Contacts of the helix formed by residues 558 - 572 (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 LEU 558 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522B MET* 4.5 10.3 - - + -
526B PRO* 4.4 28.3 - - + -
553B PHE* 3.1 26.6 + - + +
556B TYR* 3.5 35.0 - - + +
557B ASN* 1.3 75.7 - - - +
559B ILE* 1.3 62.8 + - - +
560B GLN* 3.4 8.7 - - - +
561B GLN* 3.2 39.4 + - + +
562B CYS* 3.3 20.6 + - - +
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Residues in contact with ILE 559 (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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554B MET* 4.5 25.8 - - + -
557B ASN* 3.3 22.6 - - - +
558B LEU* 1.3 70.5 - - - +
560B GLN* 1.3 82.7 + - + +
562B CYS* 3.0 19.9 + - + +
563B THR* 3.1 25.4 + - - +
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Residues in contact with GLN 560 (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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557B ASN 3.6 9.7 - - - +
558B LEU* 3.6 6.3 - - - +
559B ILE* 1.3 107.1 + - + +
561B GLN* 1.3 84.3 + - - +
563B THR* 3.8 6.7 - - - -
564B ALA* 3.4 17.8 + - - +
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Residues in contact with GLN 561 (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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526B PRO* 5.7 5.2 - - + +
530B GLN* 3.1 34.9 + - + +
553B PHE* 4.6 7.6 - - + -
558B LEU* 3.2 43.4 - - + +
560B GLN* 1.3 92.6 - - + +
562B CYS* 1.3 55.4 + - - +
563B THR 3.2 1.8 - - - -
564B ALA* 3.0 3.3 + - - +
565B PHE* 2.7 35.1 + - - +
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Residues in contact with CYS 562 (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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550B VAL* 3.7 33.4 - - - -
553B PHE* 3.9 26.4 - - + -
554B MET* 4.7 10.5 - - - -
558B LEU 3.3 12.5 + - - +
559B ILE* 3.0 14.9 + - + +
561B GLN* 1.3 75.1 - - - +
563B THR* 1.3 58.7 + - - +
565B PHE* 3.4 7.7 + - - -
566B LEU* 2.9 47.3 + - - +
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Residues in contact with THR 563 (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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559B ILE* 3.1 22.9 + - - +
560B GLN* 3.8 10.4 - - - -
562B CYS* 1.3 80.2 - - - +
564B ALA* 1.3 56.9 + - - +
566B LEU* 3.2 9.8 + - - +
567B LEU* 2.9 47.5 + - + +
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Residues in contact with ALA 564 (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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530B GLN* 3.4 15.0 - - - +
560B GLN 3.4 11.6 + - - +
561B GLN* 3.0 9.8 + - - +
563B THR* 1.3 78.3 - - - +
565B PHE* 1.3 57.5 + - - +
567B LEU* 3.5 10.6 + - - +
568B ASP* 3.1 36.3 + - - +
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Residues in contact with PHE 565 (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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530B GLN* 3.8 20.1 - - + +
533B ALA* 3.7 34.5 - - + -
534B GLN* 4.5 8.7 - - + -
537B VAL* 4.6 8.3 - - + -
546B ILE* 4.2 8.5 - - + -
549B ILE* 3.5 28.3 - - + -
550B VAL* 3.9 15.0 - - + -
553B PHE* 4.0 17.3 - + + -
561B GLN 2.7 20.2 + - - +
562B CYS* 3.5 11.4 - - - -
564B ALA* 1.3 71.5 - - - +
566B LEU* 1.3 80.3 + - + +
568B ASP* 3.3 8.0 + - + +
569B ALA* 3.0 30.7 + - + +
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Residues in contact with LEU 566 (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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546B ILE* 4.5 11.4 - - + -
550B VAL* 3.7 22.9 - - + -
562B CYS* 2.9 44.3 + - - +
563B THR* 3.2 9.6 + - + +
565B PHE* 1.3 85.8 - - + +
567B LEU* 1.3 65.8 + - + +
569B ALA* 3.3 8.5 + - + +
570B LEU* 3.2 29.5 + - + +
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Residues in contact with LEU 567 (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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563B THR* 2.9 40.1 + - + +
564B ALA* 3.8 8.5 - - - +
566B LEU* 1.3 76.9 - - + +
568B ASP* 1.3 63.8 + - - +
570B LEU* 3.4 19.9 + - + +
571B LYS* 3.3 19.6 + - - +
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Residues in contact with ASP 568 (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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534B GLN* 4.6 19.3 - - + +
564B ALA* 3.1 19.3 + - - +
565B PHE* 3.5 12.1 - - + +
566B LEU 3.2 0.2 - - - -
567B LEU* 1.3 78.7 - - - +
569B ALA* 1.3 62.3 + - - +
571B LYS* 3.3 16.6 + - - +
572B ASN* 3.3 12.8 + - - +
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Residues in contact with ALA 569 (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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537B VAL* 4.7 22.7 - - + +
546B ILE* 5.9 2.9 - - + -
565B PHE* 3.0 26.4 + - + +
566B LEU* 3.3 15.0 + - + +
568B ASP* 1.3 75.7 - - - +
570B LEU* 1.3 61.4 + - + +
572B ASN* 3.5 21.3 + - - +
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Residues in contact with LEU 570 (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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566B LEU* 3.2 19.8 + - + +
567B LEU* 3.6 23.6 - - + +
568B ASP 3.2 0.2 - - - -
569B ALA* 1.3 75.4 - - - +
571B LYS* 1.3 64.6 + - - +
572B ASN 3.1 6.4 + - - -
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Residues in contact with LYS 571 (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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567B LEU 3.3 8.7 + - - +
568B ASP* 3.3 12.9 + - - +
570B LEU* 1.3 78.3 - - - +
572B ASN* 1.3 59.4 + - - +
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Residues in contact with ASN 572 (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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537B VAL* 5.7 6.1 - - + +
538B GLN* 5.5 9.0 - - - +
539B ASP* 5.1 6.6 - - - +
568B ASP 3.3 10.5 + - - +
569B ALA* 3.7 20.0 - - - +
570B LEU 3.1 5.5 - - - -
571B LYS* 1.3 84.3 - - - +
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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