Contacts of the helix formed by residues 268 - 277 (chain J) in PDB entry 6K71
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 THR 268 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51J SER* 5.7 2.7 - - - +
53J ASP* 6.4 1.8 - - + -
131J LEU* 3.8 13.6 - - + +
152J TYR* 4.7 7.6 - - - +
260J PHE* 5.2 0.4 - - - -
267J GLN* 1.3 93.7 + - - +
269J ARG* 1.3 75.1 + - + +
270J ASP* 3.3 24.5 - - - +
271J ASP* 2.8 19.8 + - - +
272J PHE* 3.3 12.4 + - - +
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Residues in contact with ARG 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J LEU* 4.1 12.4 - - + +
150J LEU* 4.7 20.1 + - + +
152J TYR* 4.4 21.2 - - - +
183J MET* 5.2 11.7 - - - +
215J PHE* 5.9 5.1 - - - -
246J ASP* 3.9 23.1 + - - -
248J HIS* 3.8 42.0 + - + +
249J ILE 4.1 6.1 - - - +
250J SER* 3.7 27.2 + - - +
260J PHE* 5.5 2.0 - - + -
268J THR* 1.3 78.5 - - + +
270J ASP* 1.3 62.0 + - + +
272J PHE* 3.2 13.4 - - + +
273J VAL* 2.9 40.1 + - + +
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Residues in contact with ASP 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215J PHE* 4.4 19.2 - - + -
217J LYS* 4.4 20.8 - - + +
268J THR* 3.4 19.0 - - - +
269J ARG* 1.3 76.1 - - + +
271J ASP* 1.3 86.3 + - - +
272J PHE 3.1 1.1 - - - -
273J VAL* 3.2 11.8 - - - +
274J ARG* 3.0 27.4 + - - +
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Residues in contact with ASP 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265J ASP 4.4 6.9 - - - +
266J TYR* 3.2 16.9 - - + -
267J GLN* 4.3 11.2 + - - +
268J THR* 2.8 30.6 + - - +
270J ASP* 1.3 84.4 + - - +
272J PHE* 1.3 58.1 + - - -
274J ARG* 3.8 7.6 - - - +
275J GLY 2.9 23.4 + - - -
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Residues in contact with PHE 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256J VAL* 4.0 35.2 - - + -
259J LEU* 3.2 28.3 - - + -
260J PHE* 3.5 30.3 - + + -
266J TYR* 3.6 28.1 - + + -
268J THR 3.3 14.8 - - - +
269J ARG* 3.2 15.0 - - + +
271J ASP* 1.3 81.4 + - - +
273J VAL* 1.3 73.3 + - + +
275J GLY* 3.2 3.5 + - - -
276J LEU* 2.9 52.1 + - + +
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Residues in contact with VAL 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183J MET* 4.6 13.7 - - + -
215J PHE* 3.6 33.2 - - + -
269J ARG* 2.9 29.6 + - + +
270J ASP* 3.2 15.3 - - - +
272J PHE* 1.3 88.5 - - + +
274J ARG* 1.3 61.1 + - - +
276J LEU* 3.3 8.7 + - + +
277J LEU* 3.0 38.2 + - + +
287J ILE* 4.6 19.5 - - + -
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Residues in contact with ARG 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214J HIS* 5.1 16.8 - - - +
215J PHE* 4.6 22.7 + - - +
216J GLN* 4.6 27.3 + - - +
227J PRO* 5.3 10.9 - - - +
270J ASP 3.0 16.7 + - - +
271J ASP* 3.8 8.3 - - - +
273J VAL* 1.3 78.7 - - - +
275J GLY* 1.3 58.2 + - - +
277J LEU* 2.9 27.8 + - - +
278J VAL* 3.2 34.3 + - + +
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Residues in contact with GLY 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266J TYR* 3.3 28.9 - - - -
271J ASP 2.9 11.5 + - - -
272J PHE 3.6 3.1 - - - -
274J ARG* 1.3 74.3 - - - +
276J LEU* 1.3 62.5 + - - +
278J VAL* 3.3 16.7 - - - +
279J ASN* 3.0 25.4 + - - -
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Residues in contact with LEU 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180J VAL* 4.1 23.3 - - + -
259J LEU* 3.8 29.4 - - + -
266J TYR* 5.3 4.3 - - + -
272J PHE* 2.9 58.4 + - + +
273J VAL* 3.4 15.3 - - + +
275J GLY* 1.3 76.1 - - - +
277J LEU* 1.3 66.2 + - + +
278J VAL 3.4 1.8 + - - -
279J ASN* 4.1 11.0 + - - +
285J ASN* 3.6 29.7 - - + +
286J GLN* 5.3 0.8 - - - -
287J ILE* 5.3 10.3 - - + -
75P ARG* 4.9 4.9 - - - +
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Residues in contact with LEU 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212J VAL* 3.7 17.3 - - + +
213J LEU* 3.3 34.8 - - - +
214J HIS* 3.9 1.8 - - - -
215J PHE* 3.4 35.2 - - + +
273J VAL* 3.0 21.1 + - + +
274J ARG* 2.9 18.1 + - - +
276J LEU* 1.3 81.0 - - + +
278J VAL* 1.3 61.3 + - - +
286J GLN* 5.7 2.2 - - + -
287J ILE* 3.7 33.0 - - + +
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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