Contacts of the helix formed by residues 447 - 458 (chain f) in PDB entry 5T0J
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 VAL 447 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444f SER* 4.5 0.2 + - - -
445f GLY 3.3 10.4 - - - +
446f ASN* 1.3 78.3 - - - +
448f LEU* 1.3 61.2 + - + +
449f LYS 3.4 3.2 - - - +
450f VAL* 3.3 20.5 - - + +
451f GLN* 4.1 7.3 + - - +
473f LYS* 6.5 0.2 - - + -
476f LYS* 3.8 35.4 - - - +
477f ASP* 4.5 5.8 - - - +
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Residues in contact with LEU 448 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446f ASN* 2.8 37.4 + - + +
447f VAL* 1.3 80.7 - - + +
449f LYS* 1.3 62.7 + - - +
450f VAL 3.4 0.2 - - - -
451f GLN* 3.5 18.1 + - - +
452f GLN* 3.2 39.8 + - + +
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Residues in contact with LYS 449 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415f GLU* 6.3 1.2 - - - +
438f VAL 5.8 1.8 - - - +
441f TYR* 6.2 3.5 - - + +
442f ALA* 4.5 20.5 - - + +
444f SER* 3.3 41.1 - - - +
446f ASN* 4.8 4.0 - - + +
447f VAL 3.4 1.8 - - - +
448f LEU* 1.3 76.5 - - - +
450f VAL* 1.3 65.3 + - - +
452f GLN* 3.4 11.9 + - - +
453f LEU* 3.0 56.8 + - + +
472f LYS* 4.8 8.5 - - + +
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Residues in contact with VAL 450 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444f SER* 4.9 0.8 + - - -
447f VAL* 3.3 20.4 - - + +
449f LYS* 1.3 79.3 - - - +
451f GLN* 1.3 65.0 + - + +
453f LEU* 4.6 0.6 - - - +
454f LEU* 3.2 32.5 + - + +
469f ASP* 5.0 8.4 - - - +
470f LYS* 5.9 0.9 - - - -
472f LYS* 3.5 23.7 - - - +
473f LYS* 3.6 39.9 - - + +
476f LYS* 3.8 22.2 - - - -
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Residues in contact with GLN 451 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447f VAL 4.4 8.6 - - - +
448f LEU* 3.5 22.0 + - - +
449f LYS 3.2 0.6 - - - -
450f VAL* 1.3 82.4 - - + +
452f GLN* 1.3 68.6 + - + +
454f LEU* 4.0 5.0 - - - +
455f HIS* 3.3 20.8 + - + +
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Residues in contact with GLN 452 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448f LEU* 3.2 30.0 + - + +
449f LYS* 3.8 12.0 + - - +
451f GLN* 1.3 77.8 - - + +
453f LEU* 1.3 71.0 + - + +
455f HIS* 3.0 17.1 + - - +
456f ILE* 3.3 14.3 + - - +
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Residues in contact with LEU 453 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415f GLU* 3.5 40.4 - - + +
438f VAL* 3.7 32.1 - - + +
441f TYR* 5.6 0.9 - - + -
449f LYS* 3.0 42.4 + - + +
450f VAL 4.6 1.1 - - - +
452f GLN* 1.3 86.9 - - + +
454f LEU* 1.3 56.3 + - - +
456f ILE* 3.3 10.2 - - + +
457f CYS* 3.0 35.0 + - + +
469f ASP* 5.0 3.4 - - - +
472f LYS* 4.3 11.7 - - + -
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Residues in contact with LEU 454 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450f VAL* 3.2 26.6 + - + +
451f GLN* 4.0 5.4 - - - +
452f GLN 3.1 1.0 + - - -
453f LEU* 1.3 78.2 - - - +
455f HIS* 1.3 56.8 + - - +
457f CYS* 4.8 0.7 - - - -
458f SER* 2.5 56.1 + - - +
466f LYS* 5.4 8.7 - - + -
469f ASP* 3.3 28.2 + - + +
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Residues in contact with HIS 455 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451f GLN* 3.3 10.1 + - + +
452f GLN* 3.0 11.0 + - - +
454f LEU* 1.3 82.5 - - - +
456f ILE* 1.3 63.8 + - - +
458f SER* 4.2 2.5 - - - -
459f GLU* 3.8 20.1 + - - +
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Residues in contact with ILE 456 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415f GLU* 5.1 9.0 - - - +
419f ALA* 6.1 4.5 - - + -
422f GLU* 5.3 0.2 - - - +
452f GLN 3.3 11.2 + - - +
453f LEU* 3.3 24.2 - - + +
455f HIS* 1.3 81.7 + - - +
457f CYS* 1.3 65.7 + - + +
459f GLU* 2.8 32.6 - - - +
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Residues in contact with CYS 457 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422f GLU* 3.1 44.3 - - - +
453f LEU* 3.0 20.5 + - + +
454f LEU* 4.5 2.0 - - - +
456f ILE* 1.3 80.7 - - + +
458f SER* 1.3 69.7 + - - +
459f GLU* 3.8 6.6 - - - +
461f PHE 5.5 0.2 - - - -
462f ASP* 5.6 4.0 - - - +
465f GLU* 3.3 34.1 - - - -
469f ASP* 5.2 3.4 - - - +
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Residues in contact with SER 458 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454f LEU* 2.5 41.5 + - - +
455f HIS* 4.0 3.1 + - - -
457f CYS* 1.3 81.3 - - - +
459f GLU* 1.3 72.2 + - - +
460f HIS* 3.0 22.1 + - - +
461f PHE* 2.7 35.7 + - - +
462f ASP 4.5 2.0 - - - +
465f GLU* 5.9 0.2 - - - -
466f LYS* 6.0 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