Contacts of the helix formed by residues 275 - 284 (chain G) in PDB entry 6MZL
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 275 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237G SER 5.8 0.5 + - - -
238G GLN* 5.7 4.7 - - - -
241G TYR* 3.5 60.1 - + + +
271G GLN* 3.7 14.3 + - + -
272G GLU* 3.2 54.8 + - + +
274G TYR* 1.3 115.8 + + - +
276G GLN* 1.3 67.2 + - - +
277G ASP* 3.1 7.3 + - - +
278G ASP* 3.2 7.1 + - - +
279G LEU* 3.1 30.6 + - + +
649G ARG* 4.4 8.3 - - - +
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Residues in contact with GLN 276 (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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272G GLU 5.0 0.6 + - - -
273G CYS* 3.3 34.9 + - - +
274G TYR* 3.2 12.9 + - - +
275G TYR* 1.3 79.3 - - - +
277G ASP* 1.3 59.4 + - - +
279G LEU* 3.3 16.5 + - - +
280G ARG* 2.9 56.1 + - - +
649G ARG* 4.2 2.1 - - - +
7I LEU* 5.1 10.9 - - - +
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Residues in contact with ASP 277 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G TYR 3.7 1.9 - - - +
276G GLN* 1.3 73.7 - - - +
278G ASP* 1.3 75.3 + - - +
280G ARG* 3.1 17.2 + - - +
281G VAL* 2.9 33.9 + - + +
647G ALA 4.9 7.4 - - - +
649G ARG* 2.8 37.8 + - - +
671G PRO* 5.0 7.4 - - - +
52I GLN* 3.7 7.0 + - - +
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Residues in contact with ASP 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G TYR* 3.2 25.7 + - - +
245G VAL* 6.4 0.2 - - + -
275G TYR* 3.2 4.4 + - + +
277G ASP* 1.3 89.4 + - - +
279G LEU* 1.3 60.1 + - - +
281G VAL* 3.7 14.5 - - - +
282G LEU* 2.8 33.8 + - + +
296G THR* 4.3 18.2 - - - +
300G PHE* 4.3 22.2 - - - -
301G ARG* 5.0 11.7 + - - +
649G ARG* 5.5 5.9 + - - +
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Residues in contact with LEU 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G TYR* 4.2 21.3 - - + +
244G PHE* 6.1 2.0 - - + -
264G PHE* 4.2 22.6 - - + -
268G HIS* 5.0 14.6 - - + +
271G GLN* 6.0 3.8 - - + -
272G GLU 5.7 1.6 - - - +
275G TYR* 3.1 34.6 + - + +
276G GLN* 3.3 20.0 - - - +
277G ASP 3.2 0.2 - - - -
278G ASP* 1.3 76.9 - - - +
280G ARG* 1.3 56.6 + - + +
282G LEU* 3.0 9.6 + - + +
283G SER* 2.9 28.6 + - - -
7I LEU* 6.2 5.2 - - + +
9I LEU* 5.5 1.9 - - - +
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Residues in contact with ARG 280 (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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276G GLN* 2.9 58.5 + - - +
277G ASP* 3.1 16.3 + - - +
279G LEU* 1.3 76.0 - - + +
281G VAL* 1.3 60.6 + - - +
283G SER* 2.4 28.2 + - - -
284G SER* 3.6 6.8 + - - -
9I LEU* 5.4 9.2 - - + -
52I GLN* 3.6 17.0 - - - +
25M ASP 3.2 23.5 + - - +
26M MET* 3.2 36.0 + - - +
27M GLY* 3.6 14.8 + - - -
28M ILE* 5.1 6.3 - - - +
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Residues in contact with VAL 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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277G ASP* 2.9 23.2 + - + +
278G ASP* 3.7 15.7 - - - +
280G ARG* 1.3 74.4 - - - +
282G LEU* 1.3 57.9 + - + +
284G SER* 2.4 36.7 + - - +
285G LEU* 3.3 19.8 - - + +
294G ASN* 3.4 33.0 - - + +
296G THR* 6.4 1.6 - - + -
297G MET* 5.1 4.9 - - + -
301G ARG* 5.7 3.8 - - - +
52I GLN* 3.4 26.9 - - - +
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Residues in contact with LEU 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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241G TYR* 5.6 1.1 - - - +
244G PHE* 4.0 21.3 - - + -
245G VAL* 4.6 18.8 - - + +
248G TYR* 3.1 57.5 + - + -
264G PHE* 3.7 25.7 - - + -
278G ASP* 2.8 19.7 + - + +
279G LEU* 3.0 15.4 + - + +
281G VAL* 1.3 74.6 - - + +
283G SER* 1.3 64.6 + - - +
284G SER 3.4 0.3 + - - -
285G LEU* 3.8 13.9 - - + +
301G ARG* 3.9 22.9 - - - +
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Residues in contact with SER 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G TYR* 4.7 3.4 + - - -
264G PHE* 4.3 14.7 - - - -
279G LEU 2.9 11.4 + - - -
280G ARG* 2.4 30.2 + - - -
282G LEU* 1.3 78.9 - - - +
284G SER* 1.3 57.1 + - - +
285G LEU 3.4 6.8 + - - +
9I LEU* 3.7 31.2 - - - +
11I ASN* 3.7 22.1 + - - +
45I TYR* 4.3 2.9 + - - -
48I LYS* 6.1 1.6 - - - +
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Residues in contact with SER 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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280G ARG 3.8 7.4 - - - -
281G VAL* 2.4 37.4 + - - +
283G SER* 1.3 72.3 + - - +
285G LEU* 1.3 60.2 + - - +
290G HIS* 3.3 14.7 + - - -
294G ASN* 5.6 1.0 + - - -
11I ASN* 5.1 1.1 - - - -
45I TYR* 3.2 40.7 - - - +
48I LYS* 5.6 10.8 - - - -
49I GLU* 4.9 9.8 + - - +
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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