Contacts of the helix formed by residues 246 - 257 (chain A) in PDB entry 2QUK
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 GLY 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A SER* 2.9 3.8 + - - -
245A SER* 1.3 80.7 - - - +
247A PHE* 1.3 66.2 + - - +
248A TYR 3.6 1.1 - - - -
249A LYS* 3.6 13.0 - - - +
250A ASN* 3.2 29.3 + - - -
291A ASN* 3.8 16.3 + - - -
292A SER* 4.0 7.2 - - - -
294A PRO* 4.5 2.4 - - - +
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Residues in contact with PHE 247 (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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194A GLN* 4.0 11.7 - - - -
235A PHE* 4.5 6.1 - + - -
237A ASP* 4.4 8.3 - - - -
240A TYR* 3.9 17.9 - + + -
241A MET* 3.3 42.6 - - + -
244A SER* 2.8 31.1 + - - +
246A GLY* 1.3 70.5 - - - +
248A TYR* 1.3 66.8 + - - +
250A ASN* 3.1 7.3 + - - +
251A VAL* 3.1 23.7 + - + +
283A ILE* 3.9 27.6 - - + -
286A ALA* 3.4 20.4 - - + -
287A PRO* 3.7 17.3 - - + -
292A SER* 3.5 23.5 + - - +
293A PHE* 4.9 2.9 - + - -
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Residues in contact with TYR 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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241A MET* 4.1 35.8 + - + +
244A SER 4.7 5.9 + - - +
246A GLY 3.6 0.2 - - - -
247A PHE* 1.3 75.7 - - - +
249A LYS* 1.3 70.9 + - + +
251A VAL* 2.9 21.7 + - + +
252A VAL* 3.0 42.8 + - + +
255A GLN* 4.5 12.1 + - - -
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Residues in contact with LYS 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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244A SER 5.8 0.2 + - - -
245A SER* 3.3 32.4 + - - +
246A GLY* 3.6 12.3 - - - +
247A PHE 3.2 0.2 - - - -
248A TYR* 1.3 85.2 - - + +
250A ASN* 1.3 58.8 + - - +
252A VAL* 3.5 8.6 + - - +
253A LYS* 3.2 36.4 + - - +
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Residues in contact with ASN 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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246A GLY 3.2 14.5 + - - -
247A PHE 3.1 9.1 + - - +
248A TYR 3.1 0.8 - - - -
249A LYS* 1.3 78.6 - - - +
251A VAL* 1.3 64.6 + - - +
253A LYS* 3.8 9.8 - - - +
254A ILE* 3.0 33.2 + - + +
286A ALA* 4.4 8.3 - - + -
289A PHE* 4.5 4.9 + - + -
291A ASN* 3.4 27.6 + - - +
292A SER* 3.1 27.3 + - - +
329A TYR* 2.7 38.6 + - - -
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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
----------------------------------------------------------
241A MET* 3.9 15.5 - - + -
247A PHE* 3.1 21.2 + - + +
248A TYR* 2.9 23.0 + - + +
250A ASN* 1.3 77.9 - - - +
252A VAL* 1.3 52.2 + - - +
254A ILE* 3.0 6.2 + - - +
255A GLN* 2.6 54.6 + - - +
282A ALA* 3.8 23.1 - - + +
283A ILE* 4.2 19.7 - - + -
286A ALA* 4.0 17.5 - - + -
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Residues in contact with VAL 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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248A TYR* 3.0 54.9 + - + +
249A LYS* 3.6 7.2 - - - +
251A VAL* 1.3 72.7 - - - +
253A LYS* 1.3 68.1 + - - +
255A GLN* 3.0 22.8 + - + +
256A LYS* 3.3 20.2 + - + +
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Residues in contact with LYS 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 LYS* 3.2 24.0 + - - +
250A ASN* 3.8 15.7 - - - +
251A VAL 3.3 0.2 - - - -
252A VAL* 1.3 79.1 - - + +
254A ILE* 1.3 59.1 + - - +
256A LYS* 3.6 13.5 + - - +
257A HIS* 2.7 33.3 - - - -
291A ASN* 4.5 3.4 - - - +
327A ILE* 4.1 24.2 + - + +
329A TYR* 3.0 35.1 + - + -
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Residues in contact with ILE 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 ASN 3.0 15.7 + - - +
251A VAL* 3.0 5.9 + - - +
253A LYS* 1.3 75.1 - - - +
255A GLN* 1.3 65.1 + - - +
256A LYS 3.1 1.6 + - - -
257A HIS* 3.1 13.1 + - - +
258A VAL* 3.4 23.2 + - + +
282A ALA* 3.9 21.3 - - + +
285A ALA* 3.8 9.4 - - + -
286A ALA* 3.5 36.1 - - + +
289A PHE* 3.7 18.8 - - + -
319A MET* 4.4 2.5 - - + -
323A VAL* 3.9 20.9 - - + -
327A ILE* 4.1 18.8 - - + -
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Residues in contact with GLN 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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248A TYR* 4.5 8.6 + - - -
251A VAL* 2.6 36.1 + - - +
252A VAL* 3.0 27.0 + - + +
254A ILE* 1.3 72.9 - - - +
256A LYS* 1.3 57.4 + - - +
258A VAL* 3.4 18.7 - - - +
279A SER* 3.4 34.4 + - - +
282A ALA* 3.7 17.5 - - + -
283A ILE* 6.3 0.4 - - - +
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Residues in contact with LYS 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 VAL* 3.3 19.3 + - + +
253A LYS* 3.6 22.7 + - - +
254A ILE 3.2 0.8 - - - -
255A GLN* 1.3 76.9 - - + +
257A HIS* 1.3 90.8 + - + +
258A VAL 3.1 10.7 + - - +
259A THR* 5.7 1.4 - - - +
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Residues in contact with HIS 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 LYS 2.7 25.6 - - - +
254A ILE 3.1 7.4 + - - +
256A LYS* 1.3 105.8 + - + +
258A VAL* 1.3 59.4 + - - +
259A THR* 4.2 1.1 - - - -
262A GLN* 3.4 6.1 + - - -
323A VAL* 3.6 18.2 - - + +
326A ARG* 2.7 64.9 + - - +
327A ILE* 3.6 25.2 - - + +
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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