Contacts of the helix formed by residues 245 - 257 (chain B) in PDB entry 2K7A
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 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244B ILE* 1.3 77.3 - - - +
246B ARG* 1.3 69.2 + - - +
247B ASP* 3.4 9.8 + - - +
248B LYS* 3.8 25.4 - - - +
249B ALA* 2.6 36.7 + - - +
265B ARG* 3.6 5.4 - - - +
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Residues in contact with ARG 246 (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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245B SER* 1.3 80.8 + - - +
247B ASP* 1.3 56.4 + - - +
249B ALA* 2.8 8.6 + - - +
250B GLU* 2.7 49.5 + - - +
265B ARG* 3.3 36.6 - - - +
268B ARG* 5.1 11.7 - - - +
291B HIS* 5.0 5.4 - - + -
293B HIS* 5.9 4.9 + - - -
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Residues in contact with ASP 247 (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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245B SER* 3.8 5.6 + - - +
246B ARG* 1.3 81.9 - - - +
248B LYS* 1.3 66.6 + - + +
250B GLU* 3.5 14.8 + - - +
251B LYS* 3.2 23.4 + - - +
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Residues in contact with LYS 248 (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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243B SER 4.8 8.7 + - - +
244B ILE* 3.4 21.8 - - + -
245B SER* 3.3 27.0 + - - +
246B ARG 3.1 0.8 - - - -
247B ASP* 1.3 77.3 - - + +
249B ALA* 1.3 57.8 + - - +
251B LYS* 4.0 6.1 - - - +
252B LEU* 2.7 37.6 + - - +
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Residues in contact with ALA 249 (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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244B ILE* 3.9 15.3 - - + -
245B SER 2.6 23.5 + - - +
246B ARG* 3.2 9.6 - - - +
248B LYS* 1.3 72.9 - - - +
250B GLU* 1.3 64.4 + - + +
252B LEU* 4.4 0.9 - - - -
253B LEU* 3.1 35.0 + - + +
263B MET* 6.3 1.1 - - + -
265B ARG* 4.1 14.4 - - + +
276B SER* 4.2 17.7 - - - +
289B ILE* 5.4 0.2 - - - -
291B HIS* 5.5 0.4 - - + -
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Residues in contact with GLU 250 (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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246B ARG* 2.7 29.9 + - - +
247B ASP* 3.8 14.3 - - - +
249B ALA* 1.3 74.4 - - - +
251B LYS* 1.3 60.5 + - - +
254B LEU* 3.2 21.3 + - - +
289B ILE* 3.7 33.6 - - + +
291B HIS* 3.2 36.1 + - + +
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Residues in contact with LYS 251 (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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247B ASP 3.2 15.7 + - - +
248B LYS* 4.0 4.9 - - - +
250B GLU* 1.3 77.1 - - - +
252B LEU* 1.3 61.9 + - - +
254B LEU* 2.7 36.2 + - + +
255B ASP* 3.1 7.2 + - + +
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Residues in contact with LEU 252 (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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244B ILE* 3.8 20.9 - - + -
248B LYS 2.7 24.4 + - - +
249B ALA* 4.0 2.0 - - - +
251B LYS* 1.3 75.5 - - - +
253B LEU* 1.3 69.7 + - + +
255B ASP* 3.1 22.4 + - - +
256B THR* 3.7 4.9 + - - -
263B MET* 3.3 31.4 - - + -
337B VAL* 3.8 16.1 - - + +
338B CYS 4.4 12.8 - - - +
339B GLY* 4.4 13.2 - - - +
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Residues in contact with LEU 253 (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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249B ALA* 3.1 18.7 + - + +
250B GLU 4.0 3.8 - - - +
251B LYS 3.1 0.4 - - - -
252B LEU* 1.3 84.5 - - + +
254B LEU* 1.3 62.2 + - - +
256B THR* 3.0 13.6 + - - -
261B ALA* 4.6 5.2 - - + +
263B MET* 4.1 12.6 - - + -
276B SER* 3.7 37.0 - - - +
278B PHE* 2.9 49.5 - - + -
289B ILE* 4.1 11.0 - - + -
337B VAL* 3.5 37.9 - - + -
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Residues in contact with LEU 254 (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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250B GLU 3.2 12.0 + - - +
251B LYS* 2.7 25.3 + - + +
253B LEU* 1.3 75.9 - - - +
255B ASP* 1.3 61.7 - - - +
257B GLY* 3.1 15.1 + - - -
278B PHE* 4.2 8.4 - - - -
287B PRO* 3.4 35.0 - - + -
289B ILE* 5.4 3.1 - - + -
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Residues in contact with ASP 255 (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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251B LYS* 3.1 8.4 + - + +
252B LEU* 3.1 15.7 + - - +
254B LEU* 1.3 80.1 - - - +
256B THR* 1.3 65.6 + - - +
257B GLY* 3.4 0.7 + - - -
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Residues in contact with THR 256 (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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252B LEU 3.7 4.5 + - - -
253B LEU* 3.0 14.7 + - - -
255B ASP* 1.3 80.9 - - - +
257B GLY* 1.3 64.7 + - - +
258B LYS* 3.2 27.2 + - + +
261B ALA* 4.0 13.5 - - + -
335B TYR* 3.9 21.3 - - + -
337B VAL* 3.6 27.4 - - + +
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Residues in contact with GLY 257 (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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254B LEU 3.1 15.3 + - - -
255B ASP 4.3 0.7 - - - -
256B THR* 1.3 78.9 - - - +
258B LYS* 1.3 57.6 + - - +
278B PHE* 3.4 16.1 - - - -
280B LYS* 5.3 10.9 - - - +
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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