Contacts of the helix formed by residues 252 - 265 (chain A) in PDB entry 2H0A
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 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A VAL* 4.3 7.0 - - + -
198A PHE* 4.7 3.6 - - + -
201A ARG* 4.8 1.3 - - - +
226A HIS* 3.5 34.3 - - + +
250A ALA* 3.2 8.7 - - - +
251A GLY* 1.3 80.6 - - - +
253A ASP* 1.3 65.6 + - - +
254A GLN 3.3 0.2 - - - -
255A VAL* 3.3 12.5 + - + +
256A ALA 3.0 17.7 + - - -
279A PHE 3.5 12.1 - - - +
280A ASP* 4.5 5.8 - - - +
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Residues in contact with ASP 253 (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 ALA* 1.3 72.0 - - - +
254A GLN* 1.3 63.2 + - - +
256A ALA* 3.1 7.5 + - - +
257A LEU* 2.9 26.5 + - - +
278A GLY* 3.4 2.9 - - - -
279A PHE 2.7 33.1 + - - +
280A ASP* 3.2 4.3 + - - +
281A GLY* 2.9 11.1 + - - -
282A HIS* 2.8 36.3 + - + -
284A PHE* 3.6 23.5 - - + -
285A ALA* 4.3 4.1 - - - +
290A LEU* 3.8 9.2 - - + +
292A THR* 2.8 21.9 + - - -
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Residues in contact with GLN 254 (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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76A GLU* 5.8 3.2 - - - +
226A HIS* 3.6 35.5 + - + +
227A SER* 4.1 17.9 - - - -
228A GLN* 2.9 52.4 - - - +
252A ALA* 3.3 1.0 - - - +
253A ASP* 1.3 77.0 - - - +
255A VAL* 1.3 62.5 + - + +
257A LEU* 3.3 20.5 + - - +
282A HIS* 5.1 3.4 - - + -
284A PHE* 3.9 25.4 - - + -
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Residues in contact with VAL 255 (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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183A ILE* 3.7 32.3 - - + -
185A VAL* 4.3 9.0 - - + -
224A THR* 4.9 0.7 - - + -
225A ARG 4.0 7.9 - - - +
226A HIS* 4.1 7.0 - - + -
227A SER 3.3 28.0 - - - +
230A GLY 4.4 1.1 - - - -
231A GLY* 3.4 26.0 - - - +
250A ALA* 4.2 6.5 - - - +
252A ALA* 3.3 23.1 + - + +
253A ASP 3.2 0.2 - - - -
254A GLN* 1.3 72.6 - - - +
256A ALA* 1.3 61.6 + - - +
258A GLY* 2.9 17.8 + - - -
259A VAL* 3.1 11.4 + - - +
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Residues in contact with ALA 256 (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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250A ALA* 3.3 25.5 - - + +
252A ALA 3.0 9.2 + - - +
253A ASP 3.3 9.9 - - - +
255A VAL* 1.3 74.3 - - - +
257A LEU* 1.3 59.3 + - - +
259A VAL* 3.4 3.5 + - - +
260A LEU* 3.0 29.9 + - - +
276A VAL* 3.8 17.6 - - + +
278A GLY* 3.9 4.5 - - - -
290A LEU* 3.4 23.6 - - + -
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Residues in contact with LEU 257 (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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228A GLN* 3.8 26.6 + - - +
253A ASP 2.9 8.2 + - - +
254A GLN* 3.4 14.1 - - - +
255A VAL 3.1 0.4 - - - -
256A ALA* 1.3 76.7 - - - +
258A GLY* 1.3 58.1 + - - +
260A LEU* 3.4 11.7 - - + +
261A GLU* 2.8 30.6 + - - +
284A PHE* 3.3 44.4 - - + -
288A ALA* 3.8 29.6 - - + -
290A LEU* 4.7 4.0 - - + -
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Residues in contact with GLY 258 (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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228A GLN* 3.2 31.1 - - - +
232A ARG* 3.2 18.7 - - - +
254A GLN 3.6 3.8 + - - -
255A VAL 2.9 6.1 + - - -
257A LEU* 1.3 78.3 - - - +
259A VAL* 1.3 56.6 + - - +
261A GLU* 4.1 3.6 - - - -
262A GLU* 2.7 31.9 + - - +
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Residues in contact with VAL 259 (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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183A ILE* 3.6 25.1 - - + -
231A GLY 3.6 18.8 - - - +
235A LEU* 3.3 22.4 - - + +
248A VAL* 4.2 14.8 - - + -
250A ALA* 4.8 0.4 - - + -
255A VAL 3.1 14.5 + - - +
256A ALA* 3.8 10.5 - - - +
257A LEU 3.4 0.2 - - - -
258A GLY* 1.3 75.0 - - - +
260A LEU* 1.3 57.6 + - - +
263A ALA* 3.0 30.7 + - - +
274A VAL* 4.0 12.1 - - + -
276A VAL* 3.7 23.1 - - + -
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Residues in contact with LEU 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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256A ALA 3.0 15.7 + - - +
257A LEU* 3.4 11.4 - - + +
259A VAL* 1.3 78.6 - - - +
261A GLU* 1.3 61.4 + - - +
263A ALA* 3.3 4.0 + - - +
264A VAL* 3.1 31.1 + - + +
269A THR* 3.2 32.3 + - + -
276A VAL* 3.5 23.8 - - + -
288A ALA* 3.8 31.0 - - + +
290A LEU* 4.2 21.3 - - + -
333A SER* 3.6 12.8 - - - -
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Residues in contact with GLU 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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228A GLN* 3.5 21.9 + - - +
232A ARG* 3.0 40.3 + - - -
257A LEU 2.8 21.5 + - - +
258A GLY* 3.5 3.6 - - - +
260A LEU* 1.3 74.2 - - - +
262A GLU* 1.3 57.6 + - - +
264A VAL* 3.3 7.9 + - - +
265A ARG* 3.0 29.9 + - + +
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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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232A ARG* 3.1 47.7 + - + +
235A LEU* 3.9 14.6 - - + -
236A ARG* 4.0 21.6 + - + +
239A LEU* 6.0 0.7 - - + -
258A GLY 2.7 19.7 + - - +
261A GLU* 1.3 70.9 - - - +
263A ALA* 1.3 66.5 + - - +
265A ARG* 3.0 45.8 + - - -
266A LEU* 2.9 35.9 - - + +
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Residues in contact with ALA 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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235A LEU* 3.5 8.2 - - + +
259A VAL 3.0 21.0 + - - +
260A LEU* 3.5 6.5 - - - +
261A GLU 3.2 0.2 - - - -
262A GLU* 1.3 77.0 - - - +
264A VAL* 1.3 50.7 + - - +
266A LEU* 2.6 27.3 + - - +
267A GLY 2.7 25.2 + - - +
268A LEU 4.6 0.9 - - - +
269A THR* 4.3 9.2 - - + +
273A ASP* 3.2 27.8 - - - +
274A VAL* 4.3 5.2 - - + -
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Residues in contact with VAL 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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260A LEU* 3.1 17.6 + - + +
261A GLU* 3.6 9.0 - - - +
263A ALA* 1.3 69.6 - - - +
265A ARG* 1.3 54.6 + - - +
266A LEU* 2.5 24.4 + - - +
267A GLY 4.0 7.3 + - - -
269A THR* 3.2 19.5 - - + +
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Residues in contact with ARG 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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232A ARG* 3.3 18.8 - - - +
236A ARG* 5.4 8.9 - - - +
261A GLU* 3.0 18.5 + - + +
262A GLU* 3.0 49.3 + - - +
263A ALA 3.2 0.4 - - - -
264A VAL* 1.3 74.1 - - - +
266A LEU* 1.3 75.3 + - + +
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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