Contacts of the helix formed by residues 444 - 475 (chain J) in PDB entry 5KHU
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 TRP 444 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443J LYS* 3.8 27.4 - - - +
445J GLU* 3.8 29.6 - - - +
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Residues in contact with GLU 445 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444J TRP* 3.8 29.8 - - - +
446J PRO* 3.8 26.7 - - - -
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Residues in contact with PRO 446 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ARG* 4.3 23.8 - - - -
445J GLU* 3.8 25.4 - - - -
447J LEU* 3.8 29.6 - - - -
449J ASN* 4.4 17.0 - - - -
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Residues in contact with LEU 447 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446J PRO* 3.8 28.9 - - - -
448J LEU* 3.8 26.9 - - - +
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Residues in contact with LEU 448 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447J LEU* 3.8 30.1 - - - +
449J ASN* 3.8 25.6 - - - +
451J LEU* 4.4 15.5 - - - +
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Residues in contact with ASN 449 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446J PRO* 4.4 16.8 - - - -
448J LEU* 3.8 26.9 - - - +
450J ASN* 3.7 29.8 - - - +
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Residues in contact with ASN 450 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449J ASN* 3.7 29.6 - - - +
451J LEU* 3.8 25.4 - - - +
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Residues in contact with LEU 451 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448J LEU* 4.4 19.1 - - - +
450J ASN* 3.8 24.7 - - - +
452J GLY* 3.8 28.9 - - - +
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Residues in contact with GLY 452 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451J LEU* 3.8 29.2 - - - +
453J HIS* 3.8 25.8 - - - +
464J ALA* 4.1 26.5 - - - +
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Residues in contact with HIS 453 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452J GLY* 3.8 28.0 - - - +
454J VAL* 3.8 29.2 - - - +
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Residues in contact with VAL 454 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453J HIS* 3.8 28.7 - - - +
455J CYS* 3.8 25.6 - - - +
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Residues in contact with CYS 455 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454J VAL* 3.8 29.4 - - - +
456J ARG* 3.8 24.7 - - - +
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Residues in contact with ARG 456 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455J CYS* 3.8 26.7 - - - +
457J LYS* 3.8 29.4 - - - +
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Residues in contact with LYS 457 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456J ARG* 3.8 25.4 - - - +
458J LEU* 3.8 29.6 - - - +
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Residues in contact with LEU 458 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457J LYS* 3.8 29.6 - - - +
459J LYS* 3.8 25.1 - - - +
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Residues in contact with LYS 459 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458J LEU* 3.8 24.9 - - - +
460J LYS* 3.8 29.2 - - - +
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Residues in contact with LYS 460 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459J LYS* 3.8 28.5 - - - +
461J TYR* 3.7 29.4 - - - +
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Residues in contact with TYR 461 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460J LYS* 3.7 30.1 - - - +
462J ALA* 3.8 28.7 - - - +
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Residues in contact with ALA 462 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461J TYR* 3.8 26.9 - - - +
463J GLU* 3.8 29.4 - - - +
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Residues in contact with GLU 463 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462J ALA* 3.8 28.9 - - - +
464J ALA* 3.8 26.5 - - - +
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Residues in contact with ALA 464 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452J GLY* 4.1 26.2 - - - +
463J GLU* 3.8 26.7 - - - +
465J LEU* 3.8 30.1 - - - +
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Residues in contact with LEU 465 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464J ALA* 3.8 26.0 - - - +
466J ASP* 3.8 29.2 - - - +
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Residues in contact with ASP 466 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465J LEU* 3.8 25.6 - - - +
467J TYR* 3.8 30.5 - - - +
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Residues in contact with TYR 467 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466J ASP* 3.8 29.2 - - - +
468J HIS* 3.8 25.6 - - - +
470J GLN* 4.6 15.9 - - - +
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Residues in contact with HIS 468 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467J TYR* 3.8 26.0 - - - +
469J ARG* 3.8 29.8 - - - +
471J ALA* 4.5 14.4 - - - +
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Residues in contact with ARG 469 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468J HIS* 3.8 29.4 - - - +
470J GLN* 3.8 26.2 - - - +
472J LEU* 4.5 15.5 - - - +
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Residues in contact with GLN 470 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467J TYR* 4.6 13.7 - - - +
469J ARG* 3.8 29.6 - - - +
471J ALA* 3.8 24.7 - - - +
473J VAL* 4.7 14.4 - - - +
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Residues in contact with ALA 471 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468J HIS* 4.5 16.2 - - - +
470J GLN* 3.8 28.7 - - - +
472J LEU* 3.8 25.8 - - - +
----------------------------------------------------------
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Residues in contact with LEU 472 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469J ARG* 4.5 14.6 - - - +
471J ALA* 3.8 29.6 - - - +
473J VAL* 3.8 25.1 - - - +
----------------------------------------------------------
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Residues in contact with VAL 473 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470J GLN* 4.7 16.2 - - - +
472J LEU* 3.8 24.5 - - - +
474J LEU* 3.7 29.8 - - - +
----------------------------------------------------------
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Residues in contact with LEU 474 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473J VAL* 3.7 29.6 - - - +
475J ILE* 3.8 26.7 - - - +
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Residues in contact with ILE 475 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474J LEU* 3.8 29.4 - - - +
476J PRO* 3.8 29.8 - - - -
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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
------------------------------------------------------------
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