Contacts of the helix formed by residues 503 - 513 (chain A) in PDB entry 5UO5
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 ASN 503 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482A SER* 4.4 2.4 + - - -
486A ARG* 3.2 51.1 + - - +
487A TYR 2.9 28.8 + - - +
489A GLY 4.3 0.7 - - - +
500A ASP* 3.0 26.4 + - - +
502A ALA* 1.3 80.4 - - - +
504A VAL* 1.3 56.0 + - - +
505A GLN 3.3 2.5 - - - -
506A PHE* 3.4 9.9 + - + +
507A THR* 2.6 42.7 + - - +
525A LEU* 4.2 10.8 - - + -
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Residues in contact with VAL 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A GLY 3.6 24.4 - - - +
490A TYR 4.4 0.4 - - - +
491A LYS* 4.1 29.2 - - + +
497A THR* 4.1 11.7 - - + +
501A PRO* 3.3 28.1 + - + +
502A ALA 3.6 1.4 + - - -
503A ASN* 1.3 76.9 - - - +
505A GLN* 1.3 65.1 + - - +
507A THR* 3.6 1.6 - - - -
508A GLU* 3.0 44.1 + - + +
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Residues in contact with GLN 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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502A ALA 5.2 1.0 + - - +
503A ASN 3.3 0.6 - - - -
504A VAL* 1.3 78.9 - - - +
506A PHE* 1.3 63.2 + - - +
508A GLU* 3.2 15.4 + - - +
509A ILE* 3.1 29.8 + - + +
714A ASP* 5.2 1.2 - - - +
716A TRP* 3.3 39.5 - - + +
717A ASN* 5.2 1.2 + - - -
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Residues in contact with PHE 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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480A TRP* 3.7 22.0 - - + -
481A ASN* 3.4 55.6 - - - -
482A SER 5.7 1.3 - - - -
503A ASN* 3.4 13.9 + - + +
504A VAL 3.4 0.4 - - - -
505A GLN* 1.3 75.7 - - - +
507A THR* 1.3 65.4 + - - +
509A ILE* 3.2 14.0 + - + +
510A CYS* 3.0 45.3 + - - -
525A LEU* 3.8 26.9 - - + -
526A PRO 4.1 2.7 - - - -
528A LEU* 4.0 15.0 - - + -
716A TRP* 4.2 19.9 - + + -
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Residues in contact with THR 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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488A ALA* 3.5 23.4 - - + -
489A GLY 3.1 34.5 + - - +
490A TYR* 3.9 16.6 - - + -
503A ASN* 2.6 23.3 + - - +
504A VAL 3.6 1.1 - - - -
506A PHE* 1.3 78.5 - - - +
508A GLU* 1.3 62.5 + - + +
510A CYS* 3.1 4.2 + - - +
511A ILE* 3.0 31.4 + - + +
515A TRP* 4.1 6.3 - - + -
525A LEU* 3.6 13.4 - - - +
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Residues in contact with GLU 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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489A GLY 5.8 0.7 - - - +
491A LYS* 4.7 8.2 + - - +
504A VAL* 3.0 38.1 + - + +
505A GLN* 3.2 15.8 + - - +
507A THR* 1.3 76.7 - - + +
509A ILE* 1.3 56.4 + - + +
511A ILE* 3.3 11.2 + - + +
512A GLN* 2.9 29.0 + - - +
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Residues in contact with ILE 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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480A TRP* 4.4 11.7 - - + -
505A GLN* 3.1 23.2 + - + +
506A PHE* 3.2 12.5 + - + +
508A GLU* 1.3 76.2 - - + +
510A CYS* 1.3 57.6 + - - +
512A GLN* 3.2 13.2 + - - +
513A GLN* 2.9 41.3 + - + +
528A LEU* 3.8 24.5 - - + -
716A TRP* 3.5 52.3 - - + -
721A TRP* 5.8 1.6 - - + -
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Residues in contact with CYS 510 (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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506A PHE* 3.0 51.8 + - - -
507A THR* 3.1 8.5 + - - +
509A ILE* 1.3 76.7 - - - +
511A ILE* 1.3 61.7 + - - +
513A GLN* 3.1 16.4 + - - +
514A GLY 3.2 0.7 + - - -
515A TRP* 2.9 43.2 + - + +
525A LEU* 4.6 1.6 - - - -
526A PRO* 3.9 21.5 - - + -
528A LEU* 4.6 3.1 - - - -
538A LEU* 3.8 10.6 - - + +
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Residues in contact with ILE 511 (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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490A TYR* 4.2 6.7 - - + -
507A THR* 3.0 36.3 + - + +
508A GLU* 3.7 9.9 - - + +
510A CYS* 1.3 75.6 - - - +
512A GLN* 1.3 64.9 + - - +
514A GLY* 3.1 12.6 + - - -
515A TRP* 3.6 29.8 + - + +
517A PRO* 3.8 29.6 - - + -
519A ARG* 4.3 14.4 - - - +
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Residues in contact with GLN 512 (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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508A GLU 2.9 13.9 + - - +
509A ILE* 3.5 15.5 - - - +
511A ILE* 1.3 78.1 - - - +
513A GLN* 1.3 70.1 + - - +
514A GLY* 3.1 4.7 + - - -
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Residues in contact with GLN 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A ILE* 2.9 33.2 + - + +
510A CYS* 3.1 8.7 + - - +
512A GLN* 1.3 89.1 + - - +
514A GLY* 1.3 56.3 + - - +
515A TRP 3.7 0.7 - - - -
528A LEU* 4.4 13.9 - - + -
535A ASP* 6.2 0.2 - - - +
536A PRO 4.5 11.7 + - - -
538A LEU* 3.5 23.3 - - + +
721A TRP* 3.5 36.3 - - + -
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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