Contacts of the helix formed by residues 486 - 499 (chain A) in PDB entry 4XK8
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 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A LEU 3.7 1.3 - - - +
485A GLN* 1.3 79.2 - - - +
487A VAL* 1.3 64.3 + - - +
488A PHE 3.3 3.1 - - - -
489A ALA* 3.2 17.8 + - + +
490A GLN* 2.9 37.5 + - - +
534A LEU* 3.9 17.9 - - + -
535A GLY 3.1 32.3 - - - +
538A ASP* 4.6 2.0 - - + -
539A PHE* 4.1 22.4 - - + +
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Residues in contact with VAL 487 (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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485A GLN* 2.9 31.9 + - + +
486A PRO* 1.3 71.1 - - - +
488A PHE* 1.3 72.3 + - + +
490A GLN* 3.3 13.2 + - - +
491A TRP* 2.9 30.8 + - + +
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Residues in contact with PHE 488 (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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486A PRO 3.3 0.8 - - - -
487A VAL* 1.3 89.3 - - + +
489A ALA* 1.3 58.0 + - - +
491A TRP* 3.2 8.2 + - + +
492A ILE* 3.0 37.1 + - + +
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Residues in contact with ALA 489 (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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486A PRO* 3.2 15.2 + - + +
488A PHE* 1.3 78.6 - - - +
490A GLN* 1.3 57.5 + - - +
492A ILE* 3.3 11.4 + - - +
493A GLN* 2.9 32.9 + - - +
534A LEU* 3.7 22.9 - - + -
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Residues in contact with GLN 490 (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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485A GLN* 3.4 23.7 + - - +
486A PRO* 2.9 26.5 + - - +
487A VAL* 3.5 16.1 - - - +
489A ALA* 1.3 77.2 - - - +
491A TRP* 1.3 56.3 + - - +
493A GLN* 3.3 17.7 + - - +
494A ASN* 2.9 28.8 + - - +
534A LEU* 2.8 33.6 + - + +
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Residues in contact with TRP 491 (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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487A VAL* 2.9 17.0 + - + +
488A PHE* 3.2 11.6 + - + +
490A GLN* 1.3 74.1 - - - +
492A ILE* 1.3 77.4 + - + +
494A ASN* 3.4 9.0 + - - +
495A THR* 2.8 62.4 + - + -
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Residues in contact with ILE 492 (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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488A PHE* 3.0 24.3 + - + +
489A ALA* 3.6 11.0 - - - +
491A TRP* 1.3 94.0 - - + +
493A GLN* 1.3 57.6 + - - +
495A THR* 3.5 2.8 + - - -
496A HIS* 2.9 58.1 + - + +
515A TRP* 4.7 6.7 - - + -
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Residues in contact with GLN 493 (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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489A ALA 2.9 13.1 + - - +
490A GLN* 3.3 19.6 - - - +
492A ILE* 1.3 76.8 - - + +
494A ASN* 1.3 57.2 + - - +
496A HIS* 3.2 3.3 + - - +
497A ALA* 2.9 29.5 + - - +
514A THR 3.4 16.8 + - - -
515A TRP* 3.8 24.7 - - + +
516A GLY* 3.5 24.3 + - - +
532A ILE* 2.8 29.3 + - - +
533A PRO* 5.3 0.2 - - - +
534A LEU* 3.6 32.5 + - + +
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Residues in contact with ASN 494 (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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490A GLN 2.9 16.5 + - - +
491A TRP* 3.8 11.5 + - - +
493A GLN* 1.3 74.9 - - - +
495A THR* 1.3 62.1 + - - +
497A ALA* 3.1 7.8 + - - +
498A LEU* 2.9 56.9 + - - +
516A GLY* 4.8 4.2 - - - -
517A GLY 5.5 0.2 - - - +
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Residues in contact with THR 495 (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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491A TRP* 2.8 58.0 + - + -
492A ILE* 3.7 5.6 - - - -
494A ASN* 1.3 81.4 + - - +
496A HIS* 1.3 65.9 + - + +
498A LEU* 3.4 4.8 + - - +
499A ALA* 3.0 28.3 + - + +
503A THR* 5.8 4.0 - - + +
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Residues in contact with HIS 496 (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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492A ILE* 2.9 40.0 + - + +
493A GLN 3.7 0.4 - - - +
495A THR* 1.3 87.2 - - + +
497A ALA* 1.3 60.2 + - - +
499A ALA* 3.7 18.5 - - + +
500A PRO* 3.9 1.9 - - - +
510A SER* 3.5 14.2 + - - -
511A THR 5.3 0.5 + - - -
515A TRP* 3.1 56.9 - + + +
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Residues in contact with ALA 497 (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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493A GLN 2.9 16.7 + - - +
494A ASN* 3.5 7.4 - - - +
496A HIS* 1.3 79.1 - - - +
498A LEU* 1.3 66.3 + - + +
499A ALA 3.3 0.7 - - - -
500A PRO* 3.4 14.0 - - - +
510A SER* 3.5 12.3 + - - -
515A TRP* 4.1 4.9 - - + +
517A GLY* 3.5 38.8 - - - +
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Residues in contact with LEU 498 (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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494A ASN* 2.9 45.8 + - - +
495A THR* 3.7 4.7 - - - +
497A ALA* 1.3 81.5 - - + +
499A ALA* 1.3 64.4 + - - +
500A PRO* 3.4 2.5 - - - -
501A GLY* 3.3 11.2 + - - -
502A THR* 3.2 21.8 + - + +
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Residues in contact with ALA 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A THR* 3.0 17.4 + - + +
496A HIS* 3.7 15.0 - - + +
497A ALA 3.3 0.2 - - - -
498A LEU* 1.3 78.4 - - - +
500A PRO* 1.4 69.3 - - + +
501A GLY 3.1 1.2 + - - -
502A THR* 3.1 12.7 + - - -
503A THR* 3.2 14.9 + - - +
504A ALA* 2.9 30.9 + - + -
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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