Contacts of the helix formed by residues 241 - 252 (chain F) in PDB entry 1KR2
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 PRO 241 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238E TYR* 5.0 6.1 - - + -
242E ASP* 6.1 1.1 - - - +
20F ILE* 5.0 2.5 - - + +
21F THR 4.8 1.8 - - - -
22F ASN* 3.4 12.1 - - - +
25F LEU* 3.6 29.6 - - + -
72F LEU 5.3 1.3 - - - +
73F ALA* 4.0 18.8 - - + +
240F VAL* 1.3 88.8 - - + +
242F ASP* 1.3 67.5 + - - +
243F LEU* 4.5 4.5 - - + +
244F VAL* 2.9 31.2 + - + -
245F GLN* 3.0 10.4 + - - +
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Residues in contact with ASP 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ASN* 4.1 11.6 - - - +
237F ARG* 3.2 46.7 + - - +
238F TYR* 4.7 12.9 + - - -
240F VAL 3.6 2.5 + - - +
241F PRO* 1.3 70.4 - - - +
243F LEU* 1.3 59.8 + - + +
245F GLN* 3.2 5.3 + - - +
246F GLU* 2.9 42.3 + - - +
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Residues in contact with LEU 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F LEU* 3.6 45.6 - - + +
75F LYS* 4.1 27.6 - - + +
76F ASN* 5.1 7.6 - - - +
241F PRO* 3.2 4.3 - - + +
242F ASP* 1.3 81.8 - - + +
244F VAL* 1.3 58.2 + - + +
246F GLU* 3.8 17.7 - - - +
247F TYR* 3.0 27.2 + - - +
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Residues in contact with VAL 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F ILE* 4.3 16.2 - - + +
69F MET* 3.6 52.9 - - + +
72F LEU* 4.2 4.7 - - + -
73F ALA* 3.9 14.6 - - + +
240F VAL* 4.3 4.3 - - + -
241F PRO* 2.9 31.7 + - + +
243F LEU* 1.3 76.3 - - - +
245F GLN* 1.3 62.3 + - - +
247F TYR* 3.4 4.9 + - - +
248F ILE* 2.9 44.7 + - + +
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Residues in contact with GLN 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235F SER* 5.8 0.4 + - - +
236F ILE* 4.1 14.1 - - + +
237F ARG* 2.9 62.5 + - - +
240F VAL* 3.7 15.2 - - + +
241F PRO 3.0 11.3 + - - +
242F ASP* 3.4 9.2 - - - +
244F VAL* 1.3 77.4 - - - +
246F GLU* 1.3 68.8 + - - +
248F ILE* 3.1 6.7 + - - +
249F GLU* 2.9 58.3 + - - +
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Residues in contact with GLU 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F ARG* 2.9 23.4 + - - +
242F ASP* 2.9 26.5 + - - +
243F LEU* 3.8 24.1 - - - +
245F GLN* 1.3 88.3 - - - +
247F TYR* 1.3 62.6 + - - +
249F GLU* 4.0 3.9 - - - +
250F LYS* 3.0 27.4 + - - +
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Residues in contact with TYR 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F TYR* 4.3 7.6 - - - -
65F HIS* 2.6 30.9 + + + -
68F ILE* 3.8 24.4 - - + +
69F MET* 3.8 19.7 - - + -
72F LEU* 3.7 19.3 - - + -
243F LEU 3.0 20.1 + - - +
244F VAL* 3.6 5.6 - - - +
245F GLN 3.2 0.2 - - - -
246F GLU* 1.3 78.3 - - - +
248F ILE* 1.3 61.9 + - - +
250F LYS* 3.9 3.3 - - - +
251F HIS* 3.2 50.5 + + - +
253F LEU* 3.3 29.6 - - + -
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Residues in contact with ILE 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F PRO* 4.1 18.4 - - + -
69F MET* 3.6 30.7 - - - -
230F LEU* 3.5 34.5 - - + -
236F ILE* 4.2 18.6 - - + -
240F VAL* 5.3 1.1 - - + -
244F VAL* 2.9 30.8 + - + +
245F GLN* 3.6 4.0 - - - +
247F TYR* 1.3 76.4 - - - +
249F GLU* 1.3 58.2 + - - +
251F HIS 3.4 0.2 + - - -
252F ASN* 2.9 26.4 + - - -
253F LEU* 3.4 18.0 + - + +
254F TYR* 4.2 12.8 - - + +
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Residues in contact with GLU 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F LEU* 5.8 2.4 - - - +
245F GLN* 2.9 38.7 + - - +
246F GLU* 4.0 4.7 - - - +
248F ILE* 1.3 77.8 - - - +
250F LYS* 1.3 65.3 + - - +
251F HIS 3.2 1.0 + - - -
252F ASN* 3.2 20.8 + - - +
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Residues in contact with LYS 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F GLU 3.0 20.1 + - - +
247F TYR* 3.9 4.9 - - - +
248F ILE 3.4 0.2 - - - -
249F GLU* 1.3 77.3 - - - +
251F HIS* 1.3 83.6 + - + +
252F ASN* 4.6 3.8 + - - -
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Residues in contact with HIS 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F HIS* 5.1 3.4 - - - +
247F TYR* 3.2 60.0 + + - +
249F GLU 3.2 0.4 - - - -
250F LYS* 1.3 109.8 + - + +
252F ASN* 1.3 72.0 + - - +
253F LEU* 3.0 21.3 + - + +
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Residues in contact with ASN 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F ILE 2.9 10.3 + - - -
249F GLU* 3.2 13.8 + - - +
250F LYS 4.6 4.4 + - - -
251F HIS* 1.3 78.8 - - - +
253F LEU* 1.3 65.0 + - - +
254F TYR 3.4 8.5 + - - +
255F SER* 5.3 3.5 + - - -
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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