Contacts of the helix formed by residues 410 - 426 (chain B) in PDB entry 5BUK
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 PRO 410 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B ASN* 3.1 41.3 - - - +
395B ASP 6.1 0.2 - - - +
399B MET* 3.7 35.2 - - + -
407B ASP* 3.6 20.4 - - + +
409B GLU* 1.3 88.9 - - + +
411B LYS* 1.3 66.6 + - - +
412B ALA* 4.7 1.6 - - + +
413B LEU* 3.2 17.2 + - + +
414B ALA* 3.1 20.4 + - - +
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Residues in contact with LYS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PRO* 6.1 2.6 - - - +
57A ASP* 3.2 30.7 + - - -
335A ARG* 6.1 0.8 - - - +
395B ASP* 3.9 34.1 + - + +
407B ASP* 5.2 0.6 + - - -
409B GLU 3.4 3.8 + - - +
410B PRO* 1.3 72.3 - - - +
412B ALA* 1.3 63.7 + - - +
414B ALA* 3.4 4.8 + - - +
415B ALA* 3.0 25.8 + - - +
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Residues in contact with ALA 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B PHE* 3.9 10.7 - - + -
392B TYR* 5.8 0.2 - - + -
395B ASP* 3.9 35.3 + - + +
396B VAL* 3.9 20.6 - - + +
399B MET* 5.2 3.8 - - + -
410B PRO* 3.3 1.0 - - - +
411B LYS* 1.3 80.6 - - - +
413B LEU* 1.3 60.4 + - + +
415B ALA* 3.5 1.6 + - - +
416B MET* 2.9 41.4 + - + +
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ASN* 3.5 35.9 - - + +
371B GLU* 4.1 19.7 - - + +
372B PHE* 3.7 39.7 - - + +
375B ILE* 4.0 5.4 - - + +
399B MET* 4.2 13.2 - - + -
409B GLU* 6.5 0.2 - - - -
410B PRO* 3.2 35.9 + - + +
412B ALA* 1.3 73.9 - - - +
414B ALA* 1.3 60.3 + - - +
416B MET* 3.3 12.9 + - + +
417B ARG* 2.8 33.6 + - - +
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Residues in contact with ALA 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B GLU* 3.6 35.1 - - + +
410B PRO 3.1 16.4 + - - +
411B LYS* 3.8 4.7 - - - +
413B LEU* 1.3 76.5 - - - +
415B ALA* 1.3 63.3 + - - +
417B ARG* 3.5 5.8 + - - +
418B GLU* 3.2 29.0 + - - +
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Residues in contact with ALA 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B PHE* 3.8 20.2 - - + -
392B TYR* 5.6 4.7 - - + -
411B LYS 3.0 18.1 + - - +
412B ALA* 3.7 4.0 - - - +
414B ALA* 1.3 77.6 - - - +
416B MET* 1.3 63.0 + - - +
418B GLU* 3.4 8.5 + - - +
419B ILE* 3.3 25.5 + - + +
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Residues in contact with MET 416 (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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372B PHE* 4.0 19.1 - - + -
375B ILE* 3.9 24.9 - - + -
382B LEU* 3.4 27.4 - - + +
383B PHE* 4.4 7.6 - - - -
386B PHE* 3.6 42.0 - - + -
396B VAL* 4.9 3.4 - - + -
412B ALA* 2.9 31.4 + - + +
413B LEU* 3.8 26.5 - - + +
415B ALA* 1.3 74.0 - - - +
417B ARG* 1.3 65.7 + - - +
419B ILE* 3.0 3.0 + - - -
420B VAL* 2.9 22.5 + - - +
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Residues in contact with ARG 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLU* 2.9 43.1 + - - +
374B SER* 3.8 22.4 - - - -
375B ILE* 3.9 17.5 - - + +
378B ARG* 5.2 5.1 - - - +
413B LEU 2.8 21.5 + - - +
414B ALA* 3.8 6.7 - - - +
416B MET* 1.3 72.1 - - - +
418B GLU* 1.3 64.6 + - + +
420B VAL* 3.2 26.5 + - - +
421B LYS* 2.9 35.2 + - + +
424B GLU* 5.0 5.5 + - - -
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Residues in contact with GLU 418 (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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414B ALA* 3.2 16.1 + - + +
415B ALA* 3.7 10.9 - - - +
416B MET 3.2 0.4 - - - -
417B ARG* 1.3 79.8 - - + +
419B ILE* 1.3 62.6 + - + +
421B LYS* 3.5 8.8 + - - +
422B ALA* 3.1 21.5 + - - +
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Residues in contact with ILE 419 (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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90B PHE* 4.4 9.9 - - + -
379B LEU* 4.7 2.5 - - + -
382B LEU* 3.9 22.9 - - + -
386B PHE* 3.8 28.5 - - + -
392B TYR* 6.4 0.2 - - + -
415B ALA* 3.3 15.9 + - + +
416B MET 3.0 7.0 + - - +
418B GLU* 1.3 75.9 - - + +
420B VAL* 1.3 66.3 + - - +
422B ALA* 3.0 9.2 + - + +
423B VAL* 3.0 33.8 + - + +
429B HIS* 6.2 0.7 - - + +
431B TRP* 4.9 6.7 - - + -
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ILE* 4.4 18.8 - - + -
378B ARG* 3.8 21.1 - - + -
379B LEU* 4.1 21.3 - - + -
382B LEU* 3.7 15.7 - - + -
416B MET 2.9 19.4 + - - +
417B ARG* 3.6 24.2 - - - +
419B ILE* 1.3 74.4 - - - +
421B LYS* 1.3 58.1 + - - +
423B VAL* 3.3 2.4 + - - +
424B GLU* 2.9 49.6 + - + +
435B LEU* 4.8 3.6 - - + -
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Residues in contact with LYS 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B ARG* 2.9 28.9 + - + +
418B GLU* 3.6 12.3 - - - +
420B VAL* 1.3 76.1 - - - +
422B ALA* 1.3 62.0 + - - +
424B GLU* 3.2 15.8 + - - +
425B GLU* 3.0 52.7 + - - +
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Residues in contact with ALA 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLU 3.1 13.4 + - - +
419B ILE* 3.0 12.8 + - + +
421B LYS* 1.3 76.7 - - - +
423B VAL* 1.3 64.6 + - + +
425B GLU* 3.3 17.9 + - - +
426B ASP* 3.5 14.7 + - - +
429B HIS* 4.7 8.8 - - + +
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Residues in contact with VAL 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B LEU* 4.0 19.1 - - + -
419B ILE* 3.0 21.6 + - + +
420B VAL 3.7 5.6 - - - +
422B ALA* 1.3 76.3 - - + +
424B GLU* 1.3 62.8 + - - +
425B GLU 3.3 0.3 + - - -
426B ASP 3.3 10.4 + - - +
429B HIS* 4.0 31.4 - - + +
431B TRP* 3.6 12.3 - - + +
432B HIS* 3.0 53.5 + - + +
435B LEU* 4.0 14.4 - - + -
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Residues in contact with GLU 424 (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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378B ARG* 2.8 44.4 + - - +
417B ARG* 5.0 5.0 + - - -
420B VAL* 2.9 30.1 + - - +
421B LYS* 3.2 20.9 + - - +
423B VAL* 1.3 75.6 - - - +
425B GLU* 1.3 63.6 + - + +
426B ASP 3.4 0.9 + - - -
427B PRO* 5.0 0.9 - - - +
432B HIS* 3.9 11.4 - - - -
435B LEU* 4.0 20.9 - - + -
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Residues in contact with GLU 425 (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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421B LYS* 3.0 50.6 + - - +
422B ALA* 3.3 9.5 + - - +
423B VAL 3.2 0.6 - - - -
424B GLU* 1.3 78.6 - - + +
426B ASP* 1.3 58.5 + - + +
427B PRO* 3.8 8.6 - - - +
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Residues in contact with ASP 426 (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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422B ALA 3.5 11.2 + - - +
423B VAL 3.3 14.3 + - - +
424B GLU 3.2 2.0 - - - -
425B GLU* 1.3 80.7 - - + +
427B PRO* 1.3 67.2 - - - +
428B ASN* 2.9 22.2 + - - +
429B HIS* 3.0 37.7 + - + +
432B HIS* 3.3 3.7 + - - -
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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