Contacts of the helix formed by residues 458 - 464 (chain B) in PDB entry 5KJH
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 ALA 458 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444B TRP* 4.0 1.6 - - - -
445B ASP* 3.5 13.9 - - - +
449B ASN* 3.5 29.0 - - - +
457B VAL* 1.3 77.4 - - - +
459B LEU* 1.4 67.7 + - - +
460B ARG* 4.1 12.3 - - + +
461B ASP* 2.8 34.3 + - - +
462B ILE* 3.6 4.9 + - - +
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Residues in contact with LEU 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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381B LEU* 3.8 31.4 - - + -
398B LEU* 3.9 25.6 - - + -
440B PHE* 4.0 11.7 - - + -
441B THR* 3.9 28.7 - - + +
444B TRP* 3.4 44.8 - - + +
445B ASP* 3.4 10.0 + - - +
458B ALA* 1.4 71.8 - - - +
460B ARG* 1.3 55.8 + - - +
462B ILE* 3.2 9.9 + - + +
463B LEU* 2.9 49.0 + - + +
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Residues in contact with ARG 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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402B MET* 2.9 47.5 + - + +
405B GLN* 2.8 30.7 + - - +
406B PRO 3.3 6.9 + - - -
407B GLU 3.2 34.7 - - - +
417B LYS* 4.3 5.9 - - - +
441B THR* 6.0 1.2 - - - +
458B ALA* 4.4 11.4 - - + -
459B LEU* 1.3 76.9 - - - +
461B ASP* 1.4 59.4 + - - +
463B LEU* 3.4 3.0 + - - +
464B MET* 2.8 49.4 + - + +
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Residues in contact with ASP 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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370B GLN* 6.4 1.8 - - + -
374B ALA* 4.9 2.7 - - + -
449B ASN* 5.2 0.3 - - - +
456B ARG* 5.5 2.9 + - - -
457B VAL* 3.6 16.7 - - + +
458B ALA* 2.8 39.7 + - - +
460B ARG* 1.4 78.6 - - - +
462B ILE* 1.3 63.9 + - - +
464B MET* 3.9 5.7 + - - +
465B LEU* 3.4 30.0 + - + +
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Residues in contact with ILE 462 (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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306A GLN* 5.9 0.5 - - - +
374B ALA* 4.0 26.2 - - + +
377B LEU* 3.8 18.4 - - + -
378B ALA* 4.1 25.2 - - + +
381B LEU* 4.4 22.4 - - + -
395B LYS* 5.9 2.7 - - - +
444B TRP* 3.4 37.2 - - + +
457B VAL* 3.9 17.0 - - + -
458B ALA 3.6 2.4 + - - +
459B LEU* 3.2 7.8 + - + +
461B ASP* 1.3 73.4 - - - +
463B LEU* 1.4 61.1 + - + +
465B LEU* 2.9 23.2 + - - +
466B ASP* 3.3 11.0 + - + +
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Residues in contact with LEU 463 (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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381B LEU* 4.0 18.4 - - + -
395B LYS* 3.9 31.6 - - + +
398B LEU* 3.4 35.0 - - + +
399B ILE* 4.0 13.0 - - + +
402B MET* 3.9 21.8 - - + -
459B LEU* 2.9 39.4 + - + +
460B ARG 3.8 3.8 - - - +
462B ILE* 1.4 75.4 - - + +
464B MET* 1.3 61.0 + - - +
466B ASP* 3.1 22.2 + - + +
469B VAL* 3.3 14.0 - - - +
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Residues in contact with MET 464 (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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402B MET* 4.1 22.2 - - - +
416B GLN* 6.1 1.8 - - - +
460B ARG* 2.8 35.1 + - + +
461B ASP* 4.2 7.0 - - - +
462B ILE 3.3 0.2 - - - -
463B LEU* 1.3 72.5 - - - +
465B LEU* 1.3 62.1 + - + +
466B ASP 3.4 0.2 - - - -
469B VAL* 3.9 3.3 - - - +
470B GLU* 3.4 28.9 + - - +
473B PHE* 3.6 41.4 - - + -
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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