Contacts of the helix formed by residues 401 - 412 (chain L) in PDB entry 1KYO
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 SER 401 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27L ALA* 4.7 19.5 - - - -
28L GLU 6.1 0.7 - - - -
29L VAL* 5.5 10.1 - - - -
399L LYS* 3.4 6.3 + - - +
400L LEU* 1.3 76.5 - - - +
402L LEU* 1.3 59.8 + - - +
403L GLY* 4.2 3.5 - - - -
404L GLU* 2.8 61.0 + - - +
405L ALA* 3.2 5.0 + - - +
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Residues in contact with LEU 402 (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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373L LEU* 4.3 18.4 - - + +
374L GLY* 3.9 15.7 - - - -
377L TYR* 3.8 35.2 - - + -
378L GLU* 3.1 39.0 - - + +
399L LYS* 6.2 0.2 - - - +
400L LEU 3.5 3.3 + - - -
401L SER* 1.3 72.2 - - - +
403L GLY* 1.3 61.7 + - - +
405L ALA* 3.3 10.9 + - + +
406L PHE* 3.2 54.7 - - + -
27M LYS* 4.1 11.0 - - + -
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Residues in contact with GLY 403 (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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401L SER* 3.1 3.9 + - - -
402L LEU* 1.3 78.9 - - - +
404L GLU* 1.3 63.1 + - - +
406L PHE* 3.5 7.2 + - - +
407L LYS* 3.3 30.0 + - - +
27M LYS* 3.9 27.7 - - - +
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Residues in contact with GLU 404 (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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400L LEU* 3.4 24.7 - - + +
401L SER* 2.8 31.5 + - - +
403L GLY* 1.3 73.4 - - - +
405L ALA* 1.3 63.1 + - - +
407L LYS* 3.3 30.7 + - - +
408L LYS* 3.3 27.7 + - - +
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Residues in contact with ALA 405 (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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275L PHE* 4.1 26.9 - - + -
373L LEU* 4.2 19.7 - - + -
377L TYR* 5.8 3.4 - - + -
400L LEU* 4.6 6.7 - - + +
401L SER 3.2 7.1 + - - +
402L LEU* 3.4 17.5 - - + +
404L GLU* 1.3 74.0 - - - +
406L PHE* 1.3 62.0 + - - +
408L LYS* 2.8 22.9 + - - +
409L ILE* 2.8 16.6 + - - +
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Residues in contact with PHE 406 (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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370L LYS* 3.9 59.5 - - + +
373L LEU* 4.5 4.7 - - + -
374L GLY* 4.8 2.0 - - - -
402L LEU* 3.2 45.7 + - + -
403L GLY* 3.8 8.1 - - - +
404L GLU 3.4 0.2 - - - -
405L ALA* 1.3 78.0 - - + +
407L LYS* 1.3 63.4 + - + +
409L ILE* 3.7 9.8 - - + +
410L ASP* 3.0 33.6 + - - +
27M LYS* 3.8 37.5 - - + +
28M ILE* 5.7 0.4 - - + -
94M LEU* 4.7 10.8 - - + -
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Residues in contact with LYS 407 (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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403L GLY 3.3 16.2 - - - +
404L GLU* 3.4 31.9 + - - +
405L ALA 3.1 0.2 - - - -
406L PHE* 1.3 79.6 - - + +
408L LYS* 1.3 61.5 + - + +
410L ASP* 3.7 5.2 + - - +
411L ALA* 3.4 20.1 + - - +
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Residues in contact with LYS 408 (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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275L PHE* 4.0 33.2 - - + -
400L LEU* 4.8 15.7 - - + -
404L GLU* 3.3 15.2 + - - +
405L ALA 2.8 8.1 + - - +
407L LYS* 1.3 76.4 - - + +
409L ILE* 1.3 65.6 + - - +
411L ALA* 3.1 21.3 + - - +
412L ILE* 3.3 13.1 + - - +
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Residues in contact with ILE 409 (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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275L PHE* 4.2 16.4 - - + -
279L LEU* 4.4 1.3 - - + -
366L LYS* 3.3 47.3 - - + +
369L LEU* 3.6 31.9 - - + -
370L LYS* 4.2 20.4 - - + -
373L LEU* 3.5 32.8 - - + -
405L ALA 2.8 20.5 + - - +
406L PHE* 3.3 7.4 + - + +
408L LYS* 1.3 76.9 - - - +
410L ASP* 1.3 62.5 + - - +
411L ALA 3.2 0.7 + - - -
412L ILE* 3.4 17.6 + - - +
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Residues in contact with ASP 410 (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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127G LYS* 5.7 0.9 + - - -
363L GLU* 5.6 0.5 - - - +
366L LYS* 2.9 32.3 + - - +
370L LYS* 2.7 39.8 + - - -
406L PHE* 3.0 22.0 + - - +
407L LYS* 4.2 4.8 - - - +
409L ILE* 1.3 75.0 - - - +
411L ALA* 1.3 58.9 + - - +
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Residues in contact with ALA 411 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407L LYS 3.4 13.4 + - - +
408L LYS* 3.1 15.1 + - - +
410L ASP* 1.3 80.3 - - - +
412L ILE* 1.3 65.9 + - - +
413L THR* 3.3 15.6 + - - +
416L ASP* 4.2 2.5 - - - +
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Residues in contact with ILE 412 (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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275L PHE* 3.9 11.7 - - + +
276L VAL* 3.7 41.7 - - + +
279L LEU* 4.2 28.7 - - + -
362L VAL* 4.3 2.6 - - + +
366L LYS* 3.0 30.4 + - - -
408L LYS 3.4 14.4 - - - +
409L ILE* 3.5 20.6 - - + +
411L ALA* 1.3 75.6 - - - +
413L THR* 1.3 72.5 + - - +
416L ASP* 3.5 19.1 - - + +
417L VAL* 4.2 4.3 - - + -
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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