Contacts of the helix formed by residues 473 - 483 (chain A) in PDB entry 3C5R
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 HIS 473 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A SER 3.1 25.4 - - - -
437A ILE 2.9 20.1 + - - -
438A LYS 3.8 13.0 - - - -
439A GLY* 3.3 12.2 + - - -
468A ALA* 2.9 11.1 + - + +
471A HIS* 3.4 31.2 + - + +
472A GLY* 1.3 76.3 + - - +
474A LEU* 1.3 63.3 + - - +
475A LYS 3.4 2.0 - - - -
476A VAL* 3.2 22.3 + - + -
477A VAL* 2.9 23.2 + - - +
509A ILE* 4.1 2.5 - - - -
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Residues in contact with LEU 474 (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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472A GLY 3.3 6.8 + - - +
473A HIS* 1.3 72.1 - - - +
475A LYS* 1.3 59.5 + - - +
477A VAL* 3.1 4.9 + - - +
478A GLU* 2.9 28.4 + - + +
508A ASP* 3.9 45.1 - - + +
509A ILE* 3.6 27.1 - - + -
512A LEU* 3.9 20.4 - - + -
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Residues in contact with LYS 475 (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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441A ILE* 3.6 42.2 - - + -
445A GLU* 4.6 8.6 + - - -
473A HIS 3.4 0.4 - - - -
474A LEU* 1.3 80.3 - - - +
476A VAL* 1.3 56.9 + - - +
478A GLU* 3.4 23.6 + - - +
479A LEU* 2.9 55.8 + - + +
482A GLN* 5.0 3.8 + - - +
535B ASP* 6.4 0.4 - - + -
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Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A SER* 3.8 17.3 - - - +
439A GLY* 3.9 28.0 - - - -
441A ILE* 4.0 21.3 - - + -
444A VAL* 3.9 22.7 - - + -
468A ALA* 3.5 20.2 - - + -
473A HIS* 3.2 14.8 + - + +
475A LYS* 1.3 74.3 - - + +
477A VAL* 1.3 64.2 + - - +
479A LEU* 3.3 9.5 + - + +
480A LEU* 3.0 33.4 + - + +
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Residues in contact with VAL 477 (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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465A LEU* 3.8 15.7 - - + -
468A ALA* 3.6 31.2 - - + +
469A CYS* 3.7 14.6 - - - -
473A HIS 2.9 18.4 + - - +
474A LEU* 3.3 9.0 - - - +
476A VAL* 1.3 74.8 - - - +
478A GLU* 1.3 57.1 + - - +
480A LEU* 3.1 5.5 + - - +
481A LEU* 3.0 46.1 + - + +
509A ILE* 3.9 23.8 - - + -
512A LEU* 3.9 11.4 - - + -
513A LEU* 4.3 3.4 - - + -
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Residues in contact with GLU 478 (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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474A LEU* 2.9 14.1 + - + +
475A LYS* 3.6 31.9 + - - +
476A VAL 3.3 0.2 - - - -
477A VAL* 1.3 77.5 - - - +
479A LEU* 1.3 58.2 + - - +
481A LEU* 3.3 5.6 + - - +
482A GLN* 2.8 57.5 + - + +
512A LEU* 3.8 30.0 - - + +
516A TYR* 5.1 4.0 - - + +
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Residues in contact with LEU 479 (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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441A ILE* 4.0 26.9 - - + +
444A VAL* 4.2 17.0 - - + -
445A GLU* 4.0 28.9 - - + +
448A LEU* 3.8 13.2 - - + -
475A LYS* 2.9 42.2 + - + +
476A VAL* 3.6 5.8 - - - +
478A GLU* 1.3 73.9 - - - +
480A LEU* 1.3 62.9 + - - +
482A GLN* 3.3 16.1 + - - +
483A HIS* 3.0 43.7 + - + -
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Residues in contact with LEU 480 (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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432A LEU* 4.2 7.2 - - + -
436A SER* 3.8 5.2 - - - +
444A VAL* 4.6 1.1 - - + -
448A LEU* 3.8 22.9 - - + -
454A PRO* 3.9 20.5 - - + +
464A PRO* 3.5 42.8 - - + +
465A LEU* 3.6 13.7 - - + +
468A ALA* 4.0 4.9 - - + -
476A VAL* 3.0 36.3 + - + +
477A VAL 3.1 6.0 + - - +
479A LEU* 1.3 73.3 - - - +
481A LEU* 1.3 63.0 + - - +
483A HIS* 3.0 11.9 + - - +
484A LYS 3.1 0.7 + - - -
485A ALA* 3.0 32.5 + - + +
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Residues in contact with LEU 481 (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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465A LEU* 4.1 18.2 - - + -
477A VAL* 3.0 35.6 + - + +
478A GLU 3.7 5.8 - - - +
480A LEU* 1.3 72.2 - - - +
482A GLN* 1.3 65.6 + - - +
484A LYS* 3.1 13.7 + - - +
485A ALA 3.7 20.4 - - - +
487A VAL* 4.1 22.4 - - + -
512A LEU* 4.1 11.9 - - + +
513A LEU* 4.2 9.6 - - + -
516A TYR* 3.6 52.8 - - + -
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Residues in contact with GLN 482 (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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475A LYS* 5.0 3.4 + - - +
478A GLU* 2.8 49.8 + - - +
479A LEU* 3.3 26.5 + - - +
481A LEU* 1.3 73.8 - - - +
483A HIS* 1.3 64.3 + - + +
484A LYS* 3.5 10.2 + - - +
516A TYR* 3.8 18.2 + - - +
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Residues in contact with HIS 483 (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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445A GLU* 5.3 1.1 - - + -
448A LEU* 3.4 62.1 + - + +
449A GLN* 4.0 11.8 + - + +
454A PRO* 3.4 16.4 - - + +
479A LEU* 3.0 38.6 + - + +
480A LEU 3.0 8.0 + - - +
482A GLN* 1.3 83.1 - - + +
484A LYS* 1.3 66.6 + - - +
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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