Contacts of the helix formed by residues 457 - 466 (chain A) in PDB entry 1A8H
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 PRO 457 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ARG* 3.3 52.9 - - - +
86A GLY 5.1 0.4 - - - +
317A ARG* 5.9 3.1 - - - -
318A ASP* 4.5 2.2 - - - +
321A ARG* 4.0 14.1 - - - +
453A THR* 3.0 22.0 - - + +
455A ALA 3.5 7.9 - - - +
456A MET* 1.3 86.9 - - - +
458A ASP* 1.3 67.5 + - - +
460A MET* 4.2 0.7 - - - +
461A ALA* 3.2 24.3 + - - +
464A ARG* 4.9 2.1 + - - -
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Residues in contact with ASP 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ARG* 2.4 37.1 + - - -
318A ASP* 3.6 14.1 + - - +
456A MET 3.5 0.4 - - - -
457A PRO* 1.3 83.1 - - - +
459A LYS* 1.3 60.5 + - + +
461A ALA* 3.5 6.5 + - - +
462A GLU* 3.1 29.4 + - - +
465A ARG* 5.2 1.2 + - - -
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Residues in contact with LYS 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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318A ASP* 2.9 41.4 + - + +
456A MET* 4.1 3.1 - - + -
457A PRO 3.4 0.2 - - - -
458A ASP* 1.3 75.1 - - + +
460A MET* 1.3 69.4 + - + +
462A GLU* 3.0 30.6 + - - +
463A LEU* 2.8 27.0 + - - +
495A VAL 4.8 1.0 + - - -
496A LEU* 2.7 34.8 + - + +
497A PHE* 3.6 31.6 - - + -
498A PRO* 5.0 4.2 - - - +
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Residues in contact with MET 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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353A LEU* 3.8 22.7 - - + -
449A SER* 3.5 42.7 - - - +
452A LEU* 3.7 30.5 - - + +
453A THR* 3.8 11.0 - - - +
456A MET* 3.0 34.6 + - + +
457A PRO 4.3 1.3 - - - +
459A LYS* 1.3 87.3 - - + +
461A ALA* 1.3 64.7 - - - +
463A LEU* 3.2 17.7 + - + +
464A ARG* 3.2 30.6 + - - +
496A LEU* 4.6 1.6 - - + -
497A PHE* 4.5 3.8 - - + -
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Residues in contact with ALA 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 3.2 19.3 + - - +
458A ASP* 3.7 6.3 - - - +
460A MET* 1.3 77.2 - - - +
462A GLU* 1.3 57.8 + - - +
464A ARG* 3.4 20.5 + - - +
465A ARG* 3.0 36.1 + - - +
471A GLU* 4.2 21.5 - - + +
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Residues in contact with GLU 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 ASP 3.1 14.6 + - - +
459A LYS* 3.0 40.2 + - - +
461A ALA* 1.3 76.0 - - - +
463A LEU* 1.3 59.2 + - - +
465A ARG* 3.5 28.9 - - - +
466A ALA* 2.9 30.8 + - - +
494A PRO* 4.2 24.2 - - + +
495A VAL 4.6 1.9 - - - +
496A LEU* 3.5 23.9 - - + +
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Residues in contact with LEU 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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353A LEU* 3.9 22.2 - - + -
357A VAL* 3.5 29.8 - - + +
445A LEU* 4.2 15.5 - - + +
449A SER* 3.8 21.5 - - - +
459A LYS 2.8 13.2 + - - +
460A MET* 3.4 21.1 - - - +
461A ALA 3.2 0.4 - - - -
462A GLU* 1.3 77.8 - - - +
464A ARG* 1.3 66.3 + - + +
466A ALA* 3.4 6.0 + - - +
467A LEU* 3.1 36.0 + - + +
469A LEU* 5.0 1.8 - - + -
496A LEU* 3.8 21.9 - - + +
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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 ARG* 5.2 4.7 - - - -
449A SER* 2.9 45.6 + - - +
450A ILE* 3.6 4.2 - - - +
453A THR* 3.1 31.3 + - - +
457A PRO 4.9 1.0 + - - -
460A MET* 3.2 10.3 + - - +
461A ALA* 3.7 25.7 - - - +
463A LEU* 1.3 75.6 - - - +
465A ARG* 1.3 66.9 + - - +
467A LEU 3.0 1.7 + - - -
468A GLY 2.9 4.3 + - - -
469A LEU* 2.8 56.1 + - + +
470A LYS 3.1 20.4 - - - +
471A GLU* 2.7 27.9 + - - +
473A VAL* 3.7 18.4 - - - +
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Residues in contact with ARG 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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458A ASP 5.2 1.6 + - - -
461A ALA* 3.0 19.8 + - - +
462A GLU* 3.5 33.3 - - - +
464A ARG* 1.3 75.7 - - - +
466A ALA* 1.3 63.4 + - - +
468A GLY* 3.2 9.6 + - - -
469A LEU 4.4 4.2 + - - -
471A GLU* 2.8 57.3 + - + +
490A PRO* 3.2 19.5 - - - +
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Residues in contact with ALA 466 (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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357A VAL* 4.5 9.4 - - + -
361A ARG* 2.8 39.9 + - - +
462A GLU* 2.9 19.1 + - - +
463A LEU* 3.6 7.9 - - - +
464A ARG 3.2 0.2 - - - -
465A ARG* 1.3 78.2 - - - +
467A LEU* 1.3 57.6 + - - +
468A GLY 3.4 1.2 + - - -
489A ILE* 4.3 1.6 - - - +
490A PRO* 3.8 9.3 - - - +
493A ALA* 3.9 20.6 - - + -
494A PRO 5.6 2.9 - - - +
496A LEU* 5.3 4.5 - - + -
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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