Contacts of the helix formed by residues 497 - 513 (chain K) in PDB entry 6Y5D
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 497 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432K LYS* 4.8 14.6 + - - +
493K SER* 4.4 7.3 + - - +
496K ILE* 1.3 79.0 - - - +
498K LYS* 1.3 67.2 + - - +
499K ARG* 3.5 15.6 - - + +
500K SER* 3.2 46.4 + - - -
501K LYS* 3.4 7.6 + - - +
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Residues in contact with LYS 498 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475K LEU 4.1 1.6 + - - -
476K ARG* 2.8 38.0 + - - +
478K GLU* 3.8 33.2 + - + +
493K SER* 5.8 1.4 - - - +
496K ILE 3.7 0.8 + - - -
497K ASP* 1.3 73.0 - - - +
499K ARG* 1.3 64.8 + - + +
501K LYS* 2.9 13.2 + - + +
502K GLU* 2.8 55.7 + - - +
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Residues in contact with ARG 499 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429K HIS* 5.0 12.2 + - + +
497K ASP* 3.2 13.1 - - + +
498K LYS* 1.3 77.3 - - + +
500K SER* 1.3 58.5 + - - +
502K GLU* 3.3 14.3 + - - +
503K PHE* 2.9 31.3 + - - +
37V C 3.2 30.7 + - - -
38V T 5.9 0.4 + - - -
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Residues in contact with SER 500 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428K LYS 5.0 0.3 + - - -
429K HIS* 2.6 33.4 + - - +
430K LEU* 4.0 1.2 - - - +
432K LYS* 5.8 3.6 - - - +
433K PHE* 3.4 22.9 - - - -
496K ILE* 4.0 7.0 - - - -
497K ASP* 3.2 27.4 + - - -
498K LYS 3.2 0.6 - - - -
499K ARG* 1.3 77.5 - - - +
501K LYS* 1.3 58.3 + - - +
503K PHE* 3.4 5.9 + - - +
504K LEU* 2.9 23.9 + - - +
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Residues in contact with LYS 501 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433K PHE* 3.8 18.4 - - + -
475K LEU* 3.8 35.0 - - + +
478K GLU* 3.6 25.4 + - + +
491K PHE* 2.5 50.5 + - - -
492K SER 3.5 2.8 + - - -
496K ILE* 2.7 34.6 + - + +
497K ASP 3.4 10.3 + - - +
498K LYS* 2.9 12.0 + - + +
500K SER* 1.3 75.7 - - - +
502K GLU* 1.3 55.3 + - - +
504K LEU* 3.9 0.9 - - - +
505K THR* 2.6 39.9 + - - -
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Residues in contact with GLU 502 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498K LYS* 2.8 50.7 + - - +
499K ARG* 3.7 18.8 - - - +
501K LYS* 1.3 72.0 - - - +
503K PHE* 1.3 57.9 + - - +
505K THR* 3.4 7.6 + - - -
506K LYS* 2.8 31.5 + - - +
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Residues in contact with PHE 503 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424K PHE* 3.5 43.5 - + + -
427K LYS* 4.1 6.1 - - + -
429K HIS* 3.4 55.2 - + + +
430K LEU* 3.9 10.3 - - + -
499K ARG 2.9 18.0 + - - +
500K SER 3.6 3.1 - - - +
502K GLU* 1.3 74.0 - - - +
504K LEU* 1.3 61.3 + - - +
506K LYS* 3.1 11.9 + - + +
507K GLN* 2.8 65.4 + - + +
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Residues in contact with LEU 504 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417K LEU* 3.6 32.8 - - + -
420K LEU* 3.8 25.4 - - + -
430K LEU* 3.5 20.4 - - + -
433K PHE* 3.7 23.6 - - + -
471K PHE* 3.8 10.5 - - + -
475K LEU* 3.7 22.0 - - + -
500K SER 2.9 17.8 + - - +
501K LYS 4.0 2.9 - - - +
503K PHE* 1.3 77.7 - - - +
505K THR* 1.3 64.6 + - - +
507K GLN* 3.2 2.0 + - + +
508K ILE* 2.9 37.0 + - + +
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Residues in contact with THR 505 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472K LEU* 3.7 14.2 + - + +
475K LEU* 3.4 19.9 - - - +
476K ARG* 3.4 42.0 + - + +
501K LYS 2.6 25.4 + - - -
502K GLU* 3.5 8.6 - - - +
504K LEU* 1.3 76.8 - - - +
506K LYS* 1.3 57.2 + - - +
509K GLU* 2.9 47.7 + - - +
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Residues in contact with LYS 506 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502K GLU 2.8 19.5 + - - +
503K PHE* 3.4 10.3 - - + +
505K THR* 1.3 77.4 - - - +
507K GLN* 1.3 72.2 + - - +
509K GLU* 3.4 13.5 + - - +
510K TYR* 3.0 28.5 + - + +
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Residues in contact with GLN 507 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420K LEU* 4.0 20.4 - - + +
423K ARG* 4.3 5.0 + - - -
424K PHE* 2.9 37.8 - - + -
430K LEU* 5.5 0.2 - - + -
503K PHE* 2.8 53.2 + - + +
504K LEU* 3.9 4.9 - - + +
506K LYS* 1.3 86.4 - - - +
508K ILE* 1.3 60.6 + - - +
510K TYR* 3.3 13.3 + - - +
511K GLU* 2.9 34.3 + - - +
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Residues in contact with ILE 508 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416K LEU* 4.0 20.6 - - + -
417K LEU* 6.0 1.3 - - + -
420K LEU* 3.6 21.3 - - + -
468K VAL* 3.4 32.1 - - + -
471K PHE* 3.9 25.8 - - + -
472K LEU* 3.6 21.8 - - + -
475K LEU* 4.3 0.2 - - + -
504K LEU* 2.9 37.9 + - + +
507K GLN* 1.3 75.4 - - - +
509K GLU* 1.3 58.8 + - - +
511K GLU* 3.2 4.9 + - - +
512K ARG* 2.8 28.7 + - + +
516K PHE* 4.5 1.3 - - + -
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Residues in contact with GLU 509 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472K LEU* 4.2 9.9 - - + -
476K ARG* 2.7 36.6 + - - +
505K THR* 2.9 26.8 + - - +
506K LYS* 3.7 13.0 - - - +
508K ILE* 1.3 75.9 - - - +
510K TYR* 1.3 62.3 + - - +
512K ARG* 3.4 15.8 + - - +
513K ASN* 3.0 37.7 + - - +
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Residues in contact with TYR 510 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423K ARG* 5.3 5.6 - - - -
506K LYS* 3.0 15.8 + - + +
507K GLN* 3.4 19.3 - - - +
509K GLU* 1.3 76.8 - - - +
511K GLU* 1.3 84.2 + - - +
513K ASN* 3.3 8.2 + - - +
514K ASN* 2.8 47.6 + - - +
517K PRO* 4.8 9.9 - - + +
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Residues in contact with GLU 511 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416K LEU* 4.3 5.6 - - + -
420K LEU* 3.9 16.6 - - + +
423K ARG* 3.0 28.6 + - - -
507K GLN* 2.9 21.4 + - - +
508K ILE 3.6 5.2 - - - +
510K TYR* 1.3 87.6 - - - +
512K ARG* 1.3 55.6 + - - +
514K ASN 2.9 15.9 + - - -
515K GLU 3.0 0.2 + - - -
516K PHE* 2.7 39.9 + - + -
517K PRO* 3.0 16.1 - - - +
518K VAL* 2.9 42.1 + - + +
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Residues in contact with ARG 512 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465K ASP* 2.9 39.8 + - - +
468K VAL* 4.7 4.2 - - + +
469K THR* 3.7 17.2 + - - -
472K LEU* 3.7 26.1 - - - +
476K ARG* 5.2 2.2 - - - +
508K ILE* 2.8 18.6 + - + +
509K GLU* 3.7 14.7 + - - +
511K GLU* 1.3 75.4 - - - +
513K ASN* 1.3 74.5 + - - +
514K ASN 3.1 1.0 + - - -
515K GLU* 3.3 12.0 + - - +
516K PHE* 3.6 30.0 - - + -
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Residues in contact with ASN 513 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509K GLU* 3.0 29.6 + - - +
510K TYR* 3.8 6.6 - - - +
511K GLU 3.2 0.4 - - - -
512K ARG* 1.3 88.1 + - - +
514K ASN* 1.3 67.8 + - - +
515K GLU* 3.5 2.0 - - - +
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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