Contacts of the helix formed by residues 470 - 480 (chain H) in PDB entry 5WUA
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 470 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466H VAL 3.0 6.7 + - - +
467H ILE* 4.1 12.8 - - - +
468H ILE 3.0 1.6 + - - -
469H LEU* 1.3 77.5 - - - +
471H ALA* 1.3 66.3 + - - +
472H PRO 3.6 0.2 - - - -
473H VAL* 3.3 12.3 - - + +
474H GLN* 3.2 20.3 + - - +
550H ILE* 5.1 15.5 - - + -
590H LEU* 5.8 6.1 - - + -
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Residues in contact with ALA 471 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467H ILE 5.0 0.4 + - - -
468H ILE 3.0 15.5 + - - +
469H LEU 3.2 0.4 - - - -
470H LEU* 1.3 78.1 - - - +
472H PRO* 1.3 64.4 - - - +
473H VAL 3.1 0.9 + - - -
474H GLN* 3.2 3.6 + - - +
475H TYR* 3.0 24.8 + - - +
590H LEU* 5.9 8.4 - - + +
594H SER* 5.0 3.7 - - - -
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Residues in contact with PRO 472 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469H LEU 4.4 5.8 - - - +
471H ALA* 1.3 78.2 - - - +
473H VAL* 1.3 52.6 - - - +
475H TYR* 4.6 4.0 - - + -
476H PHE* 2.7 42.8 + - + +
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Residues in contact with VAL 473 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469H LEU 4.4 4.2 + - - +
470H LEU* 3.3 24.0 + - + +
471H ALA 3.1 0.6 - - - -
472H PRO* 1.3 78.3 - - - +
474H GLN* 1.3 58.2 + - - +
476H PHE* 3.8 2.2 - - - +
477H VAL* 2.9 27.2 + - - +
546H MET* 5.8 8.7 - - + -
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Residues in contact with GLN 474 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470H LEU 3.2 9.0 + - - +
471H ALA* 3.8 3.8 - - - +
473H VAL* 1.3 78.2 - - - +
475H TYR* 1.3 56.2 + - - +
477H VAL* 2.4 34.2 + - - +
478H ALA* 2.9 9.1 + - - +
591H PHE* 5.5 4.3 - - + -
594H SER* 3.4 28.3 - - - -
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Residues in contact with TYR 475 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471H ALA 3.0 16.2 + - - +
472H PRO* 4.6 4.3 - - + -
474H GLN* 1.3 75.0 - - - +
476H PHE* 1.3 56.5 + - - +
478H ALA* 3.1 13.8 - - - +
479H THR* 3.0 20.4 + - - -
594H SER* 4.4 16.3 - - - +
597H VAL* 6.1 5.4 - - + -
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Residues in contact with PHE 476 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472H PRO* 2.7 24.4 + - + +
473H VAL* 3.9 2.2 - - - +
475H TYR* 1.3 72.4 - - - +
477H VAL* 1.3 59.2 + - - +
478H ALA 3.0 1.3 - - - -
479H THR* 2.6 31.1 + - - -
480H LYS* 2.9 12.8 + - - +
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Residues in contact with VAL 477 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473H VAL 2.9 14.2 + - - +
474H GLN* 2.4 30.7 + - - +
476H PHE* 1.3 68.6 - - - +
478H ALA* 1.3 54.2 + - - -
480H LYS* 3.6 6.4 + - - +
481H LEU* 2.9 25.9 + - - +
539H TYR 5.6 3.1 - - - +
543H SER* 3.8 29.6 - - - -
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Residues in contact with ALA 478 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474H GLN 2.9 6.2 + - - +
475H TYR* 3.1 18.6 - - - +
477H VAL* 1.3 74.3 - - - +
479H THR* 1.3 56.2 + - - -
480H LYS 3.0 2.2 - - - -
481H LEU* 2.4 28.9 + - + -
482H SER* 3.0 16.1 + - - -
594H SER 5.6 4.7 - - - +
598H ARG* 6.1 6.3 - - + -
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Residues in contact with THR 479 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475H TYR 3.0 7.6 + - - -
476H PHE* 2.6 30.3 + - - -
478H ALA* 1.3 71.9 - - - +
480H LYS* 1.3 54.5 + - - -
482H SER* 4.8 3.0 + - - -
483H GLN* 5.1 6.4 + - - +
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Residues in contact with LYS 480 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476H PHE 2.9 10.9 + - - +
477H VAL* 3.7 6.3 - - - +
479H THR* 1.3 75.1 - - - +
481H LEU* 1.3 64.0 + - - +
482H SER 3.6 0.4 - - - -
483H GLN* 4.4 4.0 + - - +
484H ALA* 3.7 16.1 + - - +
539H TYR* 4.9 19.6 - - + +
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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