Contacts of the helix formed by residues 260 - 273 (chain A) in PDB entry 4ERO
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 THR 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ILE* 4.0 9.4 - - - +
258A MET 3.8 0.2 - - - -
259A ASN* 1.3 90.2 - - + +
261A ASN* 1.3 57.9 + - - +
262A GLU* 3.9 9.0 + - - +
263A GLU* 2.9 45.8 + - - +
264A ILE* 2.9 15.4 + - - +
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Residues in contact with ASN 261 (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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251A ILE* 3.7 27.2 - - - +
260A THR* 1.3 72.3 - - - +
262A GLU* 1.3 62.7 + - - +
264A ILE* 3.2 6.7 + - - +
265A SER* 2.9 27.2 + - - -
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Residues in contact with GLU 262 (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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260A THR* 3.9 9.1 + - - +
261A ASN* 1.3 77.2 - - - +
263A GLU* 1.3 56.3 + - + +
265A SER* 3.5 8.6 + - - -
266A GLN* 3.0 35.8 + - + +
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Residues in contact with GLU 263 (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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59A ARG* 5.2 1.0 + - - -
122A SER* 4.9 5.9 + - - +
125A LYS* 5.6 0.3 - - - +
258A MET* 3.3 31.5 - - + +
259A ASN* 2.6 48.3 + - - +
260A THR* 2.9 32.1 + - - +
262A GLU* 1.3 73.5 - - + +
264A ILE* 1.3 65.4 + - - +
266A GLN* 3.5 6.6 + - - +
267A ALA* 3.2 21.3 + - - +
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Residues in contact with ILE 264 (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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251A ILE* 3.4 35.0 - - + +
253A HIS* 3.8 31.6 - - + +
256A PHE* 3.7 24.2 - - + +
258A MET* 3.5 37.5 - - + +
260A THR 2.9 11.1 + - - +
261A ASN* 3.2 8.0 + - - +
263A GLU* 1.3 74.1 - - - +
265A SER* 1.3 58.4 + - - +
267A ALA* 2.9 21.0 + - - +
268A ILE* 3.1 19.0 + - + +
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Residues in contact with SER 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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261A ASN 2.9 17.4 + - - -
262A GLU* 3.5 11.4 - - - -
264A ILE* 1.3 78.5 - - - +
266A GLN* 1.3 56.9 + - - +
268A ILE* 3.7 13.0 - - - +
269A LEU* 3.2 34.8 + - - +
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Residues in contact with GLN 266 (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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59A ARG* 4.2 2.2 - - - +
262A GLU* 3.0 23.4 + - + +
263A GLU* 3.9 7.2 - - - +
265A SER* 1.3 75.1 - - - +
267A ALA* 1.3 55.1 + - - +
269A LEU* 4.3 17.8 - - - +
270A ASP* 2.7 70.1 + - - +
276A ASN* 4.5 6.1 - - - +
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Residues in contact with ALA 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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59A ARG* 3.3 29.1 - - - +
256A PHE* 3.6 36.3 - - + -
258A MET* 4.8 2.0 - - + -
263A GLU 3.2 11.4 + - - +
264A ILE* 2.9 11.7 + - - +
266A GLN* 1.3 74.9 - - - +
268A ILE* 1.3 66.0 + - - +
270A ASP* 3.6 1.2 - - - +
271A PHE* 3.0 27.4 + - - +
278A PHE* 4.2 0.5 - - - -
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Residues in contact with ILE 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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253A HIS* 3.8 31.0 - - + +
256A PHE* 3.9 22.2 - - + -
264A ILE* 3.1 19.1 + - + +
265A SER* 3.7 12.8 - - - +
267A ALA* 1.3 75.8 - - - +
269A LEU* 1.3 65.7 + - + +
271A PHE* 3.8 2.1 - - - +
272A ARG* 3.1 28.4 + - + +
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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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265A SER* 3.2 22.9 + - - +
266A GLN* 3.6 19.5 - - - +
267A ALA 3.2 0.4 - - - -
268A ILE* 1.3 79.6 - - + +
270A ASP* 1.3 58.7 + - - +
271A PHE 3.1 0.3 + - - -
272A ARG* 3.3 5.5 + - + -
273A ASN* 2.8 52.6 + - - +
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Residues in contact with ASP 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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59A ARG* 2.6 44.6 + - - +
126A MET* 4.8 2.3 - - - +
266A GLN* 2.7 48.8 + - - +
267A ALA 3.6 2.5 - - - +
269A LEU* 1.3 72.3 - - - +
271A PHE* 1.3 57.7 + - - +
274A ALA* 3.1 5.7 + - - -
275A LYS* 2.6 38.2 + - - +
276A ASN* 3.0 32.6 + - - +
278A PHE* 3.5 4.0 - - + +
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Residues in contact with PHE 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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57A PRO* 3.6 37.7 - - + -
100A LEU* 3.6 19.5 - - + -
256A PHE* 3.8 17.5 - + + -
267A ALA 3.0 17.5 + - - +
268A ILE 3.8 2.5 - - - +
270A ASP* 1.3 76.1 - - - +
272A ARG* 1.3 70.7 + - + +
273A ASN 3.2 0.2 - - - -
274A ALA* 3.1 12.8 + - - +
278A PHE* 3.5 27.7 - + + -
281A ALA* 4.2 18.9 - - + +
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Residues in contact with ARG 272 (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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268A ILE* 3.1 21.6 + - + +
269A LEU* 3.9 3.6 - - - +
271A PHE* 1.3 84.5 - - + +
273A ASN* 1.3 71.3 + - - +
274A ALA* 3.6 0.9 + - - +
282A LYS* 5.5 2.3 - - - -
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Residues in contact with ASN 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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269A LEU* 2.8 33.8 + - - +
272A ARG* 1.3 89.3 - - - +
274A ALA* 1.3 71.4 + - - +
275A LYS* 3.3 22.3 - - + +
282A LYS* 3.3 19.3 + - - +
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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