Contacts of the helix formed by residues 264 - 271 (chain A) in PDB entry 3FIE
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 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A THR* 3.4 15.9 + - - +
246A GLU* 2.9 36.4 + - + +
247A THR* 4.0 1.3 - - - +
248A ILE* 3.8 33.0 - - + -
262A ILE 4.4 0.9 - - - +
263A ARG* 1.3 72.1 - - - +
265A GLU* 1.3 57.0 - - - +
267A PHE* 3.0 10.2 + - + +
268A LEU* 2.8 41.4 + - + +
278A ILE* 3.4 45.3 - - + -
282A MET* 3.9 22.7 - - + -
286A ILE* 5.0 3.1 - - + -
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Residues in contact with GLU 265 (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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231A HIS* 2.8 25.4 + - + +
234A HIS* 2.7 38.7 + - - +
239A ALA 4.9 0.3 - - - +
240A ARG* 4.6 6.5 - - - +
243A THR* 2.9 50.1 + - - +
244A TYR* 4.0 5.8 - - + +
263A ARG* 3.1 9.8 - - + +
264A LEU* 1.3 76.7 - - - +
266A GLU* 1.3 59.4 - - - +
268A LEU* 3.7 3.0 + - - +
269A THR* 2.9 31.5 + - - -
349A TYR* 4.9 1.2 + - - -
57C ASP* 3.3 26.9 - - - +
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Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A HIS* 4.9 0.2 - - - -
231A HIS* 3.7 3.6 - - - -
262A ILE* 3.9 7.6 - - + -
263A ARG* 2.9 54.5 + - + +
265A GLU* 1.3 75.8 - - - +
267A PHE* 1.3 60.4 + - - +
269A THR* 3.3 1.4 + - - -
270A PHE* 2.9 33.4 + - - +
368A TYR* 2.8 44.1 + - + +
428A ZN 2.1 37.8 - - - -
57C ASP* 3.5 3.1 - - - -
58C DCY 3.3 10.0 + - - -
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Residues in contact with PHE 267 (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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248A ILE* 4.2 9.9 - - + -
250A VAL* 3.7 28.7 - - + -
262A ILE* 3.6 43.1 - - + -
263A ARG 3.4 13.4 + - - -
264A LEU* 3.0 16.0 + - + +
266A GLU* 1.3 78.6 - - - +
268A LEU* 1.3 56.0 + - - +
270A PHE* 4.8 3.1 - - - -
271A GLY* 3.0 29.5 + - - +
274A ASP* 3.8 35.8 - - + +
275A LEU* 3.7 7.1 - - - +
277A ILE* 3.6 34.8 - - + -
278A ILE* 4.1 8.1 - - + -
368A TYR* 4.6 9.6 - + + -
369A PHE 5.7 1.3 - - - -
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Residues in contact with LEU 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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234A HIS* 4.9 1.7 - - + -
243A THR* 3.6 31.6 - - + -
264A LEU* 2.8 23.9 + - + +
265A GLU* 4.1 4.0 - - - +
267A PHE* 1.3 73.5 - - - +
269A THR* 1.3 62.7 + - - +
271A GLY* 4.7 0.2 - - - -
275A LEU* 4.3 12.3 - - + +
278A ILE* 3.6 25.4 - - + -
283A LYS* 5.9 4.7 - - + -
286A ILE* 3.9 16.6 - - + -
345A TYR* 6.1 1.1 - - - +
349A TYR* 4.0 44.1 - - + +
351A PHE 4.0 3.1 - - - +
352A THR* 3.5 19.2 - - - +
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Residues in contact with THR 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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227A HIS* 3.6 31.9 - - + +
230A ILE* 3.5 26.2 - - + -
231A HIS* 3.2 17.2 + - + +
234A HIS* 3.3 10.6 - - - -
265A GLU* 2.9 38.8 + - - -
266A GLU 3.3 2.2 + - - -
268A LEU* 1.3 77.9 - - - +
270A PHE* 1.3 58.9 + - - +
351A PHE 4.5 0.2 - - - -
352A THR* 3.1 7.6 - - - -
353A GLU* 2.9 22.3 + - - +
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Residues in contact with PHE 270 (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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227A HIS* 4.1 3.1 - - + -
266A GLU 2.9 17.4 + - - +
267A PHE* 4.3 2.2 - - - +
269A THR* 1.3 77.1 - - - +
271A GLY* 1.3 70.6 + - - +
274A ASP* 3.8 3.8 - - + -
352A THR* 3.5 0.6 - - - -
353A GLU* 3.3 25.9 + - - +
354A ILE* 2.9 43.1 + - + +
364A CYS* 4.0 11.4 - - - -
365A ARG* 3.4 51.8 - - + -
366A ASN 3.5 12.6 - - - -
367A THR* 3.3 13.7 - - - -
368A TYR* 3.3 40.6 - + + -
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Residues in contact with GLY 271 (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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267A PHE 3.0 16.5 + - - -
269A THR 3.5 1.8 - - - -
270A PHE* 1.3 91.6 - - - +
272A GLY* 1.3 67.3 + - - +
274A ASP* 3.7 13.5 + - - +
275A LEU* 3.8 13.5 - - - -
352A THR* 3.7 18.4 - - - -
354A ILE* 4.1 0.9 - - - -
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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