Contacts of the helix formed by residues 491 - 495 (chain L) in PDB entry 1YKN
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 ILE 491 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11K GLN* 3.5 20.6 + - - +
12K THR* 4.0 16.6 - - + +
136K ASN* 5.4 0.7 - - - +
324L TYR* 3.8 23.6 - - + -
449L TRP* 3.7 27.6 - - + -
457L ARG* 3.8 18.8 - - - +
477L GLN* 4.2 5.4 - - - +
489L CYS* 3.1 9.6 - - - -
490L PRO* 1.3 76.9 - - - +
492L VAL* 1.3 62.6 + - - +
494L SER* 2.7 30.3 + - - +
5550L DHB 3.4 39.0 - - + -
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Residues in contact with VAL 492 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K GLN* 3.9 6.7 - - - -
458L PRO* 4.2 4.0 - - + -
479L TYR* 3.4 41.3 - - + +
486L ILE* 3.7 23.6 - - + +
487L PRO* 5.6 0.9 - - + -
489L CYS* 3.3 23.8 + - + +
491L ILE* 1.3 74.1 - - - +
493L LYS* 1.3 60.0 + - + +
495L ILE* 3.0 33.6 + - + +
501L VAL* 3.7 33.0 - - + +
504L LEU* 6.2 0.2 - - + -
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Residues in contact with LYS 493 (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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314H ASN* 4.2 19.2 - - - +
321L THR* 5.5 0.2 - - - -
323L ASP* 5.5 3.5 + - + +
487L PRO* 3.5 28.4 + - + +
488L MET* 4.0 14.8 + - - +
489L CYS 3.1 21.4 + - - +
490L PRO* 3.9 11.8 - - + +
491L ILE 3.3 0.6 - - - -
492L VAL* 1.3 75.2 - - + +
494L SER* 1.4 61.5 + - - +
495L ILE 3.0 12.7 + - - +
496L ALA* 4.5 1.6 + - - -
501L VAL* 5.9 0.4 - - - -
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Residues in contact with SER 494 (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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11K GLN* 3.5 9.0 + - - -
136K ASN* 3.8 14.6 + - - -
317L PRO* 3.1 38.0 - - - +
318L LYS 4.0 1.4 + - - -
321L THR* 3.8 38.3 - - - +
324L TYR* 5.2 0.7 - - - -
490L PRO 3.3 8.5 + - - -
491L ILE* 2.7 22.2 + - - +
492L VAL 3.0 1.8 + - - -
493L LYS* 1.4 76.1 - - - +
495L ILE* 1.3 59.8 + - - +
496L ALA* 3.5 3.1 + - - +
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Residues in contact with ILE 495 (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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9K PRO* 3.7 17.0 - - + -
11K GLN* 3.5 27.4 - - - +
315L TRP 3.8 9.6 - - - +
317L PRO* 4.2 14.1 - - + -
492L VAL* 3.0 15.2 + - + +
493L LYS* 3.6 11.4 - - - +
494L SER* 1.3 77.7 - - - +
496L ALA* 1.3 60.5 + - - +
497L ASN 3.8 9.8 - - - +
500L ALA* 3.3 33.9 - - + +
501L VAL* 4.0 18.2 - - + +
504L LEU* 3.6 24.9 - - + -
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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