Contacts of the helix formed by residues 494 - 504 (chain A) in PDB entry 4PK7
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 ASP 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456A PRO* 6.0 0.5 - - - +
457A ASN* 3.2 27.2 + - + +
461A VAL* 6.0 0.7 - - + -
490A GLU 3.6 13.7 + - - +
491A LEU* 3.9 10.0 - - + +
492A LEU 3.2 3.8 - - - -
493A LYS* 1.3 74.2 - - - +
495A TRP* 1.3 62.5 + - - +
496A GLU* 4.2 6.6 + - - +
497A CYS* 3.2 30.2 + - + +
498A MET* 3.3 27.2 + - - +
562A LYS* 4.6 5.5 + - - +
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Residues in contact with TRP 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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492A LEU 3.5 6.0 + - - -
493A LYS* 3.2 43.5 + - + -
494A ASP* 1.3 71.6 - - - +
496A GLU* 1.3 55.4 + - - +
498A MET* 3.1 30.4 + - + +
499A ASN* 2.7 37.8 + - - +
525A MET* 4.7 0.4 - - + -
528A THR* 3.4 23.5 + - - -
529A ILE* 3.5 21.3 - - + +
532A ALA* 3.6 33.0 - - + -
559A ASP* 3.7 22.9 - - - -
562A LYS* 3.8 26.4 - - + +
563A ILE* 3.5 30.1 - - + -
566A LEU* 3.4 17.5 - - + -
567A PHE* 3.7 12.9 - + + -
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Residues in contact with GLU 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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494A ASP* 3.5 7.1 + - - +
495A TRP* 1.3 77.9 - - - +
497A CYS* 1.3 55.7 + - - +
499A ASN* 3.7 4.0 - - - +
500A SER* 2.7 34.4 + - - -
562A LYS* 4.5 14.2 + - + +
566A LEU* 3.4 28.8 - - + +
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Residues in contact with CYS 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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455A GLY* 5.8 4.9 - - - -
457A ASN* 4.2 6.1 - - - -
458A ALA* 3.8 36.3 - - - -
461A VAL* 4.5 9.6 - - + -
494A ASP* 3.2 35.3 + - + +
495A TRP 3.2 0.2 - - - -
496A GLU* 1.3 79.1 - - - +
498A MET* 1.3 62.8 + - + +
500A SER* 3.0 13.6 + - - -
501A LEU* 2.9 28.1 - - - +
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Residues in contact with MET 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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461A VAL* 4.0 21.3 - - + -
491A LEU 5.3 2.7 - - - +
492A LEU* 3.7 15.3 - - - +
494A ASP 3.3 13.4 + - - +
495A TRP* 3.1 40.9 + - + +
497A CYS* 1.3 79.6 - - - +
499A ASN* 1.3 63.3 + - - +
501A LEU* 3.3 18.3 + - - +
502A LEU* 3.7 10.0 + - - +
521A LEU* 3.8 29.7 - - + +
524A ILE* 4.6 9.4 - - - -
525A MET* 4.0 33.7 - - + -
528A THR* 3.8 9.0 - - - +
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Residues in contact with ASN 499 (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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495A TRP 2.7 24.7 + - - +
496A GLU* 3.7 5.8 - - - +
498A MET* 1.3 74.5 - - - +
500A SER* 1.3 60.2 + - - +
501A LEU 3.5 0.7 + - - -
502A LEU* 3.5 11.0 + - - +
503A LEU* 3.6 27.3 + - - +
504A GLU* 4.9 2.5 - - - +
525A MET* 4.4 6.7 - - - -
566A LEU* 3.5 18.8 - - + +
567A PHE* 4.6 7.6 - - + -
570A ALA* 3.2 35.4 - - - +
574A LEU* 3.9 16.4 - - - +
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Residues in contact with SER 500 (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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496A GLU* 2.7 19.8 + - - +
497A CYS* 3.0 12.4 + - - -
499A ASN* 1.3 79.5 + - - +
501A LEU* 1.3 61.0 + - - +
502A LEU 3.3 0.2 - - - -
503A LEU 4.7 0.4 - - - +
504A GLU* 3.1 59.2 + - - +
505A GLU 4.4 2.3 + - - -
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Residues in contact with LEU 501 (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 ALA* 4.3 18.2 - - + +
461A VAL* 4.6 12.8 - - + -
462A LYS* 3.9 31.4 - - + -
497A CYS* 2.9 42.8 - - - +
498A MET* 3.3 9.9 + - - +
500A SER* 1.3 79.7 - - - +
502A LEU* 1.3 60.6 + - - +
503A LEU 3.3 0.8 - - - -
504A GLU 5.0 0.2 - - - -
505A GLU* 5.4 4.2 + - - +
513A LEU* 3.3 26.3 - - + +
518A GLU* 4.7 2.6 - - - +
521A LEU* 3.9 12.8 - - + -
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Residues in contact with LEU 502 (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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498A MET 3.7 5.6 + - - +
499A ASN* 3.5 8.2 + - - +
500A SER 3.3 0.6 - - - -
501A LEU* 1.3 77.9 - - - +
503A LEU* 1.3 58.7 + - - +
505A GLU* 6.2 0.4 - - - -
513A LEU* 5.1 0.7 - - + -
518A GLU* 3.4 35.2 - - + +
521A LEU* 3.8 24.7 - - + -
522A ILE* 3.6 18.6 - - + -
525A MET* 3.8 36.1 - - + -
574A LEU* 4.0 14.6 - - + -
577A LYS* 3.4 17.1 - - - +
578A TYR* 2.7 37.6 + - + +
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Residues in contact with LEU 503 (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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499A ASN* 3.6 35.4 + - - +
500A SER 3.5 1.2 + - - -
501A LEU 3.3 1.2 - - - -
502A LEU* 1.3 87.2 - - - +
504A GLU* 1.3 77.2 + - + +
505A GLU* 3.5 22.5 + - - +
570A ALA* 4.6 5.4 - - + +
573A GLN* 4.2 48.9 - - + +
574A LEU* 4.2 15.5 - - + -
577A LYS* 4.2 16.4 - - + +
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Residues in contact with GLU 504 (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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499A ASN* 4.8 2.8 - - - +
500A SER* 3.1 47.9 + - - +
503A LEU* 1.3 80.7 - - + +
505A GLU* 1.3 72.3 + - - +
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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