Contacts of the helix formed by residues 252 - 263 (chain H) in PDB entry 6D6Q
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 TYR 252 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180H LYS* 3.2 39.4 - - + +
182H GLN* 3.4 31.4 - - - +
197H LEU* 4.1 14.1 - - + -
250H MET* 4.9 4.5 - - + -
251H LEU* 1.3 83.9 - - - +
253H ASP* 1.3 82.4 + - + +
254H THR* 2.7 35.2 + - + -
255H SER* 3.1 20.7 + - - -
256H ILE* 3.1 16.6 + - - +
288H LEU* 4.5 14.2 - - + +
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Residues in contact with ASP 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182H GLN* 4.6 1.5 - - - +
187H HIS* 3.9 34.8 + - + -
189H LEU* 3.0 32.2 - - - +
197H LEU* 4.8 0.8 - - - +
252H TYR* 1.3 80.2 - - + +
254H THR* 1.3 71.8 + - + +
256H ILE* 3.1 11.4 - - - +
257H LEU* 2.9 46.3 + - - +
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Residues in contact with THR 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252H TYR* 2.7 38.0 + - + -
253H ASP* 1.3 87.6 - - + +
255H SER* 1.3 63.3 + - - +
257H LEU* 4.3 2.2 - - + -
258H TYR* 2.9 64.8 + - + +
288H LEU* 3.7 6.6 - - - +
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Residues in contact with SER 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244H LEU* 3.2 28.5 - - - +
249H MET* 3.8 8.1 - - - +
250H MET 3.8 10.8 + - - -
252H TYR* 3.1 27.9 + - - -
254H THR* 1.3 83.0 + - - +
256H ILE* 1.3 58.0 + - - +
258H TYR 3.8 0.2 - - - -
259H CYS* 3.0 29.1 + - - +
284H THR* 3.8 6.1 - - - +
288H LEU* 4.5 17.7 - - - -
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Residues in contact with ILE 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H LEU* 3.9 26.7 - - + -
195H VAL* 4.2 22.0 - - + -
197H LEU* 5.3 4.9 - - + -
237H LEU* 4.8 14.4 - - + +
240H CYS* 5.2 4.8 - - + +
241H ILE* 4.3 18.8 - - + +
244H LEU* 4.0 21.8 - - + -
251H LEU* 4.0 20.2 - - + -
252H TYR 3.1 13.2 + - - +
253H ASP* 3.1 21.8 - - - +
255H SER* 1.3 72.2 - - - +
257H LEU* 1.3 60.9 + - - +
259H CYS* 3.9 3.3 - - - +
260H TYR* 2.9 30.8 + - - +
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Residues in contact with LEU 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H LEU* 4.1 26.2 - - + -
190H PRO* 4.3 15.9 - - + -
191H CYS* 4.2 19.3 - - - -
237H LEU* 6.1 0.4 - - + -
253H ASP* 2.9 53.6 + - - +
254H THR* 3.7 7.6 - - + +
256H ILE* 1.3 77.9 - - + +
258H TYR* 1.3 71.9 + - + +
260H TYR* 3.3 7.3 - - - +
261H GLU* 2.9 32.9 + - + +
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Residues in contact with TYR 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254H THR* 2.9 42.7 + - + +
257H LEU* 1.3 92.5 - - + +
259H CYS* 1.3 60.3 + - - +
261H GLU* 3.3 7.9 + - + +
262H ALA* 2.9 28.8 + - - +
284H THR* 3.8 19.4 + - + +
287H ARG* 3.0 43.7 + - - +
288H LEU* 3.3 39.3 - - + -
291H GLN* 5.3 9.1 + - + -
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Residues in contact with CYS 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240H CYS* 3.4 32.1 - - + -
243H SER* 3.7 15.5 - - - -
244H LEU* 4.4 14.4 - - + -
255H SER 3.0 17.5 + - - +
256H ILE* 3.9 4.9 - - - +
258H TYR* 1.3 72.8 - - - +
260H TYR* 1.3 66.3 + - - +
262H ALA* 3.1 4.9 + - - +
263H SER* 2.9 21.7 + - - -
280H ILE* 3.3 24.7 - - - -
281H VAL* 5.7 0.7 - - - -
284H THR* 3.5 14.3 + - - +
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Residues in contact with TYR 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H CYS* 3.6 32.2 + - + +
233H VAL* 3.9 36.7 - - + +
236H ARG* 3.7 41.9 + - + -
237H LEU* 3.9 21.8 - - + -
240H CYS* 4.1 9.3 - - - -
256H ILE 2.9 15.5 + - - +
257H LEU* 3.3 12.1 - - - +
259H CYS* 1.3 74.3 - - - +
261H GLU* 1.3 76.0 + - - +
263H SER* 2.8 23.1 + - - -
264H LEU* 2.8 26.6 - - + +
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Residues in contact with GLU 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H CYS* 5.1 3.5 - - - -
257H LEU* 2.9 26.4 + - + +
258H TYR* 3.8 10.3 - - + +
260H TYR* 1.3 91.2 - - + +
262H ALA* 1.3 60.5 + - - +
264H LEU* 3.6 24.9 + - - +
265H PRO* 4.6 2.6 - - - +
287H ARG* 5.1 6.1 - - - +
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Residues in contact with ALA 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258H TYR 2.9 16.8 + - - +
259H CYS* 3.4 6.1 - - - +
260H TYR 2.9 0.4 + - - -
261H GLU* 1.3 79.2 - - - +
263H SER* 1.3 56.1 + - - +
264H LEU 3.3 1.6 - - - -
265H PRO* 3.3 17.8 - - - +
266H HIS* 5.0 3.1 + - - -
279H GLU* 5.2 1.6 - - - +
280H ILE* 3.8 26.0 - - + +
283H GLU* 4.0 30.7 - - + +
284H THR* 4.4 4.5 - - - +
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Residues in contact with SER 263 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H ARG* 3.7 19.5 + - - +
240H CYS* 4.0 15.0 - - - -
259H CYS 2.9 13.3 + - - -
260H TYR 2.8 15.2 + - - -
262H ALA* 1.3 69.6 - - - +
264H LEU* 1.3 58.2 + - - +
265H PRO* 3.6 0.9 - - - -
266H HIS* 2.7 17.5 + - - +
267H GLN 4.4 0.3 + - - -
271H ILE* 3.3 31.3 - - - +
280H ILE* 3.9 17.3 - - - -
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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