Contacts of the helix formed by residues 442 - 466 (chain J) in PDB entry 6AH0
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 LYS 442 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I G 4.5 2.8 + - - -
441J THR* 1.3 70.8 - - - +
443J LYS* 1.3 57.3 + - - +
445J GLN* 3.0 16.6 + - - +
446J LYS* 3.1 11.6 + - - -
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Residues in contact with LYS 443 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I G 5.0 6.8 + - - +
24I U 3.8 27.0 + - - -
441J THR 3.4 0.4 - - - -
442J LYS* 1.3 75.8 - - - +
444J GLU* 1.3 57.6 + - - +
445J GLN 3.2 0.2 - - - -
446J LYS 4.1 1.8 - - - +
447J LYS* 3.4 15.9 + - - -
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Residues in contact with GLU 444 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440J LEU* 5.7 1.3 - - - +
441J THR* 3.4 16.8 + - - +
442J LYS 3.2 0.6 - - - -
443J LYS* 1.3 74.8 - - - +
445J GLN* 1.3 62.5 + - - +
447J LYS* 4.2 2.5 - - - +
448J LEU* 3.7 12.6 + - - +
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Residues in contact with GLN 445 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441J THR 3.3 8.3 + - - -
442J LYS* 3.0 8.3 + - - +
444J GLU* 1.3 78.2 - - - +
446J LYS* 1.3 54.7 + - - +
448J LEU* 3.1 1.7 + - - -
449J ARG* 2.7 35.0 + - - -
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Residues in contact with LYS 446 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F G 5.3 7.4 - - - -
22I C 4.7 0.4 - - - -
23I G 2.6 32.3 - - - -
442J LYS 3.1 10.9 + - - -
443J LYS 4.0 0.4 + - - -
445J GLN* 1.3 71.7 - - - +
447J LYS* 1.3 65.0 + - - +
449J ARG* 2.8 3.8 + - - +
450J ARG* 2.8 24.1 + - - -
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Residues in contact with LYS 447 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I G 4.1 9.8 + - - -
24I U 5.2 5.2 - - - -
443J LYS 3.4 15.7 + - - -
444J GLU* 5.0 0.9 - - - +
445J GLN 3.2 0.8 - - - -
446J LYS* 1.3 73.1 - - - +
448J LEU* 1.3 57.5 + - - +
450J ARG* 5.3 0.7 - - - +
451J GLN* 3.1 26.3 + - - -
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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
----------------------------------------------------------
444J GLU 3.7 12.8 + - - -
445J GLN 3.1 4.4 + - - -
446J LYS 3.1 1.0 - - - -
447J LYS* 1.3 78.9 - - - +
449J ARG* 1.3 56.2 + - - +
451J GLN* 5.3 0.2 - - - +
452J THR* 3.0 25.3 + - - -
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Residues in contact with ARG 449 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F G 5.4 4.9 + - - -
10I C 5.7 0.6 + - - -
445J GLN 2.7 18.5 + - - -
446J LYS* 2.8 5.5 + - - +
448J LEU* 1.3 71.2 - - - +
450J ARG* 1.3 55.2 + - - +
452J THR* 3.9 0.3 - - - -
453J ARG* 3.0 23.9 + - - -
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Residues in contact with ARG 450 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F G 6.5 1.1 - - - -
446J LYS 2.8 17.0 + - - -
447J LYS* 4.2 0.7 - - - +
449J ARG* 1.3 69.9 - - - +
451J GLN* 1.3 54.2 + - - +
452J THR 3.3 1.6 - - - -
453J ARG* 3.8 0.8 - - - +
454J ARG* 2.7 32.7 + - - -
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Residues in contact with GLN 451 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447J LYS 3.1 17.9 + - - -
448J LEU* 5.3 0.2 - - - +
450J ARG* 1.3 73.8 - - - +
452J THR* 1.3 59.0 + - - +
454J ARG* 4.1 2.2 - - - +
455J GLU* 3.8 13.0 + - - -
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Residues in contact with THR 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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10I C 5.8 4.5 - - - -
448J LEU 3.0 20.1 + - - -
449J ARG 3.9 0.9 - - - -
451J GLN* 1.3 75.6 - - - +
453J ARG* 1.3 61.9 + - - +
455J GLU* 3.9 1.2 + - - -
456J ALA* 3.6 14.0 + - - -
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Residues in contact with ARG 453 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I C 5.8 0.4 + - - -
449J ARG 3.0 16.7 + - - -
450J ARG* 3.8 1.6 - - - +
452J THR* 1.3 73.2 - - - +
454J ARG* 1.3 66.6 + - - +
456J ALA* 3.2 2.1 + - - +
457J GLN* 3.0 20.4 + - - -
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Residues in contact with ARG 454 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450J ARG 2.7 20.8 + - - -
451J GLN* 4.7 1.3 - - - +
452J THR 3.4 0.2 - - - -
453J ARG* 1.3 73.4 - - - +
455J GLU* 1.3 64.4 + - - +
456J ALA 3.1 0.2 + - - -
457J GLN* 3.3 0.6 + - - +
458J LYS* 3.1 21.7 + - - -
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Residues in contact with GLU 455 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451J GLN 3.8 13.5 + - - -
452J THR 3.9 2.2 + - - -
453J ARG 3.3 0.6 - - - -
454J ARG* 1.3 74.3 - - - +
456J ALA* 1.3 61.1 + - - +
458J LYS* 4.3 0.2 - - - -
459J GLU* 3.2 19.9 + - - -
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Residues in contact with ALA 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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452J THR 3.6 9.8 + - - -
453J ARG* 3.2 5.9 + - - +
454J ARG 3.1 1.0 - - - -
455J GLU* 1.3 77.9 - - - +
457J GLN* 1.3 60.8 + - - +
459J GLU* 3.3 1.2 + - - -
460J LEU* 3.1 17.8 + - - -
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Residues in contact with GLN 457 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453J ARG 3.0 13.5 + - - -
454J ARG* 4.0 1.1 - - - +
456J ALA* 1.3 74.7 - - - +
458J LYS* 1.3 58.1 + - - +
460J LEU* 3.2 3.8 + - - +
461J GLN* 2.9 23.2 + - - -
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Residues in contact with LYS 458 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454J ARG 3.1 14.8 + - - -
455J GLU* 4.3 0.4 - - - +
457J GLN* 1.3 72.3 - - - +
459J GLU* 1.3 64.9 + - - +
461J GLN* 3.0 11.9 + - - +
462J GLU* 3.2 10.4 + - - -
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Residues in contact with GLU 459 (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 GLU 3.2 15.4 + - - -
456J ALA 3.7 4.3 - - - -
457J GLN 3.3 0.2 - - - -
458J LYS* 1.3 78.9 - - - +
460J LEU* 1.3 59.1 + - - +
462J GLU* 3.6 1.7 + - - -
463J LYS* 3.5 14.6 + - - -
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Residues in contact with LEU 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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456J ALA 3.1 13.3 + - - -
457J GLN* 3.2 5.5 + - - +
459J GLU* 1.3 74.3 - - - +
461J GLN* 1.3 65.5 + - - +
463J LYS* 3.2 11.8 + - - +
464J VAL* 3.4 7.8 + - - -
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Residues in contact with GLN 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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457J GLN 2.9 13.3 + - - -
458J LYS* 3.0 6.9 + - - +
460J LEU* 1.3 76.3 - - - +
462J GLU* 1.3 61.3 + - - +
464J VAL* 3.3 11.1 + - - -
465J ARG* 3.3 8.8 + - - -
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Residues in contact with GLU 462 (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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458J LYS 3.2 11.6 + - - -
459J GLU* 3.6 3.3 + - - +
461J GLN* 1.3 72.6 - - - +
463J LYS* 1.3 56.6 + - - +
465J ARG* 3.0 4.3 + - - +
466J LEU* 2.7 34.3 + - - -
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Residues in contact with LYS 463 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459J GLU 3.5 10.1 + - - -
460J LEU* 3.2 9.9 + - - +
462J GLU* 1.3 77.2 - - - +
464J VAL* 1.3 55.6 + - - +
466J LEU* 4.5 0.7 - - - +
467J GLY 3.0 3.8 + - - -
468J LEU* 2.9 32.5 + - - +
469J MET* 3.2 10.5 + - - +
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Residues in contact with VAL 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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460J LEU 3.4 6.6 + - - -
461J GLN 3.3 7.5 + - - -
462J GLU 3.1 0.4 - - - -
463J LYS* 1.3 73.7 - - - +
465J ARG* 1.3 65.4 + - - +
467J GLY* 3.3 10.4 + - - -
469J MET* 4.0 14.7 - - - +
471J PRO* 5.4 7.2 - - - -
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Residues in contact with ARG 465 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461J GLN 3.3 9.1 + - - -
462J GLU* 3.0 8.1 + - - +
464J VAL* 1.3 77.7 - - - +
466J LEU* 1.3 60.8 + - - +
467J GLY* 3.2 1.2 + - - -
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Residues in contact with LEU 466 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462J GLU 2.7 19.4 + - - -
463J LYS* 4.1 1.8 - - - +
465J ARG* 1.3 71.4 - - - +
467J GLY* 1.3 60.3 + - - +
468J LEU 3.3 2.6 + - - -
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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
------------------------------------------------------------
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