Contacts of the helix formed by residues 497 - 514 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432L LYS* 4.6 12.6 + - - +
478L GLU* 4.3 0.4 - - - -
493L SER* 4.3 7.8 + - - +
496L ILE* 1.3 79.5 - - - +
498L LYS* 1.3 66.8 + - - +
499L ARG* 3.5 14.0 - - + +
500L SER* 2.8 52.3 + - - -
501L LYS* 3.4 8.7 + - - +
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Residues in contact with LYS 498 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475L LEU 4.4 0.6 + - - -
476L ARG* 2.5 39.2 + - - +
478L GLU* 3.7 36.3 + - + +
493L SER* 5.7 0.8 - - - -
497L ASP* 1.3 72.1 - - - +
499L ARG* 1.3 64.1 + - - +
501L LYS* 3.0 8.6 + - + +
502L GLU* 2.8 57.7 + - + +
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Residues in contact with ARG 499 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37J C 3.1 37.9 + - - -
38J T 4.9 14.3 + - - -
429L HIS* 4.2 26.9 - - + +
497L ASP* 3.2 12.8 - - + +
498L LYS* 1.3 78.6 - - - +
500L SER* 1.3 57.7 + - - +
502L GLU* 3.4 13.3 + - - +
503L PHE* 2.9 28.7 + - + +
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Residues in contact with SER 500 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429L HIS* 3.2 36.1 + - - -
430L LEU* 4.2 1.7 - - - +
432L LYS* 6.1 0.4 - - - +
433L PHE* 3.8 6.5 - - - -
496L ILE* 4.0 12.8 - - - -
497L ASP* 2.8 36.1 + - - -
499L ARG* 1.3 76.5 - - - +
501L LYS* 1.3 56.9 + - - +
503L PHE* 3.3 7.3 + - - +
504L LEU* 2.9 29.3 + - - +
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Residues in contact with LYS 501 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433L PHE* 3.8 20.4 - - + -
475L LEU* 3.6 34.0 - - + +
476L ARG* 6.1 0.2 - - - -
478L GLU* 3.4 23.6 + - + +
491L PHE* 2.4 51.2 + - - -
492L SER 3.4 2.2 + - - -
496L ILE* 2.6 35.3 + - - +
497L ASP 3.4 9.8 + - - +
498L LYS* 3.0 9.5 + - + +
500L SER* 1.3 75.0 - - - +
502L GLU* 1.3 53.7 + - - +
504L LEU* 3.4 1.2 + - - +
505L THR* 2.6 42.5 + - - -
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Residues in contact with GLU 502 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476L ARG* 6.4 0.4 - - - -
498L LYS* 2.8 56.8 + - - +
499L ARG* 3.8 12.3 - - - +
501L LYS* 1.3 69.1 - - - +
503L PHE* 1.3 60.4 + - - +
505L THR* 3.4 8.4 - - - -
506L LYS* 2.9 29.5 + - - +
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Residues in contact with PHE 503 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424L PHE* 3.5 57.4 - + + -
427L LYS* 4.2 7.2 - - + -
429L HIS* 3.6 45.5 - + + +
430L LEU* 4.1 8.3 - - + -
499L ARG* 2.9 18.2 + - + +
500L SER* 3.4 6.7 - - - +
501L LYS 3.2 0.2 - - - -
502L GLU* 1.3 77.3 - - - +
504L LEU* 1.3 59.5 + - - +
506L LYS* 3.1 10.8 + - + +
507L GLN* 2.9 48.5 + - + +
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Residues in contact with LEU 504 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417L LEU* 3.6 28.9 - - + -
420L LEU* 4.0 10.1 - - + -
430L LEU* 3.6 28.7 - - + -
433L PHE* 3.6 34.5 - - + -
471L PHE* 3.9 7.2 - - + -
475L LEU* 3.7 22.2 - - + -
500L SER 2.9 13.1 + - - +
501L LYS 3.9 3.4 - - - +
503L PHE* 1.3 75.4 - - - +
505L THR* 1.3 68.4 + - - +
507L GLN* 3.2 1.7 + - + +
508L ILE* 2.9 38.8 + - + +
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Residues in contact with THR 505 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472L LEU* 3.4 16.8 - - + +
475L LEU* 3.3 20.7 - - - +
476L ARG* 3.5 39.2 + - + +
501L LYS 2.6 29.9 + - - -
502L GLU* 3.4 10.1 - - - +
503L PHE 3.3 0.2 - - - -
504L LEU* 1.3 72.0 - - - +
506L LYS* 1.3 58.3 + - - +
508L ILE 3.3 0.2 + - - -
509L GLU* 2.8 46.7 + - - +
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Residues in contact with LYS 506 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502L GLU 2.9 14.0 + - - +
503L PHE* 3.4 13.0 - - + +
505L THR* 1.3 77.5 - - - +
507L GLN* 1.3 71.9 + - - +
509L GLU* 3.4 12.7 + - + +
510L TYR* 2.8 31.2 + - + +
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Residues in contact with GLN 507 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420L LEU* 3.9 22.3 - - + +
423L ARG* 3.8 9.2 + - - -
424L PHE* 3.0 42.0 - - + -
430L LEU* 5.5 0.7 - - + -
503L PHE* 2.9 42.7 + - + +
504L LEU* 3.8 6.1 - - + +
506L LYS* 1.3 93.8 - - - +
508L ILE* 1.3 59.5 + - - +
510L TYR* 3.3 13.1 + - - +
511L GLU* 2.9 33.4 + - - +
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Residues in contact with ILE 508 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416L LEU* 4.0 18.6 - - + -
417L LEU* 5.4 3.6 - - + -
420L LEU* 3.6 21.3 - - + -
468L VAL* 3.3 31.6 - - + +
471L PHE* 3.6 37.9 - - + -
472L LEU* 3.5 16.2 - - + -
475L LEU* 4.2 3.6 - - + -
504L LEU* 2.9 30.6 + - + +
507L GLN* 1.3 77.7 - - - +
509L GLU* 1.3 56.4 + - - +
511L GLU* 3.2 5.5 + - - +
512L ARG* 2.9 27.0 + - - +
516L PHE* 4.7 0.2 - - - -
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Residues in contact with GLU 509 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472L LEU* 3.8 19.5 - - + -
476L ARG* 2.8 28.8 + - - +
505L THR* 2.8 30.7 + - - +
506L LYS* 3.7 10.7 - - - +
508L ILE* 1.3 75.8 - - - +
510L TYR* 1.3 57.9 + - - +
512L ARG* 3.4 12.6 + - - +
513L ASN* 3.0 43.3 + - - +
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Residues in contact with TYR 510 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423L ARG* 5.3 6.5 - - - -
506L LYS* 2.8 22.1 + - + +
507L GLN* 3.4 15.7 - - - +
508L ILE 3.2 0.2 - - - -
509L GLU* 1.3 73.0 - - - +
511L GLU* 1.3 89.0 + - - +
513L ASN* 3.3 4.6 + - - +
514L ASN* 2.8 52.8 + - - +
517L PRO* 4.4 13.3 - - + +
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Residues in contact with GLU 511 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416L LEU* 3.8 18.2 - - + -
420L LEU* 4.1 8.7 - - + +
423L ARG* 3.2 26.2 + - - -
507L GLN* 2.9 21.5 + - - +
508L ILE 3.6 4.7 - - - +
510L TYR* 1.3 90.7 - - - +
512L ARG* 1.3 60.8 + - - +
514L ASN 2.9 8.8 + - - -
516L PHE* 2.7 42.0 + - + -
517L PRO* 3.0 14.8 - - - +
518L VAL* 2.9 38.2 + - - +
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Residues in contact with ARG 512 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465L ASP* 2.8 51.3 + - - +
468L VAL* 4.5 6.8 - - + +
469L THR* 3.0 27.9 + - - +
472L LEU* 3.4 27.5 - - - +
476L ARG* 5.0 3.4 - - - +
508L ILE 2.9 16.8 + - - +
509L GLU* 3.8 11.0 + - - +
510L TYR 3.3 0.2 - - - -
511L GLU* 1.3 76.0 - - - +
513L ASN* 1.3 72.7 + - - +
514L ASN 3.2 1.4 + - - -
515L GLU* 3.4 9.7 + - - +
516L PHE* 3.6 30.6 - - + -
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Residues in contact with ASN 513 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509L GLU* 3.0 29.6 + - - +
510L TYR* 3.8 6.8 - - - +
511L GLU 3.2 0.2 - - - -
512L ARG* 1.3 88.0 + - - +
514L ASN* 1.3 68.5 + - - +
515L GLU* 3.6 1.9 - - - +
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Residues in contact with ASN 514 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164L LYS* 4.5 2.9 + - - -
510L TYR* 2.8 53.2 + - + +
511L GLU 2.9 2.2 + - - -
513L ASN* 1.3 88.3 + - - +
515L GLU* 1.3 73.8 + - - +
516L PHE 3.2 1.6 - - - -
517L PRO* 3.3 24.2 - - + +
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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