Contacts of the helix formed by residues 267 - 281 (chain A) in PDB entry 4OMC
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 ALA 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASP* 3.3 32.3 + - + +
265A GLY 3.6 2.6 + - - -
266A PRO* 1.3 74.8 - - - +
268A ARG* 1.3 67.0 + - - +
270A ALA* 3.2 3.2 + - - +
271A GLU* 3.0 22.4 + - - +
530B ASP* 5.6 2.2 - - - +
1H 2UC 3.8 14.8 + - - +
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASP* 3.8 0.4 + - - -
267A ALA* 1.3 76.1 - - - +
269A LEU* 1.3 56.4 + - - +
271A GLU* 3.2 17.5 + - - +
272A GLU* 2.8 38.9 + - - +
268B ARG* 5.2 16.7 - - - +
271B GLU* 3.3 35.4 + - - -
490B ARG* 3.1 33.2 - - - +
529B ASN 5.4 2.2 + - - -
530B ASP* 3.5 22.8 + - - +
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASP* 2.8 25.0 + - + +
234A ALA* 3.9 22.9 - - + +
237A ALA* 3.5 15.9 - - + +
268A ARG* 1.3 73.9 - - - +
270A ALA* 1.3 57.8 + - - +
272A GLU* 3.2 21.0 + - - +
273A ALA* 2.8 28.2 + - - +
449B LYS* 4.3 6.4 + - - +
451B ILE* 4.0 26.6 - - + +
488B GLN* 5.6 0.2 - - - +
490B ARG* 3.9 29.4 - - - +
565B LYS* 6.1 2.5 - - - -
567B THR* 4.1 14.6 - - + +
569B VAL* 4.2 12.8 - - + -
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ASP* 2.9 19.1 + - - +
236A GLU* 3.8 25.8 - - + +
237A ALA* 3.9 9.4 - - - +
240A LEU* 4.3 9.2 - - + +
266A PRO* 3.6 22.4 - - + -
267A ALA 3.6 0.4 - - - +
269A LEU* 1.3 73.1 - - - +
271A GLU* 1.3 66.7 + - - +
273A ALA* 3.1 6.3 + - - +
274A PHE* 2.9 27.1 + - - -
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Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PRO* 3.7 26.6 - - + +
267A ALA 3.0 19.0 + - - +
268A ARG* 3.5 22.5 + - - +
270A ALA* 1.3 76.2 - - - +
272A GLU* 1.3 63.7 + - + +
274A PHE* 3.0 13.8 + - - +
275A PHE* 2.9 24.6 + - - +
313A TYR* 5.1 3.0 - - + -
268B ARG* 5.2 15.8 + - - +
271B GLU* 5.6 2.0 - - - +
272B GLU* 5.3 4.3 - - - +
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ARG* 2.8 21.0 + - + +
269A LEU* 3.5 21.4 - - - +
271A GLU* 1.3 77.5 - - + +
273A ALA* 1.3 58.0 + - - +
275A PHE* 3.7 6.3 - - - +
276A ARG* 2.8 37.1 + - - +
275B PHE* 5.0 6.3 - - + -
313B TYR* 4.3 6.3 + - - +
449B LYS* 2.7 35.6 + - - +
488B GLN* 5.5 1.9 + - - -
490B ARG* 4.3 13.1 + - - -
571B TYR* 4.1 5.5 + - - -
602B FMT 3.8 18.2 - - - +
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ALA* 3.8 27.6 - - + +
240A LEU* 3.9 18.1 - - + +
241A GLY* 4.4 7.6 - - - +
269A LEU 2.8 13.6 + - - +
270A ALA 3.3 8.5 - - - +
272A GLU* 1.3 77.2 - - - +
274A PHE* 1.3 56.9 + - - +
276A ARG* 3.9 9.6 - - - +
277A GLY* 2.8 27.7 + - - -
289A PHE* 4.3 4.8 - - - -
449B LYS* 5.3 0.4 - - - +
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 3.9 18.2 - - + -
266A PRO* 4.3 14.1 - - + -
270A ALA 2.9 21.5 + - - -
271A GLU* 3.4 11.0 - - - +
273A ALA* 1.3 76.9 - - - +
275A PHE* 1.3 57.4 + - - +
277A GLY* 3.2 2.4 + - - -
278A VAL* 3.0 33.3 + - - +
289A PHE* 3.6 38.4 - + - -
291A TRP* 3.5 30.1 - + - -
308A TYR* 4.0 22.4 - + + -
311A SER* 5.2 5.4 - - - -
313A TYR* 3.7 24.2 - + + -
314A THR* 3.6 26.0 - - + -
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Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLU* 2.9 15.1 + - + +
272A GLU* 3.7 5.6 - - - +
274A PHE* 1.3 75.2 - - - +
276A ARG* 1.3 63.6 + - - +
278A VAL* 3.6 7.4 + - + +
279A SER* 2.8 38.9 + - - -
313A TYR* 3.3 24.8 - + + +
603A FMT 4.1 15.0 - - - -
604A FMT 3.6 24.9 - - - -
272B GLU* 4.1 15.3 - - + -
275B PHE* 3.3 50.7 - + + -
276B ARG* 3.9 20.9 - - + -
280B GLN* 4.7 3.1 - - - -
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Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PRO* 6.3 0.4 - - - -
272A GLU 2.8 31.0 + - - +
273A ALA* 3.9 7.2 - - - +
275A PHE* 1.3 72.1 - - - +
277A GLY* 1.3 55.5 + - - +
280A GLN* 2.7 58.8 + - - +
281A GLY 3.4 4.0 + - - -
275B PHE* 3.8 11.2 - - + -
447B GLN* 2.6 49.7 + - - -
448B ARG* 4.5 0.2 - - - +
449B LYS* 3.8 35.0 - - - +
571B TYR* 4.3 0.8 - - - -
601B FMT 3.5 9.7 + - - -
602B FMT 3.0 30.5 + - - +
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Residues in contact with GLY 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A LEU 5.9 0.4 - - - -
244A PRO* 5.5 4.9 - - - -
273A ALA 2.8 16.1 + - - -
274A PHE 3.5 4.7 - - - -
275A PHE 3.1 0.2 - - - -
276A ARG* 1.3 77.9 - - - +
278A VAL* 1.3 58.1 + - - +
281A GLY* 2.9 20.1 + - - -
287A SER* 2.8 39.8 + - - -
289A PHE* 4.1 4.3 - - - -
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A PHE 3.0 15.4 + - - +
275A PHE* 3.6 11.7 - - + +
277A GLY* 1.3 76.5 - - - +
279A SER* 1.3 64.8 + - - +
284A GLY 4.4 1.6 - - - +
285A LEU 4.3 0.7 - - - +
286A GLY* 3.2 22.3 + - - -
287A SER 4.0 8.5 - - - +
289A PHE* 4.0 11.4 - - + -
313A TYR* 3.8 45.5 - - + +
390A TRP* 3.3 41.1 + - + +
603A FMT 4.3 8.3 - - - -
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A PHE* 2.8 39.6 + - - -
278A VAL* 1.3 81.6 - - - +
280A GLN* 1.3 80.7 + - - +
284A GLY* 3.6 20.9 - - - +
603A FMT 5.1 0.3 - - - -
275B PHE* 4.1 1.9 - - - -
279B SER* 4.1 11.2 + - - -
280B GLN* 4.0 13.3 + - - +
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A PRO* 5.5 1.3 - - + -
245A ASN* 3.8 8.1 + - - +
276A ARG* 2.7 43.6 + - - +
279A SER* 1.3 92.1 - - - +
281A GLY* 1.3 68.3 + - - +
282A ARG 3.7 0.2 + - - -
283A GLY* 3.6 4.0 + - - -
284A GLY* 3.1 13.4 + - - -
275B PHE* 4.0 14.1 - - - -
279B SER* 4.0 7.3 + - - +
447B GLN* 4.7 2.1 - - - +
601B FMT 3.5 25.1 + - - +
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Residues in contact with GLY 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A PRO* 3.7 20.8 - - - +
245A ASN* 4.6 0.2 - - - -
276A ARG 3.4 3.0 + - - -
277A GLY 2.9 19.9 + - - -
280A GLN* 1.3 81.5 - - - +
282A ARG* 1.3 68.4 + - - -
284A GLY 2.9 3.5 + - - -
286A GLY 2.8 20.8 + - - -
287A SER* 3.7 9.4 - - - -
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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