Contacts of the helix formed by residues 417 - 425 (chain B) in PDB entry 1KY9
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 417 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B GLU 4.1 3.4 + - - -
257B TYR* 3.8 27.0 - - + +
261B LYS* 6.5 0.2 - - - -
378B ASN* 3.4 14.8 - - - +
382B ASP* 3.7 20.2 + - - +
385B VAL* 3.2 13.5 - - - -
415B VAL* 3.0 2.4 - - - +
416B LYS* 1.3 89.6 - - - +
418B ILE* 1.3 53.7 + - - +
419B ALA* 3.2 10.1 + - - +
420B GLU* 2.8 29.3 + - - +
421B LEU* 2.8 30.5 + - - +
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Residues in contact with ILE 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B TYR 3.5 6.7 + - - +
258B GLY* 3.9 11.0 - - - -
259B GLN* 4.9 0.9 - - - -
360B ASN* 2.8 41.1 - - - +
364B SER* 3.6 25.6 - - - +
376B MSE 4.5 1.8 - - + -
377B SER* 3.4 26.7 - - - +
378B ASN* 3.3 13.6 + - - +
385B VAL* 3.2 25.8 - - + -
417B ASN* 1.3 70.6 - - - +
419B ALA* 1.3 64.9 + - - +
421B LEU* 3.9 7.4 - - + -
422B ARG* 3.0 31.7 + - + +
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Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B VAL 3.3 15.5 - - - +
256B GLU* 3.5 6.7 - - - +
257B TYR 3.3 34.2 + - - +
258B GLY 4.3 1.1 - - - +
417B ASN* 3.2 8.6 + - - +
418B ILE* 1.3 78.4 - - - +
420B GLU* 1.3 58.7 + - + +
422B ARG* 3.8 8.4 + - - +
423B LYS* 2.9 28.5 + - - +
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Residues in contact with GLU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B ALA* 2.9 28.1 - - - +
415B VAL* 4.5 0.9 - - - -
416B LYS* 3.0 46.7 + - - +
417B ASN* 2.8 20.0 + - - +
419B ALA* 1.3 74.9 - - + +
421B LEU* 1.3 60.2 + - - +
423B LYS* 2.6 35.6 + - + +
424B VAL* 3.1 11.5 + - + +
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B SER* 4.0 19.7 - - - +
376B MSE 4.8 9.9 - - + -
385B VAL* 4.6 4.5 - - + -
407B ILE* 4.3 18.6 - - + -
410B ALA* 5.0 4.3 - - - -
415B VAL* 3.3 41.9 - - + +
417B ASN 2.8 14.1 + - - +
418B ILE* 4.0 10.1 - - + +
420B GLU* 1.3 71.3 - - - +
422B ARG* 1.3 63.7 + - + +
424B VAL* 2.9 22.2 + - + +
425B LEU* 3.1 48.3 + - + +
434B LEU* 4.8 7.2 - - + -
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Residues in contact with ARG 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B MSE 4.1 0.6 + - - -
128B VAL* 3.2 40.5 + - - +
254B MSE 3.8 5.5 + - - -
255B VAL 4.7 2.4 + - - -
258B GLY* 3.4 25.7 - - - -
360B ASN* 4.4 5.9 + - - -
363B ASP* 2.3 56.5 + - - +
364B SER* 3.4 28.7 - - - +
418B ILE* 3.0 24.9 + - - +
419B ALA* 3.9 8.0 - - - +
421B LEU* 1.3 77.2 - - + +
423B LYS* 1.3 60.3 + - - +
424B VAL 3.1 0.7 + - - -
425B LEU 3.9 1.9 - - - +
426B ASP* 3.3 25.0 + - + +
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Residues in contact with LYS 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LYS* 5.6 5.1 - - - +
419B ALA 2.9 15.7 + - - +
420B GLU* 2.6 24.5 + - + +
422B ARG* 1.3 72.3 - - - +
424B VAL* 1.3 60.0 + - + +
426B ASP* 4.3 6.9 - - - +
427B SER* 3.5 20.1 + - - -
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Residues in contact with VAL 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B ALA* 3.7 43.5 - - + +
411B ASN* 4.5 5.4 - - + +
412B GLN* 4.5 3.1 - - - +
413B GLN* 5.7 2.0 - - + +
414B ALA 5.6 0.9 - - - +
420B GLU 3.5 14.1 - - - +
421B LEU* 2.9 6.8 + - + +
423B LYS* 1.3 80.1 - - + +
425B LEU* 1.3 61.9 + - + +
426B ASP 2.8 11.0 + - - -
427B SER* 3.1 17.8 + - - +
428B LYS* 3.2 33.7 + - + +
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B SER 3.7 11.7 - - - +
365B SER* 3.0 38.4 - - - +
366B SER* 2.8 26.7 + - - -
376B MSE 6.3 0.2 - - + -
411B ASN* 4.7 4.9 - - + -
421B LEU* 3.1 44.7 + - + +
422B ARG 3.6 2.4 + - - +
424B VAL* 1.3 78.6 - - + +
426B ASP* 1.3 57.0 + - - +
428B LYS* 5.3 4.0 - - + +
429B PRO* 4.6 9.4 - - - +
432B LEU* 3.3 38.8 - - + -
434B LEU* 4.5 5.8 - - + -
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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