Contacts of the helix formed by residues 267 - 279 (chain M) in PDB entry 1OEY
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 267 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265M PRO 3.9 1.0 + - - -
266M LEU* 1.3 70.6 - - - +
268M LYS* 1.3 62.3 + - - +
270M LEU* 3.2 6.7 + - + +
271M LEU* 3.0 42.0 + - + +
285M LEU* 4.5 16.6 - - + -
297M LEU* 4.1 23.6 - - + +
298M LEU* 3.3 34.3 - - - +
299M SER* 3.7 12.1 - - - +
300M ASP* 3.0 17.7 + - - +
303M VAL* 4.1 23.9 - - + +
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Residues in contact with LYS 268 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266M LEU* 3.1 9.7 - - + +
267M LEU* 1.3 78.0 - - - +
269M ASP* 1.3 61.9 + - - +
271M LEU* 3.3 12.9 + - + +
272M GLU* 3.1 53.6 + - + +
300M ASP* 4.5 1.4 + - - +
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Residues in contact with ASP 269 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265M PRO* 4.6 7.5 - - + +
266M LEU* 3.2 40.7 + - - +
268M LYS* 1.3 79.0 - - - +
270M LEU* 1.3 64.0 + - - +
272M GLU* 3.4 18.9 + - - +
273M LEU* 3.1 24.3 + - - +
276M ARG* 5.5 0.5 + - - -
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Residues in contact with LEU 270 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240M LEU* 4.3 8.3 - - + -
265M PRO* 3.7 34.5 - - + -
266M LEU 3.3 3.9 + - - +
267M LEU* 3.2 7.3 + - + +
269M ASP* 1.3 77.4 - - - +
271M LEU* 1.3 58.5 + - - +
273M LEU* 3.5 10.6 + - + +
274M THR* 3.0 33.3 + - - -
285M LEU* 3.5 19.1 - - + -
297M LEU* 4.6 1.6 - - + -
303M VAL* 4.1 23.8 - - + -
306M MSE 4.2 8.1 - - + -
322M TRP* 4.0 14.6 - - + -
324M LEU* 3.9 31.9 - - + -
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Residues in contact with LEU 271 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267M LEU* 3.0 38.6 + - + +
268M LYS* 3.6 12.6 - - + +
269M ASP 3.2 0.4 - - - -
270M LEU* 1.3 73.9 - - - +
272M GLU* 1.3 61.5 + - + +
274M THR* 3.4 4.8 + - - -
275M ARG* 2.9 29.3 + - - +
280M ARG 5.1 0.5 - - - +
281M GLU* 5.8 0.6 - - - +
283M ILE* 4.9 16.2 - - + +
285M LEU* 3.8 26.0 - - + +
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Residues in contact with GLU 272 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268M LYS* 3.1 41.5 + - + +
269M ASP* 3.9 19.2 - - - +
270M LEU 3.4 0.4 - - - -
271M LEU* 1.3 73.4 - - + +
273M LEU* 1.3 55.9 + - - +
275M ARG* 3.2 13.3 + - - +
276M ARG* 2.8 57.9 + - - +
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Residues in contact with LEU 273 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240M LEU* 4.3 18.6 - - + -
242M VAL* 5.3 0.2 - - + -
255M ILE* 3.7 38.4 - - + -
256M ALA 4.9 1.3 - - - +
257M VAL* 3.7 29.8 - - + -
269M ASP 3.1 17.8 + - - +
270M LEU* 3.5 11.9 - - + +
272M GLU* 1.3 77.1 - - - +
274M THR* 1.3 68.8 + - - +
276M ARG* 3.3 15.4 + - - +
277M GLU* 2.9 31.0 + - - +
324M LEU* 5.2 4.5 - - + -
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Residues in contact with THR 274 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270M LEU 3.0 18.4 + - - -
271M LEU* 3.8 5.4 - - - -
273M LEU* 1.3 86.3 - - - +
275M ARG* 1.3 57.5 + - - +
278M PHE* 2.8 50.2 + - + +
280M ARG 4.3 0.3 - - - +
283M ILE* 2.9 38.6 - - + -
285M LEU* 3.6 16.5 - - + +
324M LEU* 4.3 2.4 - - - +
326M ILE* 3.8 16.6 - - + +
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Residues in contact with ARG 275 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281K GLU* 3.3 39.4 + - - +
271M LEU 2.9 18.2 + - - +
272M GLU* 3.5 12.2 + - - +
274M THR* 1.3 77.0 - - - +
276M ARG* 1.3 82.3 + - - +
279M GLN* 2.8 31.7 + - - +
280M ARG 3.5 17.4 + - - +
281M GLU* 3.8 34.1 - - + -
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Residues in contact with ARG 276 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269M ASP 5.5 0.4 + - - -
272M GLU* 2.8 49.9 + - - +
273M LEU* 3.6 11.5 - - - +
275M ARG* 1.3 95.8 - - - +
277M GLU* 1.3 63.9 + - + +
279M GLN* 4.4 8.5 + - - +
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Residues in contact with GLU 277 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411C LYS* 5.9 2.6 - - - -
253M LYS* 3.0 36.5 + - - +
255M ILE* 3.5 43.0 - - + +
273M LEU 2.9 17.0 + - - +
276M ARG* 1.3 82.7 - - - +
278M PHE* 1.3 74.3 + - + +
279M GLN* 5.0 2.9 - - - +
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Residues in contact with PHE 278 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282K ASP* 4.3 7.4 - - - +
242M VAL* 3.7 21.1 - - + -
244M TYR* 3.7 49.0 + + + -
253M LYS* 4.6 19.5 - - + -
255M ILE* 3.7 22.9 - - + -
274M THR* 2.8 37.0 + - + +
277M GLU* 1.3 81.8 - - + +
279M GLN* 1.3 73.1 + - - +
280M ARG* 3.2 21.3 + - + +
283M ILE* 5.5 0.2 - - + -
326M ILE* 3.6 20.6 - - + -
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Residues in contact with GLN 279 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281K GLU* 3.0 52.3 + - + +
282K ASP* 3.6 17.1 + - + +
329K LYS* 2.7 34.8 + - - +
275M ARG 2.8 19.9 + - - +
276M ARG 4.5 8.7 - - - +
277M GLU 5.0 2.2 - - - +
278M PHE* 1.3 80.6 - - - +
280M ARG* 1.3 58.9 + - - +
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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