Contacts of the helix formed by residues 452 - 460 (chain C) in PDB entry 1UES
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 ASP 452 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401C MET* 3.3 16.8 - - + -
450C ASN 3.9 0.8 + - - -
451C ALA* 1.3 77.2 - - - +
453C LEU* 1.3 64.6 + - - +
454C ASN* 2.8 40.1 + - - +
455C THR* 2.6 36.4 + - - -
456C ILE* 3.1 11.9 + - - +
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Residues in contact with LEU 453 (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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401C MET* 4.2 2.2 - - + +
403C HIS* 4.1 18.5 - - + +
439C LEU* 3.7 29.4 - - + -
451C ALA 3.9 0.6 + - - -
452C ASP* 1.3 74.1 + - - +
454C ASN* 1.3 65.8 + - - +
456C ILE* 3.1 6.6 + - + +
457C VAL* 2.9 32.3 + - - +
468C ALA* 4.0 22.4 - - + +
471C THR* 3.8 25.1 - - + -
472C LEU* 4.2 20.0 - - + +
475C ASN* 4.1 13.9 - - - +
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Residues in contact with ASN 454 (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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452C ASP* 2.8 19.2 + - - +
453C LEU* 1.3 78.8 - - - +
455C THR* 1.3 62.1 + - - +
457C VAL* 3.5 3.3 + - - +
458C GLN* 3.2 35.8 + - - +
472C LEU* 3.7 24.0 - - - +
546C VAL* 5.7 6.1 - - - +
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Residues in contact with THR 455 (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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448C PHE* 4.1 2.9 - - + -
451C ALA* 3.8 17.9 - - + -
452C ASP* 2.6 33.5 + - - -
454C ASN* 1.3 77.4 - - - +
456C ILE* 1.3 65.8 + - - +
458C GLN* 3.3 6.2 + - - +
459C LYS* 3.2 55.0 + - + +
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Residues in contact with ILE 456 (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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403C HIS* 3.9 19.1 - - + +
439C LEU* 4.4 12.1 - - + -
443C ILE* 4.7 2.2 - - + -
448C PHE* 3.6 39.5 - - + +
451C ALA* 3.7 22.9 - - + +
452C ASP 3.1 9.5 + - - +
453C LEU* 3.1 6.5 + - - +
455C THR* 1.3 75.6 - - - +
457C VAL* 1.3 56.1 + - - +
460C SER* 2.6 41.6 + - - -
464C ILE* 3.4 32.5 - - + -
468C ALA* 3.5 17.7 - - + -
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Residues in contact with VAL 457 (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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453C LEU 2.9 20.3 + - - +
454C ASN* 3.8 7.4 - - - +
455C THR 3.3 0.2 - - - -
456C ILE* 1.3 76.4 - - - +
458C GLN* 1.3 67.3 + - + +
460C SER* 4.2 3.1 - - - -
465C PHE* 3.1 34.2 - - + -
468C ALA* 3.7 33.9 - - + +
469C GLY* 3.8 7.2 - - - +
472C LEU* 3.7 20.2 - - + -
544C ASN* 5.5 7.0 - - + -
546C VAL* 4.7 19.7 - - + -
547C ARG* 5.8 5.2 - - + -
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Residues in contact with GLN 458 (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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454C ASN* 3.2 25.1 + - - +
455C THR* 3.8 6.2 - - - +
456C ILE 3.1 0.8 - - - -
457C VAL* 1.3 87.0 - - + +
459C LYS* 1.3 72.8 + - + +
460C SER 3.2 7.1 + - - +
465C PHE* 5.0 0.5 - - - -
546C VAL* 6.0 5.6 - - + +
547C ARG* 6.0 8.5 - - - +
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Residues in contact with LYS 459 (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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447C GLU* 4.7 9.8 - - - +
448C PHE* 3.7 18.4 - - + -
455C THR* 3.2 37.5 + - + +
458C GLN* 1.3 82.8 - - + +
460C SER* 1.3 60.7 + - - +
461C GLU* 5.1 1.4 - - - +
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Residues in contact with SER 460 (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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448C PHE* 3.5 14.7 - - - -
456C ILE* 2.6 33.5 + - - +
458C GLN 3.2 8.2 + - - +
459C LYS* 1.3 78.6 - - - +
461C GLU* 1.3 62.7 + - - +
464C ILE* 3.7 24.2 - - - -
465C PHE* 3.0 35.7 - - - +
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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