Contacts of the helix formed by residues 455 - 461 (chain B) in PDB entry 3U0Z
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 CYS 455 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451B VAL* 3.0 24.9 + - - +
452B ASN 3.8 2.2 - - - -
454B ASN* 1.3 83.5 - - - +
456B ARG* 1.3 62.2 + - - +
457B LYS 3.4 2.7 - - - -
458B LEU* 3.1 15.5 + - + +
459B VAL* 3.0 23.5 + - - +
477B LEU* 4.0 31.2 - - + -
480B LEU* 5.3 7.0 - - - -
551B TYR* 4.9 24.9 - - - -
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Residues in contact with ARG 456 (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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456A ARG* 6.1 6.4 - - + +
459A VAL* 4.6 14.7 - - - +
460A ALA* 3.9 11.9 - - + +
465A PHE 5.0 0.2 + - - -
466A ALA* 3.0 41.0 + - - +
452B ASN 3.2 10.2 + - - +
453B PHE* 2.7 74.2 + - - +
454B ASN 3.3 2.4 + - - -
455B CYS* 1.3 76.2 - - - +
457B LYS* 1.3 60.9 + - - +
459B VAL* 3.7 5.5 + - - +
460B ALA* 3.3 23.6 + - - +
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Residues in contact with LYS 457 (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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460A ALA* 3.7 34.9 - - + +
461A THR* 4.4 21.1 - - + +
454B ASN 5.0 1.8 + - - -
455B CYS 3.4 0.2 - - - -
456B ARG* 1.3 76.5 - - - +
458B LEU* 1.3 63.7 + - - +
460B ALA* 3.2 0.7 + - - +
461B THR* 2.7 42.9 + - + +
505B GLN 5.4 4.2 + - - -
506B HIS* 5.8 1.2 + - - -
523B ASP* 4.5 19.9 + - - -
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Residues in contact with LEU 458 (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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455B CYS* 3.1 20.0 + - + +
457B LYS* 1.3 79.9 - - - +
459B VAL* 1.3 63.2 + - - +
461B THR* 3.6 5.5 + - - +
462B MET* 3.3 37.9 - - + +
465B PHE* 4.0 26.5 - - + -
477B LEU* 4.8 5.8 - - + -
480B LEU* 4.8 12.8 - - + -
503B PHE* 4.7 14.1 - - + -
504B ILE 3.8 25.6 - - - +
505B GLN* 4.6 17.7 - - + +
524B GLY* 4.3 5.4 - - - +
551B TYR* 5.3 8.3 - - + -
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Residues in contact with VAL 459 (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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456A ARG* 4.6 13.9 - - - +
452B ASN* 5.1 3.6 - - - +
455B CYS 3.0 17.4 + - - +
456B ARG* 4.1 4.5 - - - +
458B LEU* 1.3 76.5 - - + +
460B ALA* 1.3 65.0 + - + +
461B THR 3.5 0.5 + - - -
462B MET* 3.5 3.8 + - - +
465B PHE* 4.1 21.1 - - + +
466B ALA* 3.2 35.4 + - - +
473B VAL* 3.5 31.6 - - + -
477B LEU* 4.1 17.0 - - + -
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Residues in contact with ALA 460 (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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456A ARG* 3.9 18.4 - - + +
457A LYS* 3.7 43.2 - - + +
460A ALA* 4.1 5.4 - - + -
456B ARG 3.3 15.8 + - - +
457B LYS 3.2 5.3 + - - +
459B VAL* 1.3 83.6 - - + +
461B THR* 1.3 57.6 + - + +
462B MET 3.4 1.9 + - - -
466B ALA* 4.1 11.9 - - - +
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Residues in contact with THR 461 (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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457A LYS* 4.4 26.2 - - + +
461A THR* 4.5 14.6 - - + -
457B LYS* 2.7 30.4 + - + +
458B LEU* 3.6 6.9 + - - +
459B VAL 3.4 0.2 - - - -
460B ALA* 1.3 75.3 - - + +
462B MET* 1.3 56.7 + - - +
463B PRO* 3.5 11.1 - - - +
523B ASP* 4.6 7.0 - - + +
524B GLY* 3.7 22.9 + - - +
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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