Contacts of the helix formed by residues 485 - 489 (chain H) 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 LEU 485 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508B LEU* 3.8 23.8 - - + -
510B MET* 4.1 14.8 - - + -
519B LEU* 3.7 24.5 - - + -
446H PRO* 3.7 23.8 - - + -
456H TRP* 4.1 22.8 - - + +
457H ARG 4.1 3.6 - - - +
458H PRO* 3.8 24.6 - - + +
483H ASP* 2.8 19.3 + - - +
484H PRO* 1.4 72.8 - - + +
486H ILE* 1.3 65.9 + - - +
487H PRO 3.4 0.4 - - - -
488H MET* 2.9 22.5 + - + +
489H CYS* 3.4 8.0 + - - +
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Residues in contact with ILE 486 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458H PRO* 3.8 20.4 - - + -
479H TYR* 3.9 29.2 - - + -
480H PHE 3.6 24.5 - - - +
482H GLY 5.0 1.8 - - - +
483H ASP* 3.6 17.7 - - + +
485H LEU* 1.3 78.8 - - - +
487H PRO* 1.3 71.9 - - + +
488H MET 3.0 1.9 + - - -
489H CYS* 3.3 8.0 + - - +
492H VAL* 3.8 33.4 - - + +
501H VAL* 4.4 7.4 - - + -
505H ILE* 3.9 28.9 - - + -
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Residues in contact with PRO 487 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483H ASP 4.1 2.5 - - - +
484H PRO* 3.4 20.2 - - + +
486H ILE* 1.3 95.9 - - + +
488H MET* 1.3 63.0 + - + +
489H CYS 3.5 0.4 - - - -
492H VAL* 5.6 1.1 - - + -
493H LYS* 3.7 23.0 + - + +
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Residues in contact with MET 488 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B LEU* 4.2 8.3 - - + -
510B MET* 3.9 30.7 - - + +
455H ASP* 5.1 2.8 - - - +
484H PRO 3.4 24.0 - - - +
485H LEU* 2.9 14.8 + - + +
487H PRO* 1.3 86.3 - - + +
489H CYS* 1.3 63.1 + - - +
490H PRO* 3.4 8.7 - - - +
493H LYS* 3.9 13.5 + - - +
1I PRO* 3.9 27.4 - - + -
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Residues in contact with CYS 489 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449H TRP* 5.0 1.6 - - - -
456H TRP 4.7 6.5 - - - +
457H ARG* 3.4 36.8 - - - -
458H PRO* 3.7 21.8 - - + -
485H LEU 3.4 2.5 + - - +
486H ILE 3.3 11.5 + - - +
487H PRO 3.5 0.4 - - - -
488H MET* 1.3 79.2 - - - +
490H PRO* 1.4 65.8 - - - +
491H ILE* 3.2 19.5 - - - -
492H VAL* 3.0 13.7 + - + +
493H LYS* 2.9 27.5 + - - +
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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