Contacts of the helix formed by residues 276 - 287 (chain O) in PDB entry 5MQF
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 ILE 276 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273O TYR 5.2 4.9 - - - +
274O ARG* 3.4 3.3 - - - -
275O ASN* 1.3 74.2 - - - +
277O THR* 1.3 57.0 + - - +
278O LEU 3.2 0.4 - - - -
279O TRP* 3.0 15.7 + - + +
280O LEU* 2.9 26.0 + - - +
306O LEU* 4.7 19.5 - - + +
308O ARG* 4.9 13.7 - - + -
311O GLN* 4.9 13.5 - - + +
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Residues in contact with THR 277 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836 A 3.3 49.7 - - - -
275O ASN* 2.9 4.1 + - - -
276O ILE* 1.3 77.8 - - - +
278O LEU* 1.3 56.6 + - - +
280O LEU* 3.1 11.3 + - - +
281O LYS* 2.9 24.6 + - - +
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Residues in contact with LEU 278 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836 A 4.7 4.8 + - + -
272O ASP* 5.3 12.6 - - + -
275O ASN* 3.0 15.1 + - + +
277O THR* 1.3 77.4 - - - +
279O TRP* 1.3 58.0 + - - +
281O LYS* 3.0 10.6 + - - +
282O TYR* 2.9 27.9 + - - +
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Residues in contact with TRP 279 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269O LEU* 6.1 6.1 - - + +
272O ASP* 6.1 2.5 - - + +
275O ASN 4.0 1.0 + - - +
276O ILE* 3.0 21.0 + - + +
278O LEU* 1.3 79.2 - - - +
280O LEU* 1.3 57.3 + - - +
282O TYR* 3.6 6.7 + - - +
283O ALA* 2.9 28.3 + - - +
302O ALA* 5.8 8.1 - - + -
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Residues in contact with LEU 280 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836 A 5.5 6.1 - - + +
276O ILE 2.9 11.4 + - - +
277O THR* 3.1 13.4 + - - +
279O TRP* 1.3 76.6 - - - +
281O LYS* 1.3 58.5 + - - +
283O ALA* 3.8 7.0 - - - +
284O GLU* 2.9 28.2 + - - +
311O GLN* 4.5 17.7 - - + -
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Residues in contact with LYS 281 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836 A 5.5 12.9 + - + +
277O THR 2.9 12.0 + - - +
278O LEU* 3.0 12.5 + - - +
280O LEU* 1.3 74.8 - - - +
282O TYR* 1.3 60.1 + - - +
284O GLU* 3.2 7.4 + - - +
285O MET* 2.9 27.0 + - - +
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Residues in contact with TYR 282 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265O TYR* 4.3 29.9 - - + +
268O ALA* 6.5 0.4 - - + -
269O LEU* 5.1 7.6 - - + +
278O LEU 2.9 14.2 + - - +
279O TRP* 4.0 7.0 - - - +
281O LYS* 1.3 76.5 - - - +
283O ALA* 1.3 57.9 + - - +
285O MET* 3.3 8.1 + - - +
286O GLU* 2.9 29.3 + - - +
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Residues in contact with ALA 283 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279O TRP 2.9 20.3 + - - +
280O LEU* 3.8 9.0 - - - +
281O LYS 3.2 0.2 - - - -
282O TYR* 1.3 75.5 - - - +
284O GLU* 1.3 57.3 + - - +
286O GLU* 3.8 5.8 - - - +
287O MET* 2.9 29.0 + - - +
295O ALA* 4.7 8.8 - - - +
298O ILE* 5.9 7.2 - - + -
299O TRP* 5.8 9.2 - - + +
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Residues in contact with GLU 284 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280O LEU 2.9 18.5 + - - +
281O LYS* 3.2 8.0 + - - +
283O ALA* 1.3 75.9 - - - +
285O MET* 1.3 63.2 + - - +
287O MET* 3.7 6.8 - - - +
288O LYS* 3.2 22.2 + - - +
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Residues in contact with MET 285 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249O ALA* 5.5 12.3 - - + +
253O GLU* 5.4 15.8 - - + +
265O TYR* 5.8 5.2 - - + -
281O LYS 2.9 14.2 + - - +
282O TYR* 3.3 11.2 + - - +
284O GLU* 1.3 77.9 - - - +
286O GLU* 1.3 59.2 + - - +
288O LYS* 3.5 13.6 + - - +
289O ASN* 3.8 8.1 + - - +
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Residues in contact with GLU 286 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265O TYR* 6.2 2.7 - - + -
282O TYR 2.9 17.0 + - - +
283O ALA* 4.1 4.5 - - - +
285O MET* 1.3 74.6 - - - +
287O MET* 1.3 64.8 + - - +
289O ASN* 3.3 22.2 + - - +
292O VAL* 4.6 2.3 + - - -
294O HIS* 5.5 1.3 - - + +
295O ALA* 3.4 26.9 - - + +
298O ILE* 5.8 4.0 - - + -
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Residues in contact with MET 287 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202N TYR* 6.4 0.4 - - - -
283O ALA 2.9 19.5 + - - +
284O GLU* 3.7 9.9 - - - +
285O MET 3.3 0.6 - - - -
286O GLU* 1.3 78.8 - - - +
288O LYS* 1.3 60.9 + - - +
289O ASN 3.3 8.5 + - - +
292O VAL* 4.6 8.3 - - - +
295O ALA* 3.8 12.3 - - + +
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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