Contacts of the helix formed by residues 273 - 281 (chain B) 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 LEU 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B CYS* 4.7 6.7 - - + +
270B LEU* 3.3 31.3 + - + +
271B PRO 3.1 1.2 - - - -
272B GLN* 1.3 88.2 - - - +
274B LEU* 1.3 65.3 + - - +
275B PRO* 3.8 3.6 - - - -
276B LEU* 3.4 36.0 - - + +
277B LEU* 4.1 5.5 + - - +
308B PHE* 6.3 0.2 - - + -
327B THR* 3.8 20.4 - - + -
330B LEU* 4.5 10.0 - - + +
223K TYR* 3.6 35.7 - - + +
224K LEU* 3.7 22.7 - - + +
227K LEU* 4.8 7.0 - - + +
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B PHE* 3.6 38.8 - - + +
256B ILE* 3.7 24.7 - - + +
269B CYS* 3.6 26.7 - - + +
270B LEU 3.3 21.1 - - - +
271B PRO* 4.1 14.8 - - + -
272B GLN* 3.6 4.4 - - - +
273B LEU* 1.3 74.8 - - - +
275B PRO* 1.4 71.9 - - + +
276B LEU 3.1 4.3 - - - -
277B LEU* 3.0 25.9 + - - +
278B LYS 3.8 1.0 + - - -
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Residues in contact with PRO 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B GLN* 5.4 2.5 - - - -
273B LEU* 3.9 2.0 - - - +
274B LEU* 1.4 90.9 - - + +
276B LEU* 1.3 68.1 + - + +
277B LEU 3.2 0.2 - - - -
278B LYS* 2.9 39.2 + - + +
279B HIS* 3.4 4.2 + - - +
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B GLN 5.3 0.7 - - - +
273B LEU* 3.4 30.5 - - + +
274B LEU 3.0 0.2 + - - -
275B PRO* 1.3 84.5 - - + +
277B LEU* 1.3 52.9 + - - +
279B HIS* 2.9 8.6 + - - +
280B THR* 2.7 36.9 + - - -
330B LEU* 3.7 29.4 - - + -
332B SER* 3.6 34.2 - - - +
227K LEU* 3.6 23.3 - - + +
228K LEU* 6.4 0.2 - - + -
229K PRO* 4.1 20.6 - - + -
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ILE* 3.9 27.6 - - + -
258B VAL* 4.5 6.1 - - + +
267B HIS* 4.3 23.1 - - + +
269B CYS* 3.6 33.0 - - + +
273B LEU 4.6 1.8 - - - +
274B LEU* 3.0 10.9 + - + +
276B LEU* 1.3 76.9 - - - +
278B LYS* 1.3 58.7 - - - +
280B THR* 2.9 5.9 + - - -
281B THR* 2.7 50.7 + - - +
282B SER 4.5 0.2 + - - -
308B PHE* 3.6 33.7 - - + -
330B LEU* 4.1 4.7 - - + +
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Residues in contact with LYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B ILE* 4.0 33.1 - - + +
257B LEU 4.5 5.9 + - - -
258B VAL* 5.1 14.4 - - + +
274B LEU 4.4 2.0 - - - +
275B PRO* 2.9 30.6 + - + +
277B LEU* 1.3 75.7 - - + +
279B HIS* 1.3 58.3 + - - +
282B SER* 4.2 9.9 + - - -
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Residues in contact with HIS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B PRO 3.4 3.9 + - - +
276B LEU* 2.9 8.9 + - - +
278B LYS* 1.3 81.3 - - - +
280B THR* 1.3 67.9 + - - +
281B THR 3.5 0.4 - - - -
282B SER* 3.3 15.5 + - - +
283B TYR* 5.3 18.2 - + - -
331B HIS* 3.1 39.9 + + - -
332B SER* 4.4 2.9 - - - -
333B ALA* 3.2 41.1 + - + +
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Residues in contact with THR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B LEU 2.7 26.1 + - - -
277B LEU* 2.9 8.9 + - - -
279B HIS* 1.3 78.4 - - - +
281B THR* 1.3 69.1 + - - +
282B SER 3.0 10.6 - - - +
283B TYR* 5.4 0.9 - - - -
308B PHE* 4.5 11.4 - - + -
329B LEU 3.7 15.5 - - - +
330B LEU* 2.3 50.9 + - + +
331B HIS* 4.6 0.8 + - - -
342B THR* 4.0 15.4 - - + +
346B LEU* 5.0 8.0 - - + +
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Residues in contact with THR 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B VAL* 3.6 27.8 - - + +
267B HIS* 3.3 37.1 + - + +
277B LEU* 2.7 47.5 + - - +
280B THR* 1.3 74.8 - - - +
282B SER* 1.3 63.4 + - - +
284B LEU* 3.2 30.2 + - + +
308B PHE* 5.6 0.7 - - - -
346B LEU* 4.8 9.7 - - - +
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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