Contacts of the helix formed by residues 498 - 508 (chain B) 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 498 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496B GLY 3.4 13.7 - - - +
497B GLN* 1.3 72.2 - - - +
499B GLN* 1.3 69.6 + - + +
500B LYS 3.3 2.2 - - - -
501B ILE* 3.2 24.0 + - + +
502B VAL* 3.7 2.3 + - - +
521B VAL* 3.9 29.2 - - + -
528B GLN* 4.1 15.5 - - + +
531B GLN* 3.9 19.7 - - + +
532B PHE* 3.8 37.5 - - + +
535B MET* 3.4 20.8 - - + +
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Residues in contact with GLN 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B GLN* 3.8 1.2 - - + +
498B VAL* 1.3 81.1 - - + +
500B LYS* 1.3 65.3 + - + +
501B ILE 3.3 0.7 + - - -
502B VAL* 3.4 5.7 + - - +
503B LEU* 3.3 39.1 + - + +
531B GLN* 5.2 9.9 + - - +
535B MET* 3.7 21.0 - - + +
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Residues in contact with LYS 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B PHE* 3.8 39.0 - - + -
497B GLN* 4.5 26.9 + - + +
498B VAL 3.3 1.0 - - - +
499B GLN* 1.3 79.2 - - + +
501B ILE* 1.3 59.9 + - - +
503B LEU* 3.9 12.2 - - + +
504B TYR* 3.0 32.6 + - - +
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Residues in contact with ILE 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B ILE* 3.8 25.0 - - + +
492B PHE* 3.4 24.7 - - + -
493B ALA* 3.7 27.8 - - + +
497B GLN 3.4 19.5 - - - +
498B VAL* 3.2 21.2 + - + +
500B LYS* 1.3 77.3 - - - +
502B VAL* 1.3 57.5 + - - +
504B TYR* 3.9 2.2 - - - +
505B ALA* 3.1 27.7 + - - +
514B TRP* 3.3 32.3 - - + -
517B LEU* 5.0 0.7 - - + -
521B VAL* 4.7 5.4 - - + -
532B PHE* 4.3 6.7 - - + -
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Residues in contact with VAL 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B VAL 4.0 0.2 - - - +
499B GLN 3.4 4.2 + - - +
501B ILE* 1.3 73.7 - - - +
503B LEU* 1.3 63.3 + - + +
505B ALA* 3.5 2.9 + - - +
506B LYS* 3.1 29.9 + - + +
514B TRP* 4.3 15.0 - - + -
532B PHE* 3.9 18.2 - - + -
535B MET* 3.7 49.1 - - + -
536B LEU* 5.5 1.6 - - + -
543B LEU* 4.3 23.3 - - + -
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Residues in contact with LEU 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B GLN* 3.3 44.1 + - + +
500B LYS* 3.9 11.4 - - + +
501B ILE 3.4 0.6 - - - -
502B VAL* 1.3 76.3 - - + +
504B TYR* 1.3 59.0 + - - +
506B LYS* 3.2 6.8 + - + +
507B LYS* 3.0 29.2 + - - +
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Residues in contact with TYR 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B LEU* 3.8 30.3 + - + +
483B ASN* 4.3 6.9 + - - -
484B VAL 4.0 1.0 + - - -
485B PRO* 3.3 44.0 - - + +
488B VAL* 3.6 28.1 - - + +
489B ILE* 3.9 18.6 - - + -
492B PHE* 4.4 9.2 - + + -
500B LYS 3.0 18.8 + - - +
501B ILE* 3.9 2.5 - - - +
503B LEU* 1.3 71.3 - - - +
505B ALA* 1.3 61.0 + - - +
506B LYS 3.0 10.6 + - - -
507B LYS* 3.1 8.9 + - + +
508B VAL* 3.0 47.7 + - + +
510B TYR* 5.5 0.4 - - + -
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Residues in contact with ALA 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B ILE* 4.2 11.0 - - + -
501B ILE 3.1 16.5 + - - +
502B VAL 3.6 4.3 - - - +
503B LEU 3.4 0.2 - - - -
504B TYR* 1.3 81.3 - - - +
506B LYS* 1.3 57.5 + - - +
509B GLY* 3.2 22.1 - - - -
510B TYR* 3.4 25.1 + - - +
514B TRP* 3.8 23.6 - - + -
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Residues in contact with LYS 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B VAL* 3.1 19.3 + - + +
503B LEU* 3.7 7.4 - - + +
504B TYR 3.0 1.0 - - - -
505B ALA* 1.3 76.7 - - - +
507B LYS* 1.3 65.9 + - - +
509B GLY* 3.4 10.8 + - - +
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Residues in contact with LYS 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B LEU 3.0 17.0 + - - +
504B TYR* 3.6 9.4 - - + +
506B LYS* 1.3 77.9 - - - +
508B VAL* 1.3 68.8 + - + +
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Residues in contact with VAL 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483B ASN* 6.0 3.4 - - - +
485B PRO* 4.8 9.4 - - + -
504B TYR* 3.0 47.0 + - + +
507B LYS* 1.3 82.2 - - + +
509B GLY* 1.3 60.3 + - - +
510B TYR* 3.6 25.8 - - + +
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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