Contacts of the helix formed by residues 457 - 461 (chain E) in PDB entry 5KRA
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 GLY 457 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377E HIS* 2.9 29.1 + - - -
378E LEU* 3.9 17.4 - - - +
381E CYS* 3.8 16.2 - - - +
453E LEU 5.0 0.2 + - - -
455E ASN 3.2 0.2 - - - -
456E SER* 1.3 78.6 - - - +
458E VAL* 1.3 62.0 + - - +
459E TYR 3.2 3.1 - - - -
460E THR* 3.0 15.6 + - - -
461E PHE* 4.0 3.6 - - - -
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Residues in contact with VAL 458 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378E LEU* 4.0 1.6 - - - +
454E LEU 3.4 15.0 - - - +
455E ASN* 3.3 20.5 + - - +
457E GLY* 1.3 78.8 - - - +
459E TYR* 1.3 84.8 + - + +
460E THR 3.2 1.6 + - - -
461E PHE* 3.6 24.4 + - + +
472E LYS* 4.3 9.6 - - + +
475E ILE* 3.9 33.2 - - + -
476E HIS* 4.0 26.3 - - + +
479E LEU* 5.2 0.9 - - + -
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Residues in contact with TYR 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455E ASN* 2.7 44.9 + - - -
456E SER 4.7 2.9 - - - -
457E GLY* 3.2 1.0 - - - -
458E VAL* 1.3 88.7 - - + +
460E THR* 1.3 63.2 + - - +
461E PHE 3.6 1.5 + - - -
476E HIS* 4.5 12.7 + + - -
479E LEU* 5.8 0.2 - - - +
515E ARG* 4.8 0.7 - - - -
427F MET* 5.0 2.1 - - - +
430F ALA* 3.4 31.8 - - + +
431F THR* 5.8 1.3 - - - -
434F ARG* 4.4 23.4 + - + -
506F GLN 4.6 0.7 + - - -
509F LEU* 3.7 20.4 + - - +
510F ILE* 3.8 23.1 + - + +
513F HIS* 3.5 53.6 + + + +
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Residues in contact with THR 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377E HIS* 2.6 43.5 + - - -
381E CYS* 5.0 4.7 - - - -
457E GLY* 3.0 11.4 + - - -
458E VAL 3.2 0.2 - - - -
459E TYR* 1.3 84.8 - - + +
461E PHE* 1.3 60.5 + - - +
427F MET* 3.9 33.0 - - + -
513F HIS* 4.3 7.6 - - + +
516F HIS* 5.6 3.6 - - + +
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Residues in contact with PHE 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374E ASP* 3.2 42.4 - - + -
377E HIS* 3.3 37.9 - + + -
378E LEU* 3.9 14.1 - - + -
457E GLY 4.2 0.4 - - - -
458E VAL* 3.6 34.3 + - + +
459E TYR 3.6 2.2 + - - -
460E THR* 1.3 81.2 - - - +
472E LYS* 4.6 13.2 - - + -
475E ILE* 3.6 25.8 - - + -
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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