Contacts of the helix formed by residues 458 - 465 (chain A) in PDB entry 2KFZ
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 MET 458 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419A GLN* 3.2 20.6 - - + +
457A ASP* 1.3 72.4 - - - +
459A ASP* 1.3 63.4 + - - +
461A LEU* 3.1 4.3 + - - -
462A ALA* 2.8 30.3 + - - +
470A THR* 3.8 32.3 - - + +
471A ILE 5.9 0.4 - - - +
500A GLU* 5.3 0.4 - - - +
501A ASP* 3.1 44.0 - - - +
504A VAL* 4.1 10.3 - - + -
505A THR* 3.7 21.8 - - - +
508A LEU* 4.0 18.6 - - + -
1006B US1 2.8 18.8 + - - +
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Residues in contact with ASP 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A ASP* 3.3 12.5 + - - +
458A MET* 1.3 82.2 + - - +
460A SER* 1.3 62.1 + - - +
462A ALA* 4.0 2.1 - - - +
463A GLU* 3.4 24.7 + - - +
468A HIS 4.7 0.7 - - - +
469A LYS* 5.8 0.5 - - - -
470A THR* 2.9 33.1 + - - +
471A ILE 4.2 8.0 - - - +
472A THR* 4.1 17.4 + - - -
1006B US1 4.9 5.2 + - - -
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Residues in contact with SER 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A ARG* 3.5 30.4 + - - +
457A ASP* 2.7 29.3 + - - -
458A MET 3.3 0.2 - - - -
459A ASP* 1.3 78.0 - - - +
461A LEU* 1.3 58.2 + - - +
463A GLU* 3.3 8.5 + - - +
464A ARG* 3.0 40.4 + - - +
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Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A GLN* 3.7 14.8 - - - +
442A THR 3.7 23.1 - - - +
446A SER* 3.2 28.3 - - - +
455A ARG 4.2 4.7 - - - +
456A HIS* 3.5 20.4 - - - +
457A ASP 2.9 17.1 + - - +
458A MET 3.1 4.2 + - - +
460A SER* 1.3 74.1 - - - +
462A ALA* 1.3 60.4 + - - +
464A ARG* 3.1 17.3 + - - +
465A TRP* 2.9 46.4 + - + +
508A LEU* 3.6 24.9 - - + +
512A MET* 4.6 3.6 - - + -
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Residues in contact with ALA 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A MET 2.8 19.9 + - - +
459A ASP 4.0 2.7 - - - +
461A LEU* 1.3 72.6 - - - +
463A GLU* 1.3 57.0 + - - +
466A LEU* 3.0 27.7 + - + +
468A HIS* 3.1 29.3 + - - +
470A THR* 3.6 23.3 - - + -
504A VAL* 3.8 14.1 - - + -
508A LEU* 4.0 10.7 - - - +
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Residues in contact with GLU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A ASP 3.4 14.8 + - - +
460A SER* 3.3 8.0 + - - +
461A LEU 3.1 0.6 - - - -
462A ALA* 1.3 79.8 - - - +
464A ARG* 1.3 63.4 + - - +
467A LYS* 3.4 25.2 + - - +
468A HIS 3.4 12.7 + - - +
469A LYS* 3.1 41.8 + - + +
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Residues in contact with ARG 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A SER* 4.1 7.7 + - - -
453A ALA* 4.1 21.1 + - - +
454A GLY* 3.4 19.8 - - - +
455A ARG 2.7 44.0 + - - +
456A HIS* 4.4 0.6 - - - -
460A SER* 3.0 27.5 + - - +
461A LEU* 3.7 17.2 - - - +
463A GLU* 1.3 81.0 - - - +
465A TRP* 1.3 76.2 + - + +
467A LYS* 3.7 18.0 + - - +
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Residues in contact with TRP 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A SER* 4.7 3.8 + - - -
449A LEU* 3.5 32.5 - - + -
461A LEU* 2.9 39.2 + - + +
464A ARG* 1.3 96.3 - - + +
466A LEU* 1.3 65.0 + - + +
467A LYS* 3.7 4.4 - - - +
508A LEU* 3.8 17.0 - - + -
511A LYS* 3.4 47.2 + - + +
512A MET* 3.7 28.6 - - + -
515A ASP* 3.6 22.0 - - - -
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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