Contacts of the helix formed by residues 471 - 485 (chain A) in PDB entry 2G4C
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 LEU 471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A LEU* 4.7 16.2 - - + -
405A GLU* 5.5 3.1 - - - +
406A LEU* 4.7 7.4 - - + -
441A VAL* 3.5 25.8 - - + -
453A ILE* 3.2 33.4 - - + -
455A LEU* 4.9 0.7 - - + -
466A MET* 3.2 24.4 - - + +
467A HIS 4.2 0.6 + - - -
468A ILE* 4.8 2.5 - - + -
469A SER* 3.4 8.4 - - - +
470A LYS* 1.3 78.6 - - - +
472A LYS* 1.3 65.6 + - - +
474A PHE* 3.4 2.0 - - + +
475A LEU* 3.0 49.1 + - + +
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Residues in contact with LYS 472 (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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405A GLU* 3.9 33.5 + - + +
406A LEU* 4.5 13.4 - - + +
409A ASN* 3.0 35.6 + - + +
411A ILE* 4.8 4.0 - - + -
469A SER 5.0 4.4 - - - +
470A LYS 3.5 0.2 - - - -
471A LEU* 1.3 78.8 - - - +
473A ASP* 1.3 93.8 + - - +
474A PHE 2.9 1.6 + - - -
475A LEU* 3.1 4.2 + - - +
476A ILE* 2.9 42.9 + - + +
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Residues in contact with ASP 473 (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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469A SER 5.4 4.2 - - - +
470A LYS* 4.3 14.8 + - + +
472A LYS* 1.3 103.1 + - - +
474A PHE* 1.3 57.4 + - - +
476A ILE* 3.9 13.3 - - - +
477A LYS* 3.1 35.4 + - - +
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Residues in contact with PHE 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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439A PHE* 4.2 19.5 - + - -
455A LEU* 3.2 34.3 - - + -
464A GLU* 5.5 4.9 - - - -
466A MET* 3.9 13.5 - - + -
470A LYS* 3.0 24.7 + - + +
471A LEU* 3.4 5.8 - - - +
472A LYS 2.9 1.0 + - - -
473A ASP* 1.3 76.8 - - - +
475A LEU* 1.3 79.8 + - + +
477A LYS* 3.0 7.8 + - + +
478A TYR* 2.9 39.7 + + + +
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Residues in contact with LEU 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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382A LYS* 5.2 2.5 - - + +
383A VAL* 4.0 15.0 - - + -
406A LEU* 3.4 32.5 - - + -
411A ILE* 3.4 28.5 - - + -
439A PHE* 3.5 37.9 - - + -
455A LEU* 5.3 0.2 - - + -
471A LEU* 3.0 33.7 + - + +
472A LYS 3.6 0.2 - - - +
474A PHE* 1.3 78.0 - - + +
476A ILE* 1.3 61.2 + - - +
478A TYR* 4.5 3.4 - - - -
479A ILE* 2.9 45.7 + - + +
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Residues in contact with ILE 476 (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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409A ASN* 4.6 17.3 - - + +
411A ILE* 4.2 14.8 - - + +
472A LYS* 2.9 47.2 + - + +
473A ASP* 3.9 15.7 - - - +
475A LEU* 1.3 76.0 - - - +
477A LYS* 1.3 62.3 + - + +
479A ILE* 4.4 3.7 - - - +
480A SER* 3.1 28.5 + - - -
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Residues in contact with LYS 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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473A ASP* 3.1 24.9 + - - +
474A PHE* 3.0 9.1 + - + +
475A LEU 3.0 0.6 - - - -
476A ILE* 1.3 80.3 - - + +
478A TYR* 1.3 59.1 + - - +
479A ILE 2.9 1.5 + - - -
480A SER* 3.0 3.8 + - - -
481A SER* 2.4 41.8 + - - -
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Residues in contact with TYR 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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376A PRO* 4.0 27.2 - - + +
438A LEU* 4.1 12.8 - - + +
439A PHE* 3.5 39.5 - + + -
459A ASP* 3.6 19.6 + - - -
474A PHE* 2.9 37.0 + + + +
475A LEU* 3.9 5.2 - - - +
477A LYS* 1.3 72.1 - - - +
479A ILE* 1.3 63.3 + - + +
481A SER* 3.1 8.3 - - - -
482A ALA* 2.9 29.3 + - + +
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Residues in contact with ILE 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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376A PRO* 4.9 4.7 - - + +
377A CYS* 4.1 10.4 - - - -
382A LYS* 3.2 45.8 - - + -
410A GLY 5.6 2.0 - - - +
411A ILE* 4.8 12.8 - - + -
438A LEU* 4.5 14.8 - - + -
439A PHE* 6.1 0.2 - - + -
475A LEU* 2.9 30.9 + - + +
476A ILE* 4.4 3.6 - - - +
477A LYS 2.9 0.2 + - - -
478A TYR* 1.3 78.2 - - + +
480A SER* 1.3 62.5 + - - +
481A SER 2.8 10.4 + - - -
482A ALA* 3.0 16.7 + - - +
483A LYS* 3.2 19.1 + - - +
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Residues in contact with SER 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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476A ILE* 3.1 21.7 + - - -
477A LYS* 3.0 4.6 + - - -
479A ILE* 1.3 79.7 - - - +
481A SER* 1.3 57.9 + - - +
483A LYS* 3.0 39.8 + - - +
484A ASN* 3.3 14.7 + - - +
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Residues in contact with SER 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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477A LYS* 2.4 30.0 + - - -
478A TYR* 3.1 11.0 - - - -
479A ILE 2.8 0.6 + - - -
480A SER* 1.3 69.2 - - - +
482A ALA* 1.3 54.8 + - - -
483A LYS 2.6 15.3 + - - -
484A ASN* 2.9 17.6 + - - +
485A VAL* 3.3 20.0 + - - +
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Residues in contact with ALA 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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265A LYS* 5.2 0.7 - - - +
375A HIS* 2.9 29.4 + - + +
376A PRO* 3.5 40.2 - - + -
478A TYR* 2.9 16.8 + - + +
479A ILE 3.0 5.6 + - - +
481A SER* 1.3 71.5 - - - +
483A LYS* 1.3 59.7 + - - +
485A VAL* 4.4 15.5 - - - +
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Residues in contact with LYS 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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113A GLU* 4.3 17.9 - - - +
265A LYS* 4.9 15.4 - - + +
266A PHE* 6.0 2.2 - - + -
375A HIS* 4.7 0.6 + - - -
377A CYS* 3.7 23.9 - - - -
479A ILE* 3.2 9.5 + - - +
480A SER* 3.0 38.9 + - - +
481A SER 2.6 5.1 + - - -
482A ALA* 1.3 76.0 - - - +
484A ASN* 1.3 74.5 + - - +
485A VAL* 3.4 6.4 + - - +
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Residues in contact with ASN 484 (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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480A SER* 3.3 13.4 + - - +
481A SER* 2.9 13.4 + - - +
483A LYS* 1.3 82.0 - - - +
485A VAL* 1.3 71.7 + - - +
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Residues in contact with VAL 485 (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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265A LYS* 5.2 9.5 - - - +
481A SER* 3.3 22.4 + - - +
482A ALA* 4.4 12.2 - - - +
483A LYS 3.4 7.3 + - - +
484A ASN* 1.3 83.5 - - + +
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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