Contacts of the helix formed by residues 457 - 472 (chain X) in PDB entry 5G04
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 THR 457 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452X LEU* 2.9 50.5 + - - +
455X PRO* 3.2 22.8 - - + +
456X VAL* 1.3 71.3 - - - +
458X GLN* 1.3 62.7 + - - +
459X GLU 3.3 4.4 + - - -
460X LYS* 3.4 23.2 + - + -
461X ALA* 3.3 3.3 + - - +
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Residues in contact with GLN 458 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452X LEU 5.3 0.2 - - - -
453X GLU* 5.2 2.7 - - + +
456X VAL* 2.8 25.8 + - - +
457X THR* 1.3 72.2 - - - +
459X GLU* 1.3 57.7 + - + +
461X ALA* 3.6 6.8 + - - +
462X LYS* 3.1 40.1 + - + +
485X LEU* 4.8 9.4 + - + +
488X ARG* 3.4 52.4 + - - +
489X GLU* 3.8 23.7 + - - +
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Residues in contact with GLU 459 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457X THR 3.3 0.6 - - - -
458X GLN* 1.3 78.7 - - + +
460X LYS* 1.3 78.2 + - + +
462X LYS* 3.5 15.0 + - - +
463X THR* 3.5 20.9 + - - +
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Residues in contact with LYS 460 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452X LEU* 3.3 25.0 - - + +
457X THR* 3.4 31.3 + - + -
459X GLU* 1.3 89.1 + - + +
461X ALA* 1.3 62.0 + - - +
463X THR* 3.4 16.6 + - - -
464X LEU* 3.4 17.0 - - - +
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Residues in contact with ALA 461 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449X THR* 3.3 20.8 - - - +
452X LEU* 3.4 30.6 - - + +
453X GLU* 3.3 26.7 - - - +
457X THR 3.3 12.0 + - - +
458X GLN* 3.9 5.2 - - - +
459X GLU 3.3 0.2 - - - -
460X LYS* 1.3 77.4 - - - +
462X LYS* 1.3 62.6 + - - +
464X LEU* 3.3 2.8 + - - +
465X LEU* 3.1 17.9 + - - +
485X LEU* 5.4 0.7 - - - -
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Residues in contact with LYS 462 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458X GLN* 3.1 28.0 + - + +
459X GLU* 3.5 7.2 + - - +
461X ALA* 1.3 74.3 - - - +
463X THR* 1.3 61.1 + - + +
465X LEU* 3.2 3.2 + - - +
466X ASP* 2.9 49.1 + - - +
482X LYS* 5.1 4.6 - - - +
485X LEU* 3.6 32.5 - - + +
486X LEU* 4.2 20.2 - - - +
489X GLU* 3.5 40.2 - - - +
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Residues in contact with THR 463 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459X GLU 3.5 14.0 + - - +
460X LYS* 3.4 15.4 + - - -
462X LYS* 1.3 76.0 - - + +
464X LEU* 1.3 67.8 + - - +
466X ASP* 3.5 10.6 + - - +
467X LYS* 3.0 36.5 + - - +
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Residues in contact with LEU 464 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434X TYR* 4.9 9.2 - - + +
445X THR* 4.0 33.0 - - + +
448X ALA* 4.9 11.7 - - + -
449X THR* 3.7 13.2 - - + +
452X LEU* 5.4 7.2 - - + -
460X LYS* 3.4 17.7 - - + +
461X ALA* 3.3 10.3 + - - +
462X LYS 3.3 0.2 - - - -
463X THR* 1.3 89.1 + - - +
465X LEU* 1.3 57.5 + - - +
467X LYS* 3.3 21.0 + - + +
468X ALA* 3.0 27.5 + - - +
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Residues in contact with LEU 465 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446X LEU* 4.9 4.9 - - - -
449X THR* 3.4 33.5 - - + +
453X GLU* 4.9 4.0 - - - +
461X ALA 3.1 8.3 + - - +
462X LYS* 3.2 9.6 + - - +
464X LEU* 1.3 72.6 - - - +
466X ASP* 1.3 66.2 + - - +
468X ALA* 3.4 9.0 + - + +
469X LEU* 3.3 23.4 + - - +
478X ALA* 3.5 31.4 - - + +
481X LYS* 3.7 16.2 - - + +
482X LYS* 3.6 31.4 - - + +
485X LEU* 3.6 22.0 - - + -
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Residues in contact with ASP 466 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462X LYS* 2.9 29.3 + - - +
463X THR* 3.5 11.8 - - - +
465X LEU* 1.3 75.9 - - - +
467X LYS* 1.3 61.2 + - + +
469X LEU* 3.4 6.6 + - - +
470X THR* 3.3 27.0 + - + +
482X LYS* 2.7 44.3 + - - +
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Residues in contact with LYS 467 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445X THR* 5.5 6.5 - - + -
463X THR* 3.0 23.2 + - - +
464X LEU* 3.5 24.7 - - + +
465X LEU 3.3 0.2 - - - -
466X ASP* 1.3 75.2 - - + +
468X ALA* 1.3 63.1 + - - +
470X THR* 2.6 26.9 + - - +
471X GLN* 3.3 18.1 + - - +
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Residues in contact with ALA 468 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442X GLN* 4.2 15.8 - - + +
445X THR* 3.3 28.0 + - - +
446X LEU* 4.5 4.9 - - - +
464X LEU 3.0 11.6 + - - +
465X LEU* 3.5 19.5 - - + +
466X ASP 3.4 0.2 - - - -
467X LYS* 1.3 73.4 - - - +
469X LEU* 1.3 62.1 + - - +
471X GLN* 3.4 18.3 + - - +
472X ARG* 3.4 11.8 + - - +
475X TYR* 5.8 1.0 - - - +
478X ALA* 4.7 9.9 - - + -
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Residues in contact with LEU 469 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465X LEU 3.3 7.4 + - - +
466X ASP* 3.8 7.2 - - - +
467X LYS 3.3 0.4 - - - -
468X ALA* 1.3 76.6 - - - +
470X THR* 1.3 65.1 + - + +
472X ARG 3.0 22.8 - - - +
473X PRO* 3.9 5.4 - - - +
474X ASP 4.7 3.4 - - - +
475X TYR 4.1 13.0 - - - +
478X ALA* 3.7 25.4 - - + +
479X VAL* 3.5 39.0 - - + -
482X LYS* 3.7 32.1 - - + +
498X LEU* 4.3 13.7 - - + -
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Residues in contact with THR 470 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466X ASP* 3.3 16.7 + - + +
467X LYS* 2.6 26.4 + - + +
469X LEU* 1.3 77.4 - - + +
471X GLN* 1.3 64.2 + - - +
472X ARG 4.8 0.7 - - - -
473X PRO* 4.9 4.9 - - - +
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Residues in contact with GLN 471 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440X ASN* 3.6 42.7 - - + +
441X ALA 3.8 13.6 + - - +
442X GLN* 3.9 16.1 + - + +
445X THR* 4.7 10.5 + - - +
467X LYS* 3.3 16.9 + - - +
468X ALA* 3.6 10.3 - - - +
469X LEU 3.3 0.2 - - - -
470X THR* 1.3 84.8 + - - +
472X ARG* 1.3 58.0 + - - +
473X PRO* 4.0 4.5 - - - +
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Residues in contact with ARG 472 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442X GLN* 3.7 30.5 - - + +
468X ALA 3.4 4.8 + - - +
469X LEU* 3.0 19.9 - - - +
471X GLN* 1.3 79.7 - - - +
473X PRO* 1.4 69.5 - - + +
474X ASP 3.4 2.4 + - - -
475X TYR* 3.8 22.1 + - + +
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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