Contacts of the helix formed by residues 261 - 274 (chain G) 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 THR 261 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259G HIS 3.4 4.7 + - - -
260G MET* 1.3 74.3 - - - +
262G SER* 1.3 58.6 + - - +
263G ASP* 3.1 25.0 + - + +
264G GLN* 3.2 20.4 + - - +
265G ARG* 2.6 37.7 + - - +
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Residues in contact with SER 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260G MET 4.1 0.8 + - - -
261G THR* 1.3 77.8 - - - +
263G ASP* 1.3 64.9 + - - +
265G ARG* 3.3 17.0 - - - +
266G LYS* 2.9 30.1 + - - +
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Residues in contact with ASP 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261G THR* 3.1 16.5 - - + +
262G SER* 1.3 79.6 + - - +
264G GLN* 1.3 60.7 + - + +
266G LYS* 3.8 2.5 - - - +
267G GLN* 2.9 30.2 + - - +
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Residues in contact with GLN 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256G ALA* 5.7 3.3 - - - +
259G HIS* 6.1 0.7 - - - -
260G MET* 4.1 15.9 - - + +
261G THR* 3.2 24.6 + - - +
263G ASP* 1.3 81.1 - - + +
265G ARG* 1.3 62.7 + - - +
267G GLN* 3.8 9.0 - - + -
268G ILE* 2.9 32.5 + - + +
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Residues in contact with ARG 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216G GLU* 4.8 11.1 - - - +
217G ILE* 4.3 19.9 - - + +
220G GLU* 4.5 20.0 - - - +
260G MET* 3.7 20.6 - - + +
261G THR 2.6 23.2 + - - +
262G SER* 3.3 16.6 - - - +
264G GLN* 1.3 75.0 - - - +
266G LYS* 1.3 59.9 + - + +
268G ILE* 3.3 1.4 + - - +
269G PHE* 2.9 64.2 + - + -
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Residues in contact with LYS 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262G SER* 2.9 21.1 + - - +
263G ASP* 4.1 2.5 - - - +
265G ARG* 1.3 71.8 - - - +
267G GLN* 1.3 61.0 + - - +
269G PHE* 3.9 13.7 - - + -
270G SER* 2.8 45.1 + - - +
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Residues in contact with GLN 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263G ASP 2.9 19.6 + - - +
264G GLN* 3.4 12.1 - - + +
265G ARG 3.1 0.2 - - - -
266G LYS* 1.3 77.3 - - - +
268G ILE* 1.3 67.5 + - + +
270G SER* 3.6 5.3 - - - -
271G ARG* 2.9 73.7 + - + +
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Residues in contact with ILE 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249G ILE* 3.1 36.6 - - + +
252G ASN* 5.9 5.8 - - + -
253G ILE* 3.3 27.6 - - + +
260G MET* 4.5 11.0 - - + -
264G GLN* 2.9 20.0 + - + +
265G ARG 4.0 2.2 - - - +
267G GLN* 1.3 81.0 - - + +
269G PHE* 1.3 61.5 + - + +
271G ARG* 3.5 10.2 - - + +
272G LEU* 2.9 27.7 + - - +
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Residues in contact with PHE 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G ILE* 4.6 13.9 - - + -
220G GLU* 4.8 19.5 - - + -
221G VAL* 5.2 9.4 - - + -
224G LEU* 3.4 29.7 - - + +
253G ILE* 4.8 20.6 - - + -
260G MET* 5.5 2.7 - - + -
265G ARG* 2.9 63.8 + - + +
266G LYS* 3.7 12.3 - - + +
267G GLN 3.2 0.2 - - - -
268G ILE* 1.3 80.1 - - + +
270G SER* 1.3 56.3 + - - +
272G LEU* 3.3 6.9 + - + -
273G ALA* 2.9 26.2 + - - +
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Residues in contact with SER 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266G LYS* 2.8 34.1 + - - +
267G GLN* 3.6 5.8 - - - -
269G PHE* 1.3 70.0 - - - +
271G ARG* 1.3 74.9 + - - +
273G ALA* 3.1 11.4 + - - +
274G GLU* 2.9 32.9 + - - +
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Residues in contact with ARG 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249G ILE* 4.9 17.7 - - + -
267G GLN* 2.9 56.4 + - + +
268G ILE* 3.5 15.9 - - + +
270G SER* 1.3 82.1 - - - +
272G LEU* 1.3 57.5 + - - +
274G GLU* 2.9 48.0 + - - +
275G SER* 3.3 5.1 + - - -
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Residues in contact with LEU 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G VAL* 5.5 8.7 - - + -
224G LEU* 3.7 23.8 - - + +
225G HIS* 3.4 39.4 - - + +
246G GLN* 4.4 7.2 + - - +
249G ILE* 3.1 33.7 - - + -
250G LEU* 4.8 1.6 - - + +
253G ILE* 3.6 25.8 - - + -
268G ILE 2.9 17.5 + - - +
269G PHE* 3.6 10.5 - - + +
271G ARG* 1.3 75.4 - - - +
273G ALA* 1.3 63.3 + - - +
275G SER* 2.7 27.8 + - - +
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Residues in contact with ALA 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G LEU* 4.3 8.9 - - + +
269G PHE 2.9 14.2 + - - +
270G SER* 3.1 13.9 + - - +
272G LEU* 1.3 75.4 - - - +
274G GLU* 1.3 59.8 + - + +
275G SER 3.4 2.4 + - - -
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Residues in contact with GLU 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270G SER* 2.9 21.3 + - - +
271G ARG* 2.9 33.1 + - - +
273G ALA* 1.3 79.9 - - + +
275G SER* 1.3 55.3 + - - +
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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