Contacts of the helix formed by residues 455 - 465 (chain A) in PDB entry 5KZX
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 TYR 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A ARG* 3.6 31.5 - - + +
413A ASP* 2.7 45.0 + - - +
415A THR* 3.7 20.0 - - + -
446A ILE* 3.8 25.5 - - + +
447A SER* 3.6 33.0 + - - -
450A GLY* 5.5 6.7 - - - -
451A PRO 4.4 0.8 + - - +
454A SER* 1.3 85.5 + - - +
456A ARG* 1.3 66.0 + - - +
457A PRO* 3.6 26.5 - - + +
458A TYR* 3.1 11.4 + - + +
459A ASP* 3.0 27.6 + - - +
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Residues in contact with ARG 456 (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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453A GLY 5.6 0.2 + - - -
454A SER 4.2 0.6 - - - -
455A TYR* 1.3 72.1 - - - +
457A PRO* 1.4 66.1 - - + +
459A ASP* 4.0 9.2 - - - -
460A GLU* 2.7 69.1 + - + +
501A ASP* 5.5 2.6 + - - +
502A MET* 4.1 11.9 - - + +
505A GLU* 2.8 42.0 + - - +
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Residues in contact with PRO 457 (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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414A PHE* 3.8 35.7 - - + +
446A ILE* 3.9 9.3 - - + +
455A TYR* 3.4 41.3 - - + +
456A ARG* 1.4 92.7 - - + +
458A TYR* 1.3 56.4 + - - +
461A GLY* 3.0 20.8 + - - -
498A TRP* 3.1 19.1 + - + +
502A MET* 3.7 20.9 - - + -
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Residues in contact with TYR 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ILE* 3.6 10.6 - - + +
447A SER 3.3 27.6 - - - +
448A SER* 3.5 41.4 + - - -
450A GLY 5.6 6.3 - - - -
455A TYR* 3.1 15.0 + - + +
457A PRO* 1.3 77.8 - - - +
459A ASP* 1.3 72.7 + - - +
461A GLY* 3.1 1.6 + - - -
462A LEU* 2.9 62.8 + - + +
467A PHE* 3.8 26.2 - + - -
475A PRO* 4.8 5.1 - - + +
477A ILE* 4.9 3.8 - - - +
486A ALA* 4.2 7.9 - - + -
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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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451A PRO 4.4 1.7 - - - +
452A ALA* 4.2 5.4 - - - -
453A GLY* 3.1 35.8 + - - -
455A TYR* 3.0 40.8 + - - +
456A ARG* 3.8 6.8 + - + +
458A TYR* 1.3 88.3 - - - +
460A GLU* 1.3 62.3 + - - +
462A LEU* 3.5 8.6 + - - +
463A ARG* 3.2 22.3 + - - +
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Residues in contact with GLU 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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456A ARG* 2.7 57.0 + - + +
459A ASP* 1.3 73.7 - - - +
461A GLY* 1.3 63.3 + - - +
463A ARG* 2.8 46.8 + - - +
464A ARG* 3.0 42.2 + - - +
498A TRP* 3.9 18.8 - - + +
501A ASP* 5.4 0.7 - - - +
502A MET* 4.4 9.4 - - + -
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Residues in contact with GLY 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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457A PRO 3.0 19.3 + - - -
458A TYR 3.1 3.5 + - - -
460A GLU* 1.3 75.0 - - - +
462A LEU* 1.3 56.4 + - - +
464A ARG 3.5 0.3 + - - -
465A GLY* 3.0 23.4 + - - -
466A VAL* 3.0 34.6 + - - +
467A PHE* 3.5 11.3 - - - -
498A TRP* 3.5 6.6 - - - +
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Residues in contact with LEU 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 TYR* 2.9 57.5 + - + +
459A ASP* 3.5 8.5 - - - +
461A GLY* 1.3 73.4 - - - +
463A ARG* 1.3 65.3 + - - +
465A GLY* 3.2 13.4 + - - -
467A PHE* 3.5 5.9 - - + -
475A PRO* 3.8 25.8 - - + -
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Residues in contact with ARG 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 3.2 10.7 + - - +
460A GLU* 2.8 48.1 + - - +
462A LEU* 1.3 80.0 - - - +
464A ARG* 1.3 82.5 + - - +
465A GLY 3.6 0.2 + - - -
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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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460A GLU* 3.0 41.3 + - - +
462A LEU 3.2 0.2 - - - -
463A ARG* 1.3 102.9 - - - +
465A GLY* 1.3 64.1 + - - +
466A VAL* 3.9 7.4 - - + -
492A ASN* 5.1 0.5 + - - -
494A THR* 3.4 37.5 + - + +
497A ALA* 3.6 22.2 - - - +
498A TRP* 3.6 27.2 - - - +
501A ASP* 3.1 26.7 + - - +
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Residues in contact with GLY 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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461A GLY 3.0 6.2 + - - -
462A LEU 3.2 10.2 + - - -
463A ARG 3.4 1.0 + - - -
464A ARG* 1.3 78.3 - - - +
466A VAL* 1.3 60.2 + - - +
467A PHE* 3.4 7.4 + - - +
492A ASN* 3.2 19.6 + - - -
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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