Contacts of the helix formed by residues 255 - 266 (chain R) in PDB entry 3K9Q
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 255 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253R ASP 3.9 10.3 - - - +
254R VAL* 1.3 78.6 - - - +
256R VAL* 1.3 63.5 + - - +
257R GLU* 3.6 18.0 + - - +
258R GLN* 3.0 37.5 + - - +
259R VAL* 3.2 25.6 + - - +
299R VAL* 3.9 5.8 - - - -
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Residues in contact with VAL 256 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255R THR* 1.3 71.2 - - - +
257R GLU* 1.3 72.9 + - - +
259R VAL* 3.3 4.0 + - - +
260R ASN* 3.0 46.7 + - - +
294R ALA 5.1 1.1 - - - +
297R THR* 4.1 34.7 - - + +
298R ARG* 4.5 0.4 - - - -
299R VAL* 3.7 26.2 - - + +
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Residues in contact with GLU 257 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255R THR* 3.2 20.3 - - - +
256R VAL* 1.3 89.2 + - + +
258R GLN* 1.3 58.4 + - + +
260R ASN* 3.3 6.3 + - - +
261R GLU* 2.8 39.2 + - + +
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Residues in contact with GLN 258 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167R PHE* 3.7 19.6 - - + -
251R LYS* 5.9 2.2 - - - +
252R GLN 5.4 0.2 - - - +
253R ASP 3.7 7.7 + - - +
254R VAL* 3.3 13.2 - - - +
255R THR* 3.0 38.5 + - - +
257R GLU* 1.3 76.8 - - + +
259R VAL* 1.3 61.2 + - - +
261R GLU* 3.7 6.0 + - - +
262R ALA* 3.1 24.9 + - - +
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Residues in contact with VAL 259 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163R LEU* 4.6 6.5 - - + -
167R PHE* 4.1 14.1 - - + -
254R VAL* 3.7 20.9 - - + -
255R THR 3.2 14.6 + - - +
256R VAL 3.6 7.0 - - - +
258R GLN* 1.3 78.4 - - - +
260R ASN* 1.3 63.2 + - - +
262R ALA* 3.3 3.8 + - - +
263R MET* 3.0 36.4 + - + +
292R PHE* 4.3 5.4 - - + -
297R THR* 3.9 11.0 - - + -
299R VAL* 5.1 0.2 - - + -
308R VAL* 3.9 17.5 - - + -
310R VAL* 3.6 31.2 - - + -
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Residues in contact with ASN 260 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256R VAL* 3.0 35.5 + - - +
257R GLU* 3.8 5.7 - - - +
259R VAL* 1.3 74.5 - - - +
261R GLU* 1.3 58.6 + - - +
263R MET* 3.3 1.6 + - - +
264R LYS* 2.9 24.8 + - - +
273R TYR* 3.3 26.4 - - - +
292R PHE* 3.3 15.4 - - - -
294R ALA* 3.4 29.0 + - + +
297R THR* 2.6 24.4 + - - -
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Residues in contact with GLU 261 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257R GLU* 2.8 24.1 + - + +
258R GLN* 3.8 6.3 - - - +
260R ASN* 1.3 75.6 - - - +
262R ALA* 1.3 58.3 + - - +
264R LYS* 3.1 22.2 + - - +
265R ASN* 2.9 51.4 + - - +
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Residues in contact with ALA 262 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162R VAL* 3.7 21.0 - - + +
166R ASP* 3.3 27.9 - - - +
167R PHE* 4.2 9.0 - - + -
258R GLN 3.1 17.3 + - - +
259R VAL 3.7 4.3 - - - +
261R GLU* 1.3 79.0 - - - +
263R MET* 1.3 60.6 + - - +
265R ASN* 3.6 9.4 + - - +
266R ALA* 3.5 17.2 + - - +
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Residues in contact with MET 263 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159R VAL* 3.6 32.8 - - + +
162R VAL* 3.7 24.5 - - + -
163R LEU* 3.8 22.9 - - + -
167R PHE* 6.0 0.2 - - + -
259R VAL* 3.0 20.2 + - + +
260R ASN 3.6 6.1 - - - +
261R GLU 3.2 0.2 - - - -
262R ALA* 1.3 74.3 - - - +
264R LYS* 1.3 65.7 + - - +
266R ALA* 3.1 13.6 + - - +
267R SER* 3.4 9.0 + - - -
271R PHE* 3.8 31.0 - - + -
273R TYR* 4.2 3.6 - - + +
292R PHE* 3.4 44.4 - - + -
310R VAL* 4.8 0.4 - - + -
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Residues in contact with LYS 264 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260R ASN 2.9 14.0 + - - +
261R GLU* 3.1 25.4 + - - +
263R MET* 1.3 75.0 - - - +
265R ASN* 1.3 67.6 + - - +
267R SER* 2.9 25.6 + - - +
273R TYR* 3.7 46.1 - - + +
275R GLU* 5.6 1.3 - - - +
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Residues in contact with ASN 265 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261R GLU* 2.9 36.6 + - - +
262R ALA* 3.9 9.3 - - - +
263R MET 3.3 0.4 - - - -
264R LYS* 1.3 82.0 - - - +
266R ALA* 1.3 56.5 + - - +
267R SER 3.3 3.2 + - - +
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Residues in contact with ALA 266 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162R VAL* 3.4 33.7 - - + -
262R ALA 3.5 4.0 + - - +
263R MET 3.1 8.6 + - - +
264R LYS 3.1 1.0 - - - -
265R ASN* 1.3 76.8 - - - +
267R SER* 1.3 64.4 + - - +
268R ASN* 3.7 12.8 + - - -
271R PHE* 3.6 15.7 - - + +
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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