Contacts of the helix formed by residues 484 - 495 (chain A) in PDB entry 5ODS
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 VAL 484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A GLU* 4.0 27.4 - - + +
479A TYR* 3.5 38.3 + - + +
482A ALA* 3.2 18.3 + - + +
483A ASN* 1.3 69.9 - - - +
485A PRO* 1.3 67.9 - - + +
486A ASN* 3.4 17.5 - - - +
487A LYS* 4.3 4.5 - - + -
488A VAL* 3.3 21.7 + - - +
504A TYR* 4.1 0.7 - - - -
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Residues in contact with PRO 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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483A ASN* 3.0 13.4 - - - +
484A VAL* 1.3 83.1 - - + +
486A ASN* 1.3 75.1 + - - +
488A VAL* 3.0 2.4 + - - +
489A ILE* 3.0 28.4 + - - +
504A TYR* 3.3 25.1 - - + +
508A VAL* 4.4 5.6 - - + -
510A TYR* 3.4 41.7 - - + -
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Residues in contact with ASN 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLU* 4.2 5.7 + - - +
484A VAL* 3.6 24.4 - - - +
485A PRO* 1.3 88.2 - - - +
487A LYS* 1.3 80.4 + - - +
489A ILE* 4.4 2.5 - - - +
490A GLN* 3.3 25.9 + - - +
510A TYR* 3.9 26.9 - - + +
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Residues in contact with LYS 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLU* 3.1 32.7 + - + +
465A ASP* 3.9 10.9 + - - +
479A TYR* 3.5 50.4 + - + +
484A VAL* 3.7 6.7 + - + +
485A PRO 3.1 0.4 - - - -
486A ASN* 1.3 95.4 - - - +
488A VAL* 1.3 62.2 + - - +
490A GLN* 3.5 28.1 + - - +
491A CYS* 3.1 28.8 + - - -
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Residues in contact with VAL 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LEU* 3.9 5.7 - - + +
479A TYR* 3.7 30.1 - - + +
480A LEU* 3.8 17.9 - - + +
484A VAL 3.3 15.0 - - - +
485A PRO 3.0 7.5 + - - +
487A LYS* 1.3 76.2 - - - +
489A ILE* 1.3 65.5 - - - +
490A GLN 3.1 1.3 - - - -
491A CYS* 3.0 15.4 + - - +
492A PHE* 3.2 35.5 + - + -
504A TYR* 3.6 33.9 - - + +
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Residues in contact with ILE 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A PRO 3.0 11.7 + - - +
486A ASN* 4.4 3.1 - - - +
488A VAL* 1.3 73.7 - - - +
490A GLN* 1.3 67.7 + - - +
492A PHE* 3.3 8.3 + - - +
493A ALA* 3.0 21.7 + - - +
501A ILE* 3.9 30.7 - - + +
504A TYR* 3.9 17.3 - - + -
505A ALA* 4.1 14.6 - - + -
510A TYR* 3.4 36.8 - - + -
512A PRO* 4.0 16.6 - - + -
517A LEU* 4.2 22.4 - - + -
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Residues in contact with GLN 490 (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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468A LYS* 5.7 3.3 + - - +
486A ASN 3.3 16.6 + - - +
487A LYS* 3.5 39.6 + - - +
488A VAL 3.1 0.4 - - - -
489A ILE* 1.3 79.9 - - - +
491A CYS* 1.3 57.4 + - - +
493A ALA* 3.3 7.3 + - + +
494A GLU* 2.8 56.9 + - - +
517A LEU* 6.5 0.2 - - - -
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Residues in contact with CYS 491 (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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468A LYS* 5.7 6.3 - - - -
472A PRO* 4.6 8.7 - - - +
475A ALA* 5.3 0.7 - - - -
476A LEU* 3.5 30.7 - - + -
479A TYR* 3.9 22.9 - - - -
487A LYS 3.1 21.5 - - - -
488A VAL 3.0 9.2 + - - +
490A GLN* 1.3 78.2 - - - +
492A PHE* 1.3 64.4 + - - +
494A GLU* 3.4 8.5 + - - +
495A THR* 2.9 31.8 + - - +
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Residues in contact with PHE 492 (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 LEU* 3.9 32.1 - - + -
480A LEU* 4.8 5.8 - - + -
488A VAL* 3.2 35.1 + - + -
489A ILE* 3.3 6.3 + - - +
491A CYS* 1.3 77.7 - - - +
493A ALA* 1.3 57.6 + - - +
495A THR* 3.4 2.9 + - - -
496A GLY 3.1 7.4 + - - -
497A GLN* 2.9 65.4 + - - +
500A LYS* 3.8 48.9 - - + -
501A ILE* 3.4 12.6 - - + -
504A TYR* 4.4 9.4 - + + -
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Residues in contact with ALA 493 (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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489A ILE 3.0 17.4 + - - +
490A GLN* 3.5 9.0 - - + +
491A CYS 3.1 0.2 - - - -
492A PHE* 1.3 76.8 - - - +
494A GLU* 1.3 69.4 + - - +
496A GLY* 3.2 11.8 + - - -
501A ILE* 3.9 15.7 - - + +
517A LEU* 4.8 16.2 - - + -
520A ASN* 6.2 3.6 - - + +
521A VAL* 6.5 1.8 - - + -
524A ILE* 6.1 1.2 - - - +
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Residues in contact with GLU 494 (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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468A LYS* 4.8 12.7 + - - +
490A GLN* 2.8 53.2 + - - +
491A CYS* 3.9 9.4 - - - +
493A ALA* 1.3 80.5 - - - +
495A THR* 1.3 63.9 + - + +
496A GLY 3.4 2.3 + - - -
524A ILE* 5.6 5.7 - - - +
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Residues in contact with THR 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A PRO* 6.2 4.3 - - + -
473A THR* 5.6 10.3 - - + -
491A CYS 2.9 18.5 + - - +
492A PHE* 3.4 5.5 + - - -
493A ALA 3.2 0.2 - - - -
494A GLU* 1.3 81.4 - - + +
496A GLY* 1.3 55.0 + - - +
497A GLN* 2.7 38.1 + - - +
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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