + - - +
359B LYS 3.1 0.2 - - - -
360B GLU* 3.6 0.8 + - - -
361B ALA* 3.1 22.0 + - - +
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Residues in contact with LYS 358 (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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349B LEU 4.0 10.3 - - - +
350B LEU* 3.5 25.9 - - - +
351B SER* 4.3 4.7 + - - +
352B SER 2.6 30.0 + - - +
353B PRO* 4.7 9.2 + - - +
354B LYS 3.3 5.3 + - - +
355B GLU* 3.2 27.8 + - - +
357B ILE* 1.3 77.3 - - - +
359B LYS* 1.3 65.6 + - - +
361B ALA* 3.4 4.3 + - - +
362B CYS* 3.2 24.6 + - - -
391B LEU* 4.2 21.1 - - + +
399B THR* 4.3 12.3 - - + -
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Residues in contact with LYS 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ASN* 5.4 5.9 + - - -
493A GLU* 5.1 10.5 + - - -
355B GLU 3.2 9.8 + - - +
356B ASN* 3.4 34.9 + - - +
358B LYS* 1.3 77.7 - - - +
360B GLU* 1.3 72.5 + - - +
362B CYS* 2.8 22.3 + - - +
363B TRP* 2.9 12.0 + - + +
398B LYS* 3.6 43.7 - - + +
399B THR* 3.9 18.1 + - - +
402B GLU* 3.7 15.1 - - + +
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Residues in contact with GLU 360 (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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493A GLU* 3.8 10.0 - - - +
317B THR* 4.5 3.1 - - - +
320B LEU* 3.7 19.1 - - + +
321B ARG* 3.1 57.2 + - - -
356B ASN* 3.2 19.6 + - + +
359B LYS* 1.3 89.2 + - - +
361B ALA* 1.3 57.2 + - - +
362B CYS 3.2 0.2 - - - -
363B TRP* 3.3 24.0 - - + +
364B THR* 2.8 33.1 + - - -
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Residues in contact with ALA 361 (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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320B LEU* 3.9 5.7 - - + +
346B LEU* 4.1 15.3 - - + +
349B LEU* 4.1 20.2 - - + -
350B LEU* 3.6 20.0 - - + -
357B ILE 3.1 17.9 + - - +
358B LYS* 3.5 7.2 - - - +
359B LYS 3.1 0.8 - - - -
360B GLU* 1.3 77.3 - - - +
362B CYS* 1.3 57.9 + - - +
364B THR* 3.4 2.6 + - - -
365B ILE* 3.0 35.3 + - - +
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Residues in contact with CYS 362 (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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350B LEU* 4.2 3.1 - - - -
358B LYS 3.2 14.4 + - - -
359B LYS 2.8 9.1 + - - +
361B ALA* 1.3 77.5 - - - +
363B TRP* 1.3 59.1 + - - +
365B ILE* 3.4 9.0 + - - +
366B SER* 2.8 30.3 + - - -
388B LEU* 3.9 22.9 - - + -
391B LEU* 4.0 20.0 - - - -
399B THR* 4.3 9.2 - - - -
402B GLU* 3.5 18.1 - - + +
403B ALA* 3.9 17.9 - - - +
406B ALA* 4.2 3.6 - - - +
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Residues in contact with TRP 363 (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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320B LEU 4.8 3.1 - - - -
321B ARG* 4.4 17.5 - - - -
324B GLY* 3.6 27.6 - - - -
325B ASN* 3.6 24.0 - - - -
328B THR* 4.6 3.8 - - - -
359B LYS* 2.9 8.9 + - + +
360B GLU* 3.3 34.3 - - + +
362B CYS* 1.3 76.4 - - - +
364B THR* 1.3 68.1 + - - +
366B SER* 2.7 23.4 + - - -
367B ASN* 3.2 17.9 + - - +
402B GLU* 3.4 33.1 - - + +
129F LYS* 3.5 37.0 + - - +
130F ALA* 5.0 2.6 - - - +
131F ALA 4.2 21.7 + - - -
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Residues in contact with THR 364 (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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320B LEU* 3.9 9.9 - - - +
323B VAL* 4.3 14.1 - - + -
324B GLY* 3.4 20.9 - - - -
327B VAL* 3.7 24.7 - - + -
342B VAL* 5.3 0.2 - - + -
346B LEU* 4.0 23.8 - - + -
360B GLU 2.8 20.2 + - - -
361B ALA 3.7 4.5 - - - -
363B TRP* 1.3 80.6 - - - +
365B ILE* 1.3 66.7 + - - +
367B ASN* 2.9 15.5 + - - +
368B ILE* 3.2 17.2 + - + +
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Residues in contact with ILE 365 (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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343B LEU* 5.7 0.7 - - + -
346B LEU* 3.8 22.7 - - + -
350B LEU* 4.0 28.5 - - + -
361B ALA 3.0 18.5 + - - +
362B CYS* 3.6 5.4 - - - +
364B THR* 1.3 74.9 - - - +
366B SER* 1.3 64.4 + - - +
368B ILE* 3.0 20.6 + - - +
369B THR* 3.0 16.6 + - + +
379B VAL* 4.2 22.2 - - + -
384B LEU* 4.0 18.6 - - + -
388B LEU* 3.9 32.5 - - + -
406B ALA* 4.2 2.9 - - + -
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Residues in contact with SER 366 (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 2.8 14.7 + - - -
363B TRP* 2.7 21.0 + - - -
364B THR 3.0 0.4 + - - -
365B ILE* 1.3 77.9 - - - +
367B ASN* 1.3 60.2 + - - +
368B ILE 3.1 0.4 - - - -
369B THR* 2.9 20.7 + - - -
370B ALA* 3.3 8.8 + - - +
402B GLU 4.3 1.6 - - - -
405B TRP* 3.9 5.6 - - - -
406B ALA* 3.4 27.6 - - - +
409B ASN* 3.3 15.4 + - - -
127F ALA 5.7 0.2 - - - -
129F LYS* 3.8 19.1 + - - -
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Residues in contact with ASN 367 (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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324B GLY 4.6 4.4 + - - -
327B VAL* 3.6 22.6 - - + +
328B THR* 4.1 8.7 + - - -
363B TRP* 3.2 31.7 + - - +
364B THR 2.9 8.4 + - - +
366B SER* 1.3 81.7 + - - +
368B ILE* 1.3 58.6 + - - +
370B ALA* 3.7 7.6 - - - +
127F ALA 4.2 1.2 - - - +
128F LYS* 2.5 42.6 + - + +
129F LYS* 2.6 50.0 + - - +
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Residues in contact with ILE 368 (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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327B VAL* 3.8 29.6 - - + -
334B THR* 4.2 9.0 - - + -
338B ILE* 3.9 28.7 - - + -
342B VAL* 4.4 12.3 - - + -
343B LEU* 4.0 21.3 - - + -
346B LEU* 4.6 3.6 - - + -
364B THR* 3.5 23.8 - - + +
365B ILE* 3.0 9.5 + - - +
367B ASN* 1.3 78.3 - - - +
369B THR* 1.3 56.6 + - - +
370B ALA 3.0 4.7 - - - -
371B GLY* 3.3 16.5 + - - -
375B GLN* 3.9 13.7 - - + +
379B VAL* 3.9 20.9 - - + -
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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