Contacts of the helix formed by residues 475 - 485 (chain G) in PDB entry 3DBL
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 LYS 475 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419G PRO* 3.7 21.0 + - + +
420G ASP* 3.2 28.0 + - - -
424G VAL* 5.2 1.0 - - - +
473G MET* 3.7 22.8 + - + -
474G VAL* 1.3 79.0 - - - +
476G ASP* 1.3 63.6 + - - +
477G ASP* 3.0 24.7 + - - +
478G TYR* 3.4 41.7 + - + +
479G VAL* 3.9 5.7 + - - +
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Residues in contact with ASP 476 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454G ILE* 6.0 0.2 - - - +
458G LYS* 2.9 30.1 + - - -
474G VAL 4.1 5.7 - - - +
475G LYS* 1.3 72.1 - - - +
477G ASP* 1.3 67.1 + - - +
478G TYR 3.3 0.2 - - - -
479G VAL* 3.3 18.9 + - + +
480G HIS* 3.4 22.0 + - + +
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Residues in contact with ASP 477 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475G LYS* 3.8 28.7 + - + +
476G ASP* 1.3 77.7 - - - +
478G TYR* 1.3 62.6 + - + +
480G HIS* 3.1 18.4 + - - +
481G GLU 3.3 9.9 + - - -
29H PRO* 3.5 30.3 - - - +
30H PHE* 3.8 20.5 - - + -
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Residues in contact with TYR 478 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419G PRO 3.5 18.4 - - - -
420G ASP* 2.9 37.2 + - - +
424G VAL* 4.2 22.2 - - + -
425G LEU* 3.9 31.0 - - + -
428G MET* 4.3 17.5 - - + -
474G VAL* 4.7 0.2 - - + -
475G LYS* 3.4 32.7 + - + +
476G ASP 3.3 0.2 - - - -
477G ASP* 1.3 78.9 - - + +
479G VAL* 1.3 60.0 + - - +
481G GLU* 3.7 6.4 + - + +
482G PHE* 3.2 33.8 + + - +
525G MET* 5.7 2.7 - - + -
30H PHE* 3.8 32.3 - + - -
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Residues in contact with VAL 479 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428G MET* 4.0 12.1 - - + -
454G ILE* 3.6 28.5 - - + +
457G LEU* 3.6 20.0 - - + +
458G LYS* 4.0 25.8 - - + +
461G LEU* 4.1 25.8 - - + -
474G VAL 5.4 0.7 - - - +
475G LYS 4.1 13.0 - - - +
476G ASP* 3.3 13.4 + - + +
477G ASP 3.2 1.2 - - - -
478G TYR* 1.3 74.5 - - - +
480G HIS* 1.3 66.5 + - - +
483G CYS* 3.6 15.4 + - - -
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Residues in contact with HIS 480 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454G ILE* 3.1 47.8 - - + +
476G ASP* 3.4 22.1 + - + +
477G ASP* 3.1 5.2 + - - +
479G VAL* 1.3 76.5 - - - +
481G GLU* 1.3 57.0 + - - +
483G CYS* 2.5 36.7 + - - +
484G ARG* 3.3 5.4 + - - +
29H PRO* 3.2 36.1 - - + -
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Residues in contact with GLU 481 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477G ASP 3.3 3.3 + - - +
478G TYR* 3.8 7.9 - - + +
480G HIS* 1.3 79.7 - - - +
482G PHE* 1.3 64.2 + - + +
484G ARG* 3.1 36.7 + - - +
485G TYR* 2.9 43.2 + - + +
525G MET* 3.5 15.3 - - + -
29H PRO* 4.1 4.7 - - - +
30H PHE* 3.6 31.1 + - + -
315H TYR* 2.5 43.3 + - - -
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Residues in contact with PHE 482 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G TYR* 3.9 39.2 - + - -
159G VAL* 3.7 23.8 - - + -
425G LEU* 3.8 30.1 - - + -
428G MET* 3.6 43.1 - - + -
429G LEU* 4.5 12.3 - - + -
432G VAL* 3.9 12.6 - - + -
443G PRO* 4.0 10.7 - - - +
457G LEU* 4.1 9.4 - - + -
478G TYR* 3.2 28.0 + + - +
480G HIS 2.8 4.2 + - - -
481G GLU* 1.3 79.2 - - + +
483G CYS* 1.3 60.4 + - - +
485G TYR* 3.6 29.0 - + - +
486G GLY 4.0 0.3 + - - -
525G MET* 6.2 0.2 - - - -
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Residues in contact with CYS 483 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443G PRO* 3.8 21.1 - - - +
444G GLY* 3.5 6.8 - - - +
450G VAL* 4.2 15.7 - - + +
453G ASP* 4.2 5.2 - - - -
454G ILE* 3.8 37.7 - - + -
457G LEU* 3.8 16.6 - - - -
479G VAL 3.6 15.7 - - - -
480G HIS 2.5 17.4 + - - +
482G PHE* 1.3 70.5 - - - +
484G ARG* 1.3 58.2 + - - +
485G TYR 3.1 2.0 - - - -
486G GLY 3.3 5.2 + - - -
26H ARG* 2.9 21.1 + - - -
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Residues in contact with ARG 484 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450G VAL* 4.7 5.5 - - + +
480G HIS 3.3 3.2 + - - +
481G GLU* 3.1 27.6 + - - +
483G CYS* 1.3 80.8 - - - +
485G TYR* 1.3 62.6 + - + +
22H LYS* 3.6 28.4 + - - +
23H PHE* 3.1 29.0 + - + +
26H ARG* 3.2 39.0 + - + +
27H SER* 3.2 27.8 - - - +
28H GLY* 4.0 5.9 - - - -
31H THR* 4.4 11.2 + - - +
35H PHE* 4.1 5.3 - - - -
314H ALA* 3.0 28.5 + - - +
315H TYR* 3.1 39.9 + - - +
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Residues in contact with TYR 485 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G TYR* 3.9 24.5 - + + -
157G GLY* 3.4 27.1 - - - -
158G LEU* 3.3 27.5 + - + +
159G VAL* 4.1 11.9 - - + +
481G GLU* 2.9 40.6 + - + +
482G PHE* 3.6 30.4 - + - +
483G CYS 3.1 0.2 - - - -
484G ARG* 1.3 78.8 - - - +
486G GLY* 1.3 64.2 + - - +
487G ALA 4.1 0.9 - - - +
488G ALA* 3.0 25.3 + - - +
525G MET* 2.7 35.7 - - - -
22H LYS* 3.1 5.0 - - - +
23H PHE* 3.9 12.8 - + - -
315H TYR* 3.4 1.6 - - - -
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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