Contacts of the helix formed by residues 413 - 419 (chain A) in PDB entry 1O6K
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 ASN 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A SER 3.9 2.6 + - - +
412A ILE* 1.3 72.9 - - - +
414A TRP* 1.3 59.0 + - - +
415A GLN* 3.0 22.7 + - - +
416A ASP* 3.1 50.3 + - + +
417A VAL* 3.2 14.6 + - - +
422A LEU* 5.1 3.4 - - + +
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Residues in contact with TRP 414 (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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257A ALA* 3.2 47.1 - - + -
260A VAL* 3.9 24.0 - - + -
261A SER* 4.4 9.3 + - - -
404A MET* 3.3 58.3 + - + +
405A GLU* 4.8 7.6 + - - -
409A PHE* 3.8 27.6 + + + -
412A ILE* 3.7 24.3 + - + +
413A ASN* 1.3 72.6 + - - +
415A GLN* 1.3 64.8 + - + +
417A VAL* 3.8 11.4 - - + +
418A VAL* 3.5 22.2 + - - +
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Residues in contact with GLN 415 (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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413A ASN* 3.0 10.1 + - - +
414A TRP* 1.3 80.8 + - + +
416A ASP* 1.3 67.3 + - - +
417A VAL 3.2 0.2 - - - -
418A VAL* 3.5 14.3 - - - +
419A GLN* 3.2 50.8 + - - +
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Residues in contact with ASP 416 (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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413A ASN* 3.1 40.6 + - + +
415A GLN* 1.3 78.2 - - - +
417A VAL* 1.3 61.6 + - - +
419A GLN 3.8 0.2 + - - -
420A LYS 3.4 1.7 + - - -
421A LYS* 2.9 67.4 + - + +
422A LEU* 3.8 21.1 + - + +
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Residues in contact with VAL 417 (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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211A PHE* 3.1 37.9 - - + -
257A ALA* 3.8 31.2 - - + +
258A GLU* 4.1 8.6 - - + +
261A SER* 4.1 6.5 - - - -
412A ILE* 3.6 24.7 - - + -
413A ASN 3.2 15.0 + - - +
414A TRP* 3.8 12.3 - - + +
415A GLN 3.2 0.2 - - - -
416A ASP* 1.3 75.5 - - - +
418A VAL* 1.3 58.2 + - - +
420A LYS* 3.1 15.1 + - - -
422A LEU* 3.9 20.6 - - + -
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Residues in contact with VAL 418 (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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209A HIS* 3.7 30.1 - - + +
210A PRO* 3.3 27.1 - - + +
211A PHE* 4.1 7.6 - - - -
261A SER* 3.9 7.9 - - - +
414A TRP 3.5 12.0 + - - +
415A GLN* 3.5 28.3 - - - +
417A VAL* 1.3 78.6 - - - +
419A GLN* 1.3 66.0 + - + +
420A LYS* 3.3 1.3 + - - +
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Residues in contact with GLN 419 (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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415A GLN* 3.2 41.0 + - - +
416A ASP 3.8 0.2 + - - -
418A VAL* 1.3 81.9 - - + +
420A LYS* 1.3 68.0 + - - +
421A LYS* 3.3 40.1 + - + +
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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