Contacts of the helix formed by residues 259 - 268 (chain A) in PDB entry 2DFS
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 TYR 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A SER 3.9 4.5 - - - +
206A ILE 3.3 13.7 - - - +
207A GLY* 3.4 23.6 - - - -
208A ASN 3.5 17.3 - - - -
209A ALA* 4.0 3.1 - - + +
219A ARG* 3.9 9.8 - - + +
244A LEU* 3.3 19.4 - - + +
245A GLU* 2.7 41.1 + - - +
248A ARG* 4.0 17.2 - - + +
249A VAL* 3.9 15.9 - - + -
258A ASN* 1.3 100.2 + - - +
260A HIS* 1.4 67.0 + - - +
261A ILE* 3.2 2.3 + - + -
262A PHE* 3.4 18.5 + - + -
263A TYR* 3.7 5.0 - - - -
408A TYR* 3.4 34.5 - + - +
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Residues in contact with HIS 260 (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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204A GLU* 3.5 12.8 - - + -
205A SER* 3.3 8.4 + - - +
208A ASN* 3.1 33.1 + - + +
209A ALA* 3.6 20.6 + - - -
210A LYS 4.0 1.5 + - - -
215A ASP 3.7 20.2 - - - -
216A ASN* 4.0 17.6 + - + -
257A ARG* 3.7 17.9 + - - +
258A ASN 3.6 2.5 + - - -
259A TYR* 1.4 71.4 - - - +
261A ILE* 1.4 57.7 + - - +
263A TYR* 2.9 28.3 + - - +
264A GLN* 3.1 28.0 + - + +
296A ILE* 3.9 13.9 - - + -
301A ASP* 4.9 0.8 + - - +
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Residues in contact with ILE 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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205A SER* 2.9 43.9 + - - +
206A ILE* 4.2 9.4 - - + -
259A TYR 4.5 0.4 - - - +
260A HIS* 1.4 70.1 - - - +
262A PHE* 1.3 66.5 + - + +
264A GLN* 3.2 9.0 + - - +
265A LEU* 3.0 28.9 + - + +
305A MET* 3.8 30.1 - - + -
308A THR* 4.2 10.5 - - + -
325A ILE* 6.1 0.7 - - + -
326A PHE* 4.4 7.9 - - + -
329A LEU* 3.6 35.2 - - + -
408A TYR* 4.0 17.9 - - - +
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Residues in contact with PHE 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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249A VAL* 4.8 4.9 - - + -
258A ASN* 3.5 33.0 - - - -
259A TYR* 3.4 21.7 + + + +
260A HIS 3.1 0.6 + - - -
261A ILE* 1.3 77.5 - - + +
263A TYR* 1.3 58.0 + - + +
265A LEU* 3.5 8.3 - - - +
266A CYS* 3.1 31.2 + - - -
287A TYR* 6.3 0.9 - + - -
288A THR* 3.8 19.3 - - + -
329A LEU* 3.8 35.0 - - + -
332A ILE* 4.6 14.8 - - + -
333A LEU* 3.6 29.5 - - + +
408A TYR* 3.5 40.8 - + - -
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Residues in contact with TYR 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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252A GLN* 4.3 1.4 + - - -
256A GLU 5.0 0.5 + - - -
257A ARG* 3.3 63.3 - - + +
258A ASN* 3.2 44.4 + - + -
259A TYR 3.7 11.2 - - - -
260A HIS* 2.9 8.9 + - - +
262A PHE* 1.3 72.0 - - - +
264A GLN* 1.3 60.3 + - - +
266A CYS* 3.2 5.8 + - - +
267A ALA* 3.0 31.9 + - - +
282A ALA* 3.9 17.5 - - + -
288A THR* 2.8 49.0 + - + -
293A SER 4.5 4.1 + - - -
294A PRO* 3.6 9.4 - - + -
301A ASP* 3.9 7.9 - - - +
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Residues in contact with GLN 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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205A SER* 3.3 13.7 - - - -
260A HIS* 3.1 36.4 - - + +
261A ILE* 3.2 12.8 + - - +
263A TYR* 1.3 74.5 - - - +
265A LEU* 1.3 57.1 + - - +
267A ALA* 3.8 0.9 + - - +
268A SER* 2.7 32.9 + - - -
301A ASP* 3.5 35.1 - - - +
304A GLU* 3.3 25.5 + - + +
305A MET* 3.5 16.5 - - - +
308A THR* 3.0 27.3 + - - -
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Residues in contact with LEU 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 ILE* 3.0 17.6 + - + +
262A PHE* 3.5 7.9 - - - +
263A TYR 3.2 0.2 - - - -
264A GLN* 1.3 74.1 - - - +
266A CYS* 1.4 63.8 + - - +
268A SER* 3.2 13.0 + - - -
269A ALA 3.3 8.8 + - - -
274A PHE* 4.2 10.0 - - + -
277A LEU* 3.8 20.4 - - + -
279A LEU* 3.7 23.7 - - + +
305A MET* 3.9 23.0 - - + -
326A PHE* 3.9 28.7 - - + +
329A LEU* 4.2 13.0 - - + -
330A ALA* 4.0 13.9 - - - +
333A LEU* 4.3 14.1 - - + -
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Residues in contact with CYS 266 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A PHE 3.1 21.3 + - - +
263A TYR* 3.2 8.7 + - + +
265A LEU* 1.4 73.6 - - - +
267A ALA* 1.3 62.4 + - - +
269A ALA* 3.2 21.4 - - - +
279A LEU* 4.7 3.6 - - - -
280A GLY 3.8 23.8 - - - +
281A ASN* 4.4 3.1 - - - -
282A ALA* 4.2 25.1 - - + +
285A PHE* 4.2 23.1 - - - -
288A THR* 4.7 5.4 - - - -
333A LEU* 4.4 9.0 - - - -
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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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263A TYR 3.0 16.5 + - - +
264A GLN 4.2 0.9 - - - +
266A CYS* 1.3 75.5 - - - +
268A SER* 1.3 57.6 + - - +
269A ALA 3.4 1.8 + - - -
270A ALA 5.1 1.0 + - - -
271A LEU* 5.6 0.2 - - - +
301A ASP* 3.9 9.4 - - + +
302A ALA* 3.9 34.5 - - + +
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Residues in contact with SER 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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264A GLN 2.7 22.5 + - - -
265A LEU* 3.2 8.8 + - - -
266A CYS 3.2 0.8 - - - -
267A ALA* 1.3 76.4 - - - +
269A ALA* 1.3 59.9 + - - +
270A ALA 3.5 2.5 - - - -
271A LEU* 3.3 41.9 - - - +
274A PHE* 3.4 24.1 - - - -
302A ALA* 3.9 11.1 + - - +
305A MET* 3.5 19.6 - - - +
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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