Contacts of the helix formed by residues 497 - 509 (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 GLN 497 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476A LEU* 5.9 1.6 - - - +
492A PHE* 2.9 44.3 + - + +
495A THR* 2.7 31.3 + - - +
496A GLY* 1.3 70.1 - - - +
498A VAL* 1.3 61.5 - - - +
499A GLN* 3.5 2.0 - - + +
500A LYS* 3.5 41.5 - - + +
501A ILE* 3.4 8.6 + - - +
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Residues in contact with VAL 498 (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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496A GLY* 2.8 18.8 + - - +
497A GLN* 1.3 71.8 - - - +
499A GLN* 1.3 68.2 + - - +
500A LYS 3.3 0.4 - - - -
501A ILE* 3.1 28.5 + - + +
502A VAL* 3.3 8.5 + - - +
521A VAL* 4.1 28.7 - - + -
528A GLN* 4.2 14.3 + - + +
531A GLN* 5.4 7.9 - - - +
532A PHE* 3.2 46.4 - - + +
535A MET* 4.2 8.7 - - - -
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Residues in contact with GLN 499 (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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497A GLN* 3.5 0.6 - - - +
498A VAL* 1.3 81.2 - - - +
500A LYS* 1.3 57.9 + - + +
502A VAL* 3.3 5.2 + - - +
503A LEU* 3.1 45.6 + - + +
531A GLN* 3.4 24.0 - - - +
535A MET* 3.7 26.2 - - + +
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Residues in contact with LYS 500 (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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492A PHE* 3.8 33.5 - - + -
497A GLN* 3.5 36.4 + - + +
498A VAL 3.3 0.4 - - - -
499A GLN* 1.3 76.4 - - + +
501A ILE* 1.3 65.2 + - - +
503A LEU* 4.1 15.2 - - + +
504A TYR* 3.0 27.7 + - - +
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Residues in contact with ILE 501 (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* 3.9 29.0 - - + +
492A PHE* 3.4 23.6 - - + -
493A ALA* 3.9 28.5 - - + +
497A GLN 3.4 13.4 + - - +
498A VAL* 3.1 23.5 + - + +
500A LYS* 1.3 77.8 - - - +
502A VAL* 1.3 60.2 + - + +
504A TYR* 3.9 1.9 - - - +
505A ALA* 3.1 28.6 + - - +
514A TRP* 3.8 24.5 - - + -
517A LEU* 4.3 9.6 - - + -
521A VAL* 6.0 3.4 - - + -
532A PHE* 5.0 6.5 - - + -
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Residues in contact with VAL 502 (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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498A VAL 3.3 14.3 + - - +
499A GLN 3.7 0.4 - - - +
500A LYS 3.3 0.2 - - - -
501A ILE* 1.3 74.1 - - - +
503A LEU* 1.3 65.9 + - + +
505A ALA* 4.1 0.9 - - - +
506A LYS* 3.2 36.8 + - + +
514A TRP* 4.4 11.1 - - + -
532A PHE* 4.1 21.8 - - + -
535A MET* 3.7 43.7 - - + +
543A LEU* 3.5 28.9 - - + -
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Residues in contact with LEU 503 (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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499A GLN* 3.1 41.0 + - + +
500A LYS* 4.1 13.2 - - + +
501A ILE 3.4 0.2 - - - -
502A VAL* 1.3 76.2 - - + +
504A TYR* 1.3 62.3 + - - +
506A LYS* 3.5 6.5 + - + +
507A LYS* 3.1 27.7 + - + +
535A MET* 5.4 4.0 - - + -
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Residues in contact with TYR 504 (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 LEU* 3.7 29.9 + - + +
483A ASN* 4.2 7.1 + - - -
484A VAL 4.0 1.6 + - - -
485A PRO* 3.3 44.2 - - + +
488A VAL* 3.6 29.3 - - + +
489A ILE* 3.9 17.9 - - + -
492A PHE* 4.4 9.0 - + + -
500A LYS 3.0 19.3 + - - +
501A ILE* 3.9 2.5 - - - +
503A LEU* 1.3 77.4 - - - +
505A ALA* 1.3 59.6 + - - +
507A LYS* 3.0 6.7 + - + +
508A VAL* 2.9 56.7 + - + +
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Residues in contact with ALA 505 (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* 4.1 14.6 - - + -
501A ILE 3.1 16.8 + - - +
502A VAL 4.3 0.7 - - - +
504A TYR* 1.3 84.5 - - - +
506A LYS* 1.3 57.7 + - - +
508A VAL* 4.3 3.6 - - - -
509A GLY* 3.2 20.7 + - - -
510A TYR 3.2 26.5 + - - +
512A PRO* 4.4 0.2 - - + -
514A TRP* 3.7 25.8 - - + -
543A LEU* 6.2 0.2 - - - -
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Residues in contact with LYS 506 (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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502A VAL* 3.2 28.9 + - + +
503A LEU* 3.9 6.1 - - + +
504A TYR 3.2 0.6 - - - -
505A ALA* 1.3 77.7 - - - +
507A LYS* 1.3 65.2 + - + +
509A GLY* 3.9 6.1 + - - -
535A MET 5.0 3.2 + - - -
538A GLN* 4.6 19.2 + - - +
541A GLU* 4.4 28.1 + - - +
543A LEU* 4.1 37.0 - - + +
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Residues in contact with LYS 507 (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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503A LEU 3.1 17.6 + - - +
504A TYR* 3.0 7.7 + - + +
506A LYS* 1.3 81.2 - - + +
508A VAL* 1.3 66.0 + - + +
509A GLY* 3.5 1.0 + - - -
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Residues in contact with VAL 508 (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* 6.0 3.4 - - - +
485A PRO* 4.4 7.0 - - + -
504A TYR* 2.9 57.0 + - + +
505A ALA* 4.3 0.7 - - - -
507A LYS* 1.3 79.2 - - + +
509A GLY* 1.3 60.5 + - - +
510A TYR* 3.4 26.6 + - + +
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Residues in contact with GLY 509 (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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505A ALA 3.2 12.5 + - - -
506A LYS* 4.4 4.9 - - - -
507A LYS 3.3 4.2 - - - -
508A VAL* 1.3 77.8 - - - +
510A TYR* 1.3 63.4 + - - +
511A THR* 3.7 7.5 + - - -
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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