Contacts of the helix formed by residues 496 - 507 (chain A) in PDB entry 3C51
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 496 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A LYS* 4.4 7.0 - - - +
494A ALA 4.4 3.5 - - - +
495A PHE* 1.3 83.8 - - - +
497A LYS* 1.3 65.4 + - - +
498A ALA* 3.2 9.6 - - + +
499A ASP* 3.3 24.3 + - - +
500A THR* 2.9 18.2 + - - -
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Residues in contact with LYS 497 (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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496A GLU* 1.3 75.0 + - - +
498A ALA* 1.3 62.1 + - - +
500A THR* 3.1 17.2 + - - +
501A GLU* 3.4 15.6 + - - +
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Residues in contact with ALA 498 (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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496A GLU* 3.2 7.9 - - + +
497A LYS* 1.3 78.5 - - - +
499A ASP* 1.3 64.5 + - - +
501A GLU* 4.4 8.1 + - - +
502A PHE* 4.3 9.5 + - - +
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Residues in contact with ASP 499 (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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224A LYS* 2.5 45.0 + - + +
229A TYR* 3.7 24.4 + - - +
495A PHE* 4.2 4.4 - - + -
496A GLU* 3.3 21.7 + - - +
497A LYS 3.2 0.6 - - - -
498A ALA* 1.3 78.8 - - - +
500A THR* 1.3 57.2 + - - +
501A GLU 3.2 1.8 - - - -
502A PHE* 2.7 33.1 + - - +
503A PHE* 3.1 21.5 + - + -
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Residues in contact with THR 500 (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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220A LYS* 5.5 3.6 - - - +
255A GLU* 5.3 4.5 - - - +
495A PHE* 5.7 9.4 - - + -
496A GLU 2.9 16.9 + - - +
497A LYS* 3.1 12.9 + - - +
499A ASP* 1.3 75.0 - - + +
501A GLU* 1.3 61.8 + - - +
503A PHE* 2.9 32.6 + - + +
504A GLN* 3.0 31.4 + - + +
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Residues in contact with GLU 501 (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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497A LYS 3.4 13.7 + - - +
498A ALA* 4.5 8.0 - - - +
499A ASP 3.1 0.8 + - - -
500A THR* 1.3 78.0 - - - +
502A PHE* 1.3 59.8 + - - +
504A GLN* 3.9 8.5 + - - +
505A GLU* 3.3 22.6 + - - +
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Residues in contact with PHE 502 (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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223A LEU* 5.5 0.9 - - + -
229A TYR* 3.2 66.6 - + + -
230A GLN* 5.5 0.9 - - - -
232A ALA* 5.5 0.9 - - + -
233A MET* 3.1 43.3 - - + -
260A LEU* 4.3 8.1 - - + -
498A ALA 4.3 6.3 + - - +
499A ASP* 2.7 20.7 + - - +
501A GLU* 1.3 71.7 - - - +
503A PHE* 1.3 59.2 + + - -
505A GLU* 2.9 16.8 + - - +
506A PHE* 2.6 47.9 + + + -
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Residues in contact with PHE 503 (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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220A LYS* 3.7 54.1 - - + -
223A LEU* 5.2 1.6 - - + -
229A TYR* 3.5 36.1 - + - -
255A GLU* 3.7 18.0 - - - +
260A LEU* 3.4 31.0 - - + +
495A PHE* 4.2 15.7 - + - -
499A ASP* 3.1 14.9 + - + -
500A THR* 2.9 30.5 + - + +
502A PHE* 1.3 83.0 - + - +
504A GLN* 1.3 57.7 + - - +
506A PHE* 3.4 3.9 + - - +
507A ALA* 2.8 29.5 + - - +
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Residues in contact with GLN 504 (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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255A GLU* 3.7 20.2 - - - +
500A THR* 3.0 32.1 + - + +
501A GLU* 4.2 7.1 - - - +
503A PHE* 1.3 75.5 - - - +
505A GLU* 1.3 63.4 + - - +
507A ALA* 3.2 21.4 + - - +
508A SER* 4.1 1.6 + - - -
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Residues in contact with GLU 505 (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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233A MET* 3.6 33.2 - - - +
236A LYS* 4.2 9.0 + - - -
237A LYS* 4.0 18.6 + - - -
501A GLU 3.3 13.3 + - - +
502A PHE* 2.9 17.8 + - - +
504A GLN* 1.3 77.2 - - - +
506A PHE* 1.3 59.0 + - - +
508A SER* 4.6 3.2 + - - -
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Residues in contact with PHE 506 (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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218A LEU* 4.3 7.9 - - + -
232A ALA* 3.3 31.4 - - + -
233A MET* 3.5 31.8 - - + +
236A LYS* 3.0 38.7 - - + +
253A ALA* 4.3 1.9 - - + +
254A PHE 5.0 1.8 - - - -
260A LEU* 3.4 45.5 - - + -
261A CYS 4.3 4.9 - - - -
262A LEU* 4.0 32.5 - - + -
502A PHE* 2.6 19.5 + + + +
503A PHE 3.5 8.5 - - - +
505A GLU* 1.3 72.6 - - - +
507A ALA* 1.3 56.2 + - - +
508A SER 2.7 18.0 + - - -
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Residues in contact with ALA 507 (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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253A ALA 3.4 8.8 - - - +
254A PHE* 3.7 6.5 - - + +
255A GLU* 3.4 41.5 - - + +
503A PHE 2.8 18.6 + - - +
504A GLN* 3.2 11.5 + - - +
506A PHE* 1.3 74.1 - - + +
508A SER* 1.3 65.3 + - - +
509A GLY* 3.1 4.6 + - - -
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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