Contacts of the helix formed by residues 251 - 265 (chain A) in PDB entry 4PAR
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 ASP 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A SER* 3.4 2.8 + - - +
250A THR* 1.3 89.1 + - - +
252A GLU* 1.3 63.6 + - - +
253A THR* 3.4 11.2 + - + +
254A ILE* 3.5 28.0 + - + +
255A THR* 3.2 22.9 + - - +
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Residues in contact with GLU 252 (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 LYS* 5.2 16.5 + - - -
249A SER 5.6 0.2 - - - +
250A THR 3.6 6.1 + - - +
251A ASP* 1.3 68.8 - - - +
253A THR* 1.3 63.1 + - + +
255A THR* 2.3 32.6 + - + +
256A LEU* 2.9 24.4 + - + +
298A LEU* 5.0 15.9 - - + +
299A LYS 6.4 0.2 - - - +
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Residues in contact with THR 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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251A ASP* 3.8 10.2 + - + +
252A GLU* 1.3 80.4 - - + +
254A ILE* 1.3 75.2 + - - +
256A LEU* 3.1 14.0 + - + +
257A LYS* 2.9 28.3 + - - +
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Residues in contact with ILE 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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234A TRP* 5.0 12.3 - - + -
249A SER* 3.1 35.0 - - - +
251A ASP* 3.6 24.9 - - + +
252A GLU 3.3 0.2 - - - -
253A THR* 1.3 78.5 - - - +
255A THR* 1.3 63.8 + - - +
257A LYS* 3.3 19.4 - - + +
258A LYS* 2.9 36.5 + - + +
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Residues in contact with THR 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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248A LYS* 4.2 12.3 - - + -
249A SER* 3.4 36.1 - - - +
251A ASP 3.2 15.7 - - - +
252A GLU* 2.3 33.7 + - + +
254A ILE* 1.3 77.8 - - - +
256A LEU* 1.3 62.8 + - - +
258A LYS* 3.3 5.4 + - - +
259A LEU* 2.9 31.7 + - - +
262A TRP* 4.3 14.0 - - + -
297A ASP 5.4 6.5 + - - +
298A LEU* 5.7 4.9 - - - +
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Residues in contact with LEU 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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252A GLU* 2.9 25.2 + - + +
253A THR* 3.3 14.4 - - + +
255A THR* 1.3 87.7 + - - +
257A LYS* 1.3 59.9 + - - +
259A LEU* 3.4 27.6 + - + +
260A GLU* 4.2 5.0 + - - +
297A ASP 5.9 2.0 - - - +
298A LEU* 5.6 9.6 - - + -
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Residues in contact with LYS 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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253A THR 2.9 9.5 + - - +
254A ILE* 3.3 30.3 - - + +
256A LEU* 1.3 77.7 - - - +
258A LYS* 1.3 65.5 + - + +
259A LEU 3.3 0.2 - - - -
260A GLU* 3.4 26.9 - - - +
261A GLU* 4.1 4.9 + - - +
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Residues in contact with LYS 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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234A TRP* 6.3 4.3 - - + -
247A GLU* 5.8 1.6 - - - +
254A ILE* 2.9 26.1 + - + +
255A THR* 3.6 4.7 - - - +
256A LEU 3.2 0.2 - - - -
257A LYS* 1.3 79.4 - - + +
259A LEU* 1.3 59.2 + - - +
260A GLU 3.5 0.2 - - - -
261A GLU* 3.3 33.8 + - + +
262A TRP* 2.9 61.6 + - + +
269A ARG* 5.0 7.6 - - - +
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Residues in contact with LEU 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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255A THR 2.9 15.7 + - - +
256A LEU* 3.4 20.6 - - + +
257A LYS 3.3 0.8 - - - -
258A LYS* 1.3 75.6 - - - +
260A GLU* 1.3 62.0 + - + +
262A TRP* 3.2 14.4 + - + +
263A LYS* 2.9 49.5 + - + +
296A ALA* 3.6 23.7 - - + +
297A ASP* 3.6 34.5 - - - +
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Residues in contact with GLU 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 LEU 4.2 2.9 + - - +
257A LYS* 3.4 24.2 - - - +
259A LEU* 1.3 79.8 - - + +
261A GLU* 1.3 63.2 - - - +
263A LYS* 3.0 9.3 + - - +
264A ASN* 2.9 33.7 + - - +
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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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257A LYS 4.2 3.8 - - - +
258A LYS* 3.3 51.5 + - + +
260A GLU* 1.3 83.5 - - + +
262A TRP* 1.3 59.3 + - + +
264A ASN* 3.0 18.9 + - - +
265A GLY 2.9 36.8 + - - +
266A PRO* 5.1 2.4 - - - +
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Residues in contact with TRP 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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234A TRP* 6.5 0.2 - + - -
247A GLU* 3.6 46.8 + - + -
248A LYS* 4.6 8.5 - - - -
249A SER* 6.3 0.2 - - - -
255A THR* 4.3 22.2 - - + -
258A LYS* 2.9 46.8 + - + +
259A LEU* 3.4 17.3 - - + +
261A GLU* 1.3 79.6 - - + +
263A LYS* 1.3 62.0 + - - +
264A ASN 3.5 0.2 + - - -
265A GLY* 3.7 3.6 + - - -
266A PRO 5.1 1.9 - - - +
267A GLN* 3.1 16.3 - - - +
269A ARG* 3.8 21.2 - - - +
293A PHE* 3.8 26.6 - + + -
296A ALA* 5.4 3.6 - - + -
297A ASP 5.2 4.3 - - - -
301A GLY* 4.6 4.5 - - - -
302A ALA* 3.5 37.7 - - + -
304A TRP* 4.2 9.9 - + - -
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Residues in contact with LYS 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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259A LEU* 2.9 32.5 + - + +
260A GLU* 3.0 9.8 + - - +
262A TRP* 1.3 78.1 - - - +
264A ASN* 1.3 60.7 + - - +
267A GLN* 3.5 9.9 + - - +
293A PHE* 4.4 12.2 - - + -
296A ALA* 3.6 30.3 - - + +
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Residues in contact with ASN 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 GLU 2.9 26.2 + - - +
261A GLU* 3.0 24.7 + - - +
263A LYS* 1.3 79.9 - - - +
265A GLY* 1.3 80.4 + - - +
267A GLN* 3.7 8.2 - - - +
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Residues in contact with GLY 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 GLU* 2.9 26.4 + - - +
262A TRP* 3.7 2.2 + - - -
263A LYS 3.6 0.2 - - - -
264A ASN* 1.3 92.7 + - - +
266A PRO* 1.3 75.8 - - - +
267A GLN* 3.4 9.7 + - - -
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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