Contacts of the helix formed by residues 277 - 288 (chain G) in PDB entry 3Q3G
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 SER 277 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244G GLU* 5.1 1.0 + - - -
274G ALA 4.7 1.0 + - - -
276G ARG* 1.3 81.0 - - - +
278G GLU* 1.4 61.0 - - - +
279G LYS* 4.0 7.6 + - - +
280G SER* 2.6 45.2 + - - -
281G ARG* 3.2 23.8 + - - +
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Residues in contact with GLU 278 (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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277G SER* 1.4 69.3 - - - +
279G LYS* 1.4 64.9 + - - +
281G ARG* 3.4 14.4 + - - +
282G GLN* 3.0 53.0 + - - +
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Residues in contact with LYS 279 (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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32C SER* 3.3 31.4 + - - +
244G GLU* 3.3 17.9 + - - +
277G SER* 4.0 6.7 + - - +
278G GLU* 1.4 77.2 + - - +
280G SER* 1.4 62.7 + - - +
282G GLN* 3.3 35.1 + - - +
283G GLU* 3.5 6.6 + - - +
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Residues in contact with SER 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G GLU* 3.7 25.1 + - - -
274G ALA 3.2 20.8 + - - -
275G PHE* 3.3 23.3 - - - -
277G SER* 2.6 45.5 + - - -
279G LYS* 1.4 79.0 - - - +
281G ARG* 1.3 58.9 + - - +
283G GLU* 3.1 20.0 + - - +
284G LEU 3.4 3.8 + - - -
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Residues in contact with ARG 281 (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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275G PHE 3.1 15.3 + - - +
276G ARG* 3.5 44.9 + - - +
277G SER* 3.2 20.3 + - - +
278G GLU* 3.4 10.6 + - - +
280G SER* 1.3 74.1 + - - +
282G GLN* 1.4 59.8 + - - +
284G LEU* 3.2 13.2 + - + +
285G ASN* 3.0 34.8 + - - +
298G GLN* 3.5 24.8 + - - +
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Residues in contact with GLN 282 (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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278G GLU* 3.0 42.9 + - - +
279G LYS* 3.4 20.9 + - - +
280G SER 3.2 0.4 - - - -
281G ARG* 1.4 72.3 - - - +
283G GLU* 1.4 55.3 + - - +
285G ASN* 3.3 15.5 + - - +
286G THR* 2.7 37.5 + - - +
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Residues in contact with GLU 283 (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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211G THR* 4.9 0.3 + - - -
243G GLY 4.9 0.5 - - - +
244G GLU* 3.3 30.6 - - + +
245G LYS* 2.8 29.4 + - - +
252G TYR* 2.6 39.5 + - + +
275G PHE* 5.1 4.5 - - + -
279G LYS* 3.5 5.6 + - - +
280G SER* 3.1 16.2 + - - +
282G GLN* 1.4 74.8 - - - +
284G LEU* 1.4 63.8 + - - +
286G THR* 3.2 9.3 + - - -
287G ILE* 3.1 33.7 + - + +
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Residues in contact with LEU 284 (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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241G THR* 4.8 3.1 - - + -
268G VAL* 3.4 29.4 - - + +
270G GLY* 3.8 17.7 - - - +
275G PHE* 3.6 43.1 - - + -
280G SER 3.4 2.0 + - - +
281G ARG* 3.2 14.5 + - + +
283G GLU* 1.4 75.4 - - - +
285G ASN* 1.4 57.3 + - - +
287G ILE* 3.1 7.8 + - + +
288G ALA* 3.0 25.6 + - - +
296G VAL* 3.9 19.5 - - + -
297G PHE 4.6 0.2 - - - +
298G GLN* 3.7 39.3 - - + +
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Residues in contact with ASN 285 (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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281G ARG* 3.0 23.8 + - - +
282G GLN* 3.3 17.6 + - - +
284G LEU* 1.4 74.1 - - - +
286G THR* 1.3 56.5 + - - +
288G ALA* 3.0 21.7 - - - +
289G SER 5.3 0.5 - - - +
290G LYS* 5.5 4.2 - - - +
292G PRO* 3.5 36.3 - - + +
296G VAL* 3.6 16.9 - - - +
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Residues in contact with THR 286 (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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252G TYR* 3.6 37.2 - - + -
256G ILE* 3.4 27.6 - - + +
266G ARG* 4.5 0.2 + - - -
282G GLN* 2.7 20.6 + - - +
283G GLU* 3.2 12.5 + - - -
285G ASN* 1.3 74.6 - - - +
287G ILE* 1.4 63.6 + - - +
288G ALA 3.8 3.3 - - - +
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Residues in contact with ILE 287 (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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211G THR* 4.4 8.7 - - + -
215G ILE* 3.9 12.3 - - + -
239G VAL* 3.8 31.0 - - + -
241G THR* 5.1 7.2 - - + -
252G TYR* 3.5 37.2 - - + +
256G ILE* 3.7 7.5 - - - +
266G ARG* 2.7 39.3 + - + +
267G TYR 5.3 0.2 - - - +
268G VAL* 3.8 24.9 - - + -
275G PHE* 6.1 0.4 - - + -
283G GLU* 3.1 26.8 + - + +
284G LEU* 3.1 9.6 + - + +
286G THR* 1.4 76.0 - - - +
288G ALA* 1.3 51.7 + - - +
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Residues in contact with ALA 288 (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 ARG* 3.6 16.4 + - - +
268G VAL* 3.8 11.4 - - + -
284G LEU 3.0 7.9 + - - +
285G ASN 3.0 17.7 - - - +
286G THR 3.8 1.7 - - - +
287G ILE* 1.3 79.6 - - - +
289G SER* 1.3 66.2 + - - +
290G LYS* 3.8 2.1 + - - +
295G HIS* 3.8 17.0 - - + +
296G VAL* 3.6 31.2 - - + -
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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