Contacts of the helix formed by residues 495 - 505 (chain A) in PDB entry 5UFL
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 GLY 495 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442A THR* 4.0 6.0 - - - +
493A VAL 3.6 0.6 + - - -
494A PRO* 1.3 70.1 - - - +
496A MET* 1.3 63.5 + - - +
497A GLU* 3.2 7.6 + - - +
498A VAL* 3.5 16.6 + - - +
499A SER* 3.4 20.8 + - - -
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Residues in contact with MET 496 (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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440A LEU 4.3 3.6 - - - +
441A THR 4.0 7.6 - - - +
442A THR* 3.3 53.9 + - + +
445A CYS* 4.5 13.9 - - + -
486A ILE* 3.6 31.9 - - + +
489A LEU* 3.7 36.8 - - + +
490A LYS* 4.4 5.4 - - - +
493A VAL* 3.4 27.6 - - + +
494A PRO 3.3 3.0 - - - -
495A GLY* 1.3 73.1 - - - +
497A GLU* 1.3 65.8 + - - +
499A SER* 3.9 0.6 - - - -
500A PHE* 3.0 24.3 + - - +
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Residues in contact with GLU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A LYS* 3.6 43.3 + - - +
491A PRO* 4.3 5.2 - - - +
493A VAL 4.3 2.7 + - - +
495A GLY 4.3 5.6 - - - +
496A MET* 1.3 80.6 - - - +
498A VAL* 1.3 68.2 + - + +
500A PHE* 3.5 3.1 - - - +
501A TYR* 3.2 53.5 + - + -
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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
----------------------------------------------------------
495A GLY* 3.5 17.4 + - - +
497A GLU* 1.3 82.1 - - + +
499A SER* 1.3 64.4 + - - +
501A TYR* 3.5 7.4 + - - +
502A LYS* 3.0 29.0 + - - +
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Residues in contact with SER 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A THR* 3.5 24.5 - - - -
446A THR* 3.0 32.4 - - - +
486A ILE* 6.3 0.2 - - - -
495A GLY 3.4 5.1 + - - -
496A MET* 3.9 2.2 - - - -
498A VAL* 1.3 80.7 - - - +
500A PHE* 1.3 65.1 + - - +
502A LYS* 3.3 7.8 + - - +
503A ILE* 3.0 28.7 + - - +
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Residues in contact with PHE 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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483A LEU* 3.5 31.6 - - + -
486A ILE* 3.5 27.3 - - + +
487A ASN* 3.7 31.6 - - + -
490A LYS* 3.6 21.1 - - + -
496A MET 3.0 18.7 + - - +
497A GLU 3.5 3.8 - - - +
499A SER* 1.3 76.8 - - - +
501A TYR* 1.3 68.8 + + - +
503A ILE* 3.2 8.7 + - - +
504A LEU* 3.1 57.5 + - + +
531A ILE* 4.2 9.2 - - + -
534A GLU* 3.7 23.3 - - + -
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Residues in contact with TYR 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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490A LYS* 3.2 22.9 + - - -
497A GLU* 3.2 45.3 + - + -
498A VAL* 3.5 9.0 + - - +
499A SER 3.4 0.2 - - - -
500A PHE* 1.3 84.9 - + - +
502A LYS* 1.3 63.5 + - - +
504A LEU* 3.7 7.8 + - + -
505A GLN* 3.0 27.8 + - - +
534A GLU* 3.3 33.1 + - + -
538A LEU* 3.3 34.9 - - + +
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Residues in contact with LYS 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 3.0 18.8 + - - +
499A SER* 3.5 9.2 - - - +
500A PHE 3.2 0.4 - - - -
501A TYR* 1.3 74.4 - - - +
503A ILE* 1.3 68.8 + - + +
505A GLN* 3.3 29.2 + - + +
506A ASP* 3.7 15.7 + - - +
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Residues in contact with ILE 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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446A THR* 4.0 26.7 - - + -
449A ILE* 4.3 30.3 - - + -
453A PHE* 5.2 4.3 - - + -
483A LEU* 3.8 25.4 - - + -
486A ILE* 4.4 20.9 - - + -
499A SER* 3.0 25.8 + - - +
500A PHE* 3.2 7.8 + - - +
502A LYS* 1.3 79.7 - - + +
504A LEU* 1.3 58.5 + - - +
506A ASP* 3.0 31.2 + - + +
509A LEU* 3.9 8.5 - - + +
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Residues in contact with LEU 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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483A LEU* 3.6 25.8 - - + -
500A PHE* 3.1 40.8 + - + +
501A TYR* 3.9 15.5 - - + +
502A LYS 3.3 0.4 - - - -
503A ILE* 1.3 77.8 - - - +
505A GLN* 1.3 58.8 + - - +
506A ASP 3.6 2.4 + - - +
509A LEU* 3.7 21.5 - - + +
531A ILE* 4.3 8.7 - - + +
534A GLU* 3.8 19.7 - - + +
535A ALA* 3.7 49.7 - - + +
538A LEU* 4.3 4.5 - - + -
541A PHE* 4.2 11.4 - - - -
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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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501A TYR* 3.0 24.5 + - - +
502A LYS* 3.3 22.9 + - - +
503A ILE 3.2 1.0 - - - -
504A LEU* 1.3 74.5 - - - +
506A ASP* 1.3 63.2 + - - +
507A PRO* 3.3 9.4 - - - +
538A LEU* 3.7 22.9 - - + +
539A PRO* 4.3 30.1 - - - +
540A ASP* 5.1 8.8 - - + +
541A PHE* 5.6 6.3 - - + +
542A PRO* 5.5 4.2 - - - +
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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