Contacts of the helix formed by residues 247 - 257 (chain A) in PDB entry 3KHU
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 ASP 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A CYS* 3.6 2.5 - - - -
245A GLY 5.0 0.2 - - - +
246A ALA* 1.3 74.8 - - - +
248A VAL* 1.3 64.8 + - - +
249A GLU* 3.0 27.9 + - - +
250A GLU* 3.0 36.7 + - + +
251A VAL* 3.0 21.5 + - - +
443A ARG* 3.0 27.5 + - - -
463A GLY 3.6 4.7 - - - +
464A LYS* 4.4 13.6 + - - +
212B ASN* 4.8 4.3 - - - +
215B SER* 3.0 7.3 + - - -
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ILE* 3.8 40.2 - - + +
237A ILE* 4.4 5.4 - - + -
238A SER* 3.8 12.8 - - - +
241A CYS* 3.5 9.7 - - - -
247A ASP* 1.3 72.3 - - - +
249A GLU* 1.3 67.5 + - + +
251A VAL* 4.4 2.0 - - - -
252A ALA* 2.8 32.4 + - + +
268A ALA* 4.0 18.4 - - + -
443A ARG* 3.6 22.4 - - - +
462A ILE 4.1 2.0 - - - +
463A GLY* 3.0 27.5 + - - -
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Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ASP* 3.0 10.3 + - - +
248A VAL* 1.3 82.7 - - + +
250A GLU* 1.3 61.1 + - + +
252A ALA* 3.9 5.0 - - - +
253A THR* 2.8 33.8 + - - +
266A LEU 4.6 4.5 - - - +
267A LYS* 4.6 11.8 - - - +
268A ALA* 4.4 15.1 + - - +
443A ARG* 3.6 36.7 - - - +
446A ASP* 3.7 11.7 - - - +
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Residues in contact with GLU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ASP* 3.0 31.4 + - - +
249A GLU* 1.3 77.4 - - + +
251A VAL* 1.3 61.5 + - - +
253A THR* 3.4 5.5 + - - -
254A ALA* 3.1 22.7 + - - +
209B LEU* 4.3 4.2 - - - +
210B THR 5.1 1.5 - - - +
211B THR* 3.4 21.8 - - + +
212B ASN* 3.1 27.7 + - - +
215B SER* 2.8 31.2 + - - +
219B SER* 4.8 0.2 - - - -
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Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ILE* 5.1 0.4 - - + -
237A ILE* 3.8 24.9 - - + -
241A CYS* 4.1 14.6 - - - -
246A ALA* 4.3 2.5 - - + -
247A ASP 3.0 16.4 + - - +
248A VAL 3.9 4.3 - - - +
250A GLU* 1.3 71.7 - - - +
252A ALA* 1.3 60.4 + - - +
254A ALA* 3.1 2.9 + - - +
255A ILE* 2.9 45.6 + - + +
215B SER* 3.8 21.3 - - - +
218B LEU* 4.4 6.3 - - + -
219B SER* 3.5 28.9 - - - +
222B ALA* 4.5 3.6 - - + -
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ILE* 3.9 17.9 - - + +
248A VAL* 2.8 23.9 + - + +
249A GLU* 3.9 10.5 - - - +
251A VAL* 1.3 71.9 - - - +
253A THR* 1.3 58.0 + - - +
255A ILE* 3.4 3.7 + - - +
256A GLY* 2.8 28.6 + - - -
266A LEU* 3.4 36.0 - - + +
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Residues in contact with THR 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A GLU* 2.8 26.7 + - - +
250A GLU* 3.6 6.9 - - - -
252A ALA* 1.3 77.5 - - - +
254A ALA* 1.3 62.2 + - - +
256A GLY* 3.8 1.4 - - - -
257A MET* 3.2 38.7 + - + +
209B LEU* 4.0 25.8 - - + -
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Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A GLU 3.1 11.4 + - - +
251A VAL 3.1 1.8 + - - +
253A THR* 1.3 77.8 - - - +
255A ILE* 1.3 63.5 + - - +
257A MET* 3.6 3.8 + - - -
177B ARG* 3.0 33.3 + - + +
179B LEU* 4.2 14.1 - - + -
209B LEU* 3.5 19.9 - - + +
211B THR* 5.4 0.4 - - + -
219B SER* 3.5 31.9 - - - +
223B ALA* 5.9 0.2 - - - -
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Residues in contact with ILE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ILE* 4.1 14.1 - - + -
237A ILE* 5.2 0.7 - - + -
251A VAL* 2.9 37.7 + - + +
252A ALA* 3.7 3.1 - - - +
254A ALA* 1.3 76.7 - - - +
256A GLY* 1.3 62.2 + - - +
257A MET 3.2 1.4 + - - -
258A ASP* 3.2 21.7 + - - +
261A ILE* 3.6 35.4 - - + +
266A LEU* 4.2 9.0 - - + -
177B ARG* 4.3 5.2 - - - +
219B SER* 4.5 4.9 - - - +
222B ALA* 4.0 9.2 - - + -
223B ALA* 4.2 17.3 - - - +
226B PHE* 3.8 33.7 - - + -
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Residues in contact with GLY 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ALA 2.8 17.2 + - - -
253A THR* 3.3 2.7 + - - -
255A ILE* 1.3 77.3 - - - +
257A MET* 1.3 61.3 + - - +
258A ASP 3.2 3.9 + - - +
259A GLN* 5.2 0.5 - - - +
262A GLY* 3.3 37.6 - - - -
263A ASN* 3.4 17.0 + - - +
266A LEU* 3.8 7.4 - - - -
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Residues in contact with MET 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A THR* 3.2 31.7 + - + +
254A ALA 4.0 1.1 - - - +
255A ILE 3.2 1.0 + - - -
256A GLY* 1.3 75.3 - - - +
258A ASP* 1.3 63.3 + - - +
259A GLN* 3.3 8.2 + - - +
263A ASN* 5.6 0.9 - - + -
176B ASP* 3.3 27.3 - - - +
177B ARG* 3.9 37.9 - - + -
206B GLU 3.7 22.7 - - - +
207B LYS* 4.1 11.4 - - + -
209B LEU* 4.4 16.4 - - + -
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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