Contacts of the helix formed by residues 392 - 401 (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 TYR 392 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B PHE* 3.6 27.8 - + - -
386B PHE* 3.3 50.3 - + + +
389B ASP* 2.8 19.0 + - + -
391B ARG* 1.3 122.4 + - + +
393B ARG* 1.3 67.9 + - - +
394B ILE 3.3 2.7 - - - -
395B ASP* 3.1 14.3 + - + +
396B VAL* 3.0 21.3 + - - +
412B ALA* 6.1 0.2 - - - -
415B ALA* 5.6 4.3 - - + -
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Residues in contact with ARG 393 (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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101B GLU 2.7 22.8 + - - -
102B ILE* 3.2 18.8 - - + +
106B GLU* 2.8 42.8 + - - +
386B PHE 3.4 10.1 + - - -
387B VAL* 2.8 40.4 + - - +
388B GLN* 3.1 33.4 + - - +
389B ASP 2.9 14.3 + - - +
390B PRO* 4.1 11.6 + - + +
391B ARG 3.7 0.2 - - - -
392B TYR* 1.3 76.8 - - - +
394B ILE* 1.3 66.5 + - + +
396B VAL* 3.2 3.5 + - - +
397B LEU* 2.8 30.3 + - + +
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Residues in contact with ILE 394 (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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110A SER* 4.3 31.4 - - - +
106B GLU* 3.6 34.5 - - + +
107B ARG* 3.6 32.3 + - + +
390B PRO 5.0 7.2 + - - +
391B ARG 5.5 0.4 - - - -
392B TYR 3.2 0.6 + - - -
393B ARG* 1.3 89.1 - - + +
395B ASP* 1.3 66.5 + - - +
397B LEU* 3.4 4.6 + - + +
398B LYS* 3.2 18.4 + - - +
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Residues in contact with ASP 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A SER* 5.3 3.7 + - - -
391B ARG 4.3 12.8 - - - +
392B TYR* 3.1 11.7 + - + +
394B ILE* 1.3 78.8 - - - +
396B VAL* 1.3 65.4 + - - +
398B LYS* 3.5 21.9 - - - +
399B MET* 3.9 7.8 + - - +
410B PRO* 6.1 0.2 - - - +
411B LYS* 3.9 32.5 + - + +
412B ALA* 3.9 26.6 + - + +
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Residues in contact with VAL 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B PHE* 3.8 20.4 - - + -
383B PHE* 4.8 0.9 - - + -
386B PHE* 3.5 41.7 - - + +
387B VAL* 3.9 17.0 - - + -
392B TYR 3.0 15.8 + - - +
393B ARG* 3.6 6.3 - - - +
395B ASP* 1.3 74.4 - - - +
397B LEU* 1.3 66.7 + - - +
399B MET* 2.9 18.9 + - - +
400B LEU* 3.1 28.5 + - + +
412B ALA* 3.9 11.7 - - + -
416B MET* 4.9 2.7 - - + -
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Residues in contact with LEU 397 (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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102B ILE* 4.1 38.4 - - + -
103B MET 3.7 11.0 - - - +
104B PHE* 4.2 7.6 - - + +
106B GLU* 3.6 31.9 - - + -
107B ARG* 3.6 22.7 - - + +
393B ARG* 2.8 17.9 + - + +
394B ILE* 3.6 10.3 - - + +
395B ASP 3.3 0.4 - - - -
396B VAL* 1.3 77.5 - - - +
398B LYS* 1.3 53.4 + - - +
400B LEU* 3.1 12.3 + - + -
401B GLN* 2.8 52.6 + - + +
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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
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361A MET* 5.6 1.6 - - - +
107B ARG* 3.4 44.8 - - - +
394B ILE 3.2 10.0 + - - +
395B ASP* 3.5 16.4 - - - +
397B LEU* 1.3 76.4 - - - +
399B MET* 1.3 65.2 + - + +
401B GLN* 3.5 6.4 + - - +
403B ASP* 3.1 58.9 + - + +
406B ASP* 3.5 26.4 + - - +
407B ASP* 2.9 31.6 + - - +
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Residues in contact with MET 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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368B ASN* 4.5 3.4 - - - +
369B TRP* 3.1 18.5 - - - -
372B PHE* 3.6 23.3 - - + -
395B ASP 4.1 9.0 - - - +
396B VAL* 2.9 12.7 + - - +
398B LYS* 1.3 92.9 - - + +
400B LEU* 1.3 60.4 + - - +
401B GLN 3.1 0.2 - - - -
402B GLY* 3.0 16.8 + - - -
403B ASP 3.3 26.0 - - - +
404B VAL* 4.0 22.4 - - + +
407B ASP* 4.5 1.1 - - - +
410B PRO* 3.7 39.0 - - + -
412B ALA* 5.2 2.7 - - + -
413B LEU* 4.2 24.9 - - + -
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Residues in contact with LEU 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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48B VAL* 3.4 22.7 - - - +
77B TRP* 3.6 32.8 - - + -
102B ILE* 4.3 15.0 - - + -
104B PHE* 3.8 8.2 - - + -
323B PHE* 3.5 30.3 - - + +
369B TRP* 4.6 3.7 - - - -
372B PHE* 3.4 25.8 - - + -
383B PHE* 4.4 1.1 - - + -
387B VAL* 4.3 11.2 - - + -
396B VAL* 3.1 27.9 + - + +
397B LEU* 3.1 17.8 + - + +
399B MET* 1.3 76.1 - - - +
401B GLN* 1.3 60.1 + - - +
402B GLY 3.2 0.4 + - - -
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Residues in contact with GLN 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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48B VAL* 3.6 3.8 - - - +
49B PRO* 3.5 10.9 - - + -
50B ALA* 2.9 28.6 + - - +
104B PHE* 2.9 45.8 + - + +
107B ARG* 2.9 53.8 + - - +
109B GLN* 3.3 30.4 + - - +
397B LEU* 2.8 25.9 + - + +
398B LYS* 3.7 5.1 - - - +
399B MET 3.1 0.4 - - - -
400B LEU* 1.3 76.4 - - - +
402B GLY* 1.3 58.1 + - - +
403B ASP* 4.7 0.2 - - + -
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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