Contacts of the helix formed by residues 462 - 469 (chain C) in PDB entry 5U03
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 SER 462 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457C PHE* 4.3 0.2 - - - -
459C THR* 4.2 6.5 - - - -
460C LYS 2.8 4.8 + - - -
461C ASN* 1.3 77.1 + - - +
463C VAL* 1.3 62.5 + - - +
464C MET* 3.3 1.4 + - - +
465C ARG* 3.0 28.5 + - - +
466C LYS* 3.1 27.1 + - - +
500C VAL* 3.4 27.0 - - - +
513C GLU* 2.6 27.4 + - - -
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Residues in contact with VAL 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C ASN* 5.4 1.3 + - - +
462C SER* 1.3 74.2 + - - +
464C MET* 1.3 61.4 + - + +
466C LYS* 3.0 14.6 + - + +
467C LEU* 2.9 42.8 + - + +
513C GLU* 3.2 17.2 + - - +
519C PHE* 5.8 5.6 - - + -
551C LEU* 5.2 11.4 - - + -
555C LEU* 4.5 18.8 - - + -
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Residues in contact with MET 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C PHE* 4.8 4.5 - - + -
462C SER* 3.8 2.0 - - - +
463C VAL* 1.3 76.3 - - + +
465C ARG* 1.3 67.2 + - - +
467C LEU* 2.9 21.1 + - - +
468C TYR* 2.8 57.1 + - + -
511C ILE* 4.6 16.6 - - + -
513C GLU* 3.0 23.5 + - + +
519C PHE* 5.3 4.5 - - - -
521C VAL* 4.8 18.6 - - + -
523C VAL* 5.3 3.4 - - + -
525C TYR* 4.1 8.1 - - - +
538C PRO* 4.0 4.9 - - + -
539C PRO* 3.6 42.2 - - + -
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Residues in contact with ARG 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C PHE* 3.4 41.6 + - + +
459C THR 3.6 13.0 + - - -
460C LYS* 3.5 32.8 - - - +
462C SER* 3.0 24.7 + - - +
464C MET* 1.3 75.1 - - - +
466C LYS* 1.3 52.0 + - - +
468C TYR* 3.0 4.5 + - - +
469C GLY 2.7 30.3 + - - -
470C ASP* 2.8 46.2 + - - -
471C ALA 2.9 29.9 + - - +
472C ASP* 2.7 32.9 + - - +
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Residues in contact with LYS 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C LYS 4.9 7.9 - - - +
461C ASN* 4.5 16.2 + - - +
462C SER 3.1 21.4 + - - +
463C VAL* 3.0 17.3 + - + +
465C ARG* 1.3 77.2 - - + +
467C LEU* 1.3 60.7 + - - +
469C GLY* 3.1 12.9 + - - +
470C ASP* 4.3 5.8 - - + +
555C LEU* 4.6 22.8 - - + +
559C CYS* 3.5 17.8 - - - -
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Residues in contact with LEU 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463C VAL* 2.9 26.9 + - + +
464C MET* 2.9 32.5 + - - +
466C LYS* 1.3 76.9 - - - +
468C TYR* 1.3 61.0 + - - +
469C GLY* 4.4 0.3 - - - -
519C PHE* 5.2 3.1 - - + -
538C PRO* 3.7 35.8 - - + +
541C PHE* 5.6 2.9 - - + -
542C GLY* 4.3 13.7 - - - +
545C LEU* 5.1 0.9 - - + -
551C LEU* 4.4 12.6 - - + -
554C TYR* 4.0 18.7 + - + +
555C LEU* 3.9 23.3 - - + -
559C CYS* 4.4 8.5 - - - -
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Residues in contact with TYR 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C PHE* 3.8 20.9 - + + -
464C MET* 2.8 44.4 + - + +
465C ARG* 3.4 8.1 - - - +
467C LEU* 1.3 78.7 - - - +
469C GLY* 1.3 58.4 + - - +
471C ALA* 4.8 15.6 - - + +
474C LEU* 3.4 25.5 - - + +
476C GLU* 2.8 28.0 + - - -
511C ILE* 5.2 0.7 - - + -
525C TYR* 2.9 21.1 + - - -
527C PRO* 4.9 0.2 - - - +
538C PRO* 3.5 29.5 - - + +
539C PRO* 4.5 2.3 - - - +
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Residues in contact with GLY 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465C ARG 2.7 6.3 + - - -
466C LYS 3.1 10.4 + - - -
467C LEU 4.4 0.4 - - - -
468C TYR* 1.3 76.8 - - - +
470C ASP* 1.3 76.1 + - - +
471C ALA* 3.3 4.1 + - - +
559C CYS* 5.7 2.0 - - - -
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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