Contacts of the helix formed by residues 445 - 452 (chain C) in PDB entry 4U1D
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 GLN 445 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B LYS* 3.4 18.6 + - - +
443C VAL 3.6 2.7 + - - -
444C SER* 1.3 70.6 - - - +
446C SER* 1.3 57.5 + - - +
448C LEU* 4.6 5.2 - - - -
449C TYR* 2.9 58.1 + - + +
466C GLU* 3.1 25.3 + - - -
482C ILE* 3.3 19.8 - - - +
483C ASP 4.9 0.4 - - - -
484C HIS* 3.8 9.7 - - - -
487C ALA* 2.8 47.4 + - + +
488C LYS 3.9 1.3 - - - +
489C VAL* 3.7 19.3 - - + -
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Residues in contact with SER 446 (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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444C SER* 3.1 11.9 + - - -
445C GLN* 1.3 78.4 - - - +
447C GLU* 1.3 63.1 + - - +
449C TYR* 4.3 2.0 - - - +
450C LYS* 3.2 29.8 + - - +
487C ALA* 4.6 4.5 + - - +
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Residues in contact with GLU 447 (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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439C LYS* 5.8 0.5 - - - -
440C PHE* 4.2 15.4 - - + -
443C VAL* 3.6 18.8 - - + -
444C SER* 3.0 19.4 + - - +
446C SER* 1.3 80.8 - - - +
448C LEU* 1.3 61.7 + - - +
450C LYS* 3.4 29.5 + - - +
451C LEU* 3.0 40.4 + - + +
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Residues in contact with LEU 448 (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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432C VAL* 6.4 0.2 - - + -
433C PHE* 3.6 34.3 - - + -
436C ALA* 4.7 14.8 - - + -
440C PHE* 5.5 2.0 - - + -
443C VAL* 3.6 29.4 - - + +
444C SER 2.9 17.7 + - - +
445C GLN* 4.0 4.0 - - - +
447C GLU* 1.3 74.1 - - - +
449C TYR* 1.3 62.7 + - + +
451C LEU* 3.1 9.7 + - + +
452C ALA* 3.0 24.2 + - + +
469C LEU* 4.0 10.1 - - + -
489C VAL* 3.7 31.6 - - + -
491C PHE* 3.9 12.3 - - + -
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Residues in contact with TYR 449 (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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77B LYS* 5.9 1.8 - - - -
433C PHE* 5.2 0.4 - + - -
445C GLN* 2.9 52.3 + - + +
446C SER* 4.5 1.6 - - - +
448C LEU* 1.3 87.0 - - + +
450C LYS* 1.3 59.0 + - - +
452C ALA 3.1 10.4 + - - -
453C THR* 2.7 25.1 + - - -
462C ALA* 4.2 23.1 - - + +
465C ILE* 3.5 28.4 - - + +
466C GLU* 2.6 51.3 + - + +
469C LEU* 3.8 29.0 - - + +
482C ILE* 4.2 2.9 - - - +
489C VAL* 4.3 0.6 - - + +
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Residues in contact with LYS 450 (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 LYS* 2.6 32.3 + - - -
446C SER 3.2 16.4 + - - +
447C GLU* 3.4 35.4 + - - +
449C TYR* 1.3 77.3 - - - +
451C LEU* 1.3 55.4 + - - +
453C THR* 3.3 14.0 + - - -
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Residues in contact with LEU 451 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397C VAL* 3.5 32.8 - - + +
398C ASP* 5.1 5.8 - - - +
400C VAL* 5.8 1.4 - - - +
401C LYS* 3.3 22.4 + - - +
432C VAL* 3.7 14.4 - - + +
436C ALA* 4.5 16.6 - - + -
439C LYS* 4.7 9.6 - - + -
440C PHE* 3.7 31.6 - - + -
447C GLU* 3.0 30.2 + - - +
448C LEU* 3.3 8.3 - - + +
450C LYS* 1.3 79.3 - - + +
452C ALA* 1.3 56.8 + - + +
453C THR 3.4 1.3 - - - -
454C LEU* 5.9 0.9 - - - +
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Residues in contact with ALA 452 (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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429C MET* 3.2 34.2 - - + +
432C VAL* 4.0 16.2 - - + -
433C PHE* 3.6 28.5 - - + -
448C LEU* 3.0 14.2 + - + +
449C TYR 3.1 7.0 + - - +
451C LEU* 1.3 78.9 - - + +
453C THR* 1.3 57.9 + - - +
454C LEU* 3.4 9.0 + - - +
465C ILE* 4.1 5.9 - - + +
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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