Contacts of the helix formed by residues 2409 - 2417 (chain C) in PDB entry 1KY5
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 THR2409 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2407C LYS 4.6 3.4 - - - +
2408C LEU* 1.3 75.3 - - - +
2410C GLU* 1.3 69.1 + - - +
2411C LYS* 3.6 11.2 + - - +
2412C GLN* 2.8 44.5 + - - +
2413C ALA 2.8 13.3 + - - -
2420C ILE* 2.6 14.1 - - - +
3279D ASP* 5.0 1.2 + - - -
3284D ARG* 6.3 0.7 - - - +
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Residues in contact with GLU2410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2409C THR* 1.3 71.4 - - - +
2411C LYS* 1.3 63.1 + - - +
2413C ALA* 3.8 11.8 - - - +
2414C GLN* 2.5 52.3 + - - +
2420C ILE* 3.2 15.0 - - + +
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Residues in contact with LYS2411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2409C THR* 2.9 10.2 + - - +
2410C GLU* 1.3 80.1 - - - +
2412C GLN* 1.3 57.1 + - - +
2414C GLN* 3.2 13.3 - - - +
2415C TYR* 3.0 24.3 + - - +
3278D VAL* 5.0 7.9 - - + -
3279D ASP* 3.2 35.2 + - - +
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Residues in contact with GLN2412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2406C THR* 5.8 0.8 - - - +
2407C LYS 3.7 5.3 + - - -
2408C LEU* 3.0 30.3 - - + +
2409C THR* 2.8 55.0 + - - +
2411C LYS* 1.3 68.7 - - - +
2413C ALA* 1.3 64.8 + - - +
2414C GLN 2.7 5.8 + - - -
2415C TYR* 2.7 20.9 + - - +
2416C LEU* 3.0 15.6 + - - +
3277D CYS* 3.8 15.9 - - - -
3278D VAL* 2.7 30.9 - - + +
3279D ASP* 3.5 19.8 - - - +
3432D NAI 4.0 8.8 + - - -
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Residues in contact with ALA2413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2408C LEU* 4.1 11.7 - - - +
2409C THR 2.8 9.5 + - - +
2410C GLU* 3.7 11.0 - - - +
2412C GLN* 1.3 72.9 - - - +
2414C GLN* 1.3 57.2 + - - +
2416C LEU* 5.2 1.3 - - - -
2417C GLY* 2.9 19.2 + - - -
2418C MET 2.8 22.7 + - - +
2420C ILE* 3.3 51.8 - - + +
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Residues in contact with GLN2414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2410C GLU* 2.5 49.7 + - - +
2411C LYS* 3.2 14.8 - - - +
2412C GLN 2.7 1.0 + - - -
2413C ALA* 1.3 74.0 - - - +
2415C TYR* 1.3 69.7 + - - +
2417C GLY* 2.7 18.8 + - - -
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Residues in contact with TYR2415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2411C LYS 3.0 6.4 + - - +
2412C GLN 2.7 12.2 + - - +
2414C GLN* 1.3 76.9 - - - +
2416C LEU* 1.3 66.6 + - + +
3165D LYS* 3.9 13.5 + - - -
3276D GLY 4.2 13.7 - - - -
3277D CYS* 4.1 6.7 - - - -
3278D VAL* 3.4 57.9 - - + -
3301D PHE* 4.9 12.3 - - - +
3303D VAL* 3.5 17.4 - - + +
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Residues in contact with LEU2416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2408C LEU* 3.9 24.7 - - + -
2412C GLN 3.0 8.7 + - - +
2413C ALA 4.4 0.2 - - - +
2414C GLN 2.9 0.4 + - - -
2415C TYR* 1.3 83.8 - - + +
2417C GLY* 1.3 60.5 + - - +
2418C MET* 3.3 31.9 - - + +
2424C PHE* 5.5 0.9 - - + -
3161D HIS* 2.9 39.8 + - + +
3165D LYS* 3.4 10.7 - - - +
3243D ILE* 5.3 2.5 - - + -
3276D GLY 3.9 13.9 - - - +
3277D CYS* 3.3 37.9 - - + -
3432D NAI 4.8 10.1 - - + +
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Residues in contact with GLY2417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2413C ALA 2.9 4.0 + - - -
2414C GLN* 2.7 19.8 + - - -
2416C LEU* 1.3 75.1 - - - +
2418C MET* 1.3 70.1 + - - +
3165D LYS* 4.8 6.7 - - - -
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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