Contacts of the helix formed by residues 251 - 265 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249B SER* 2.7 30.8 + - - +
250B THR* 1.3 89.4 + - - +
252B GLU* 1.3 64.5 + - - +
253B THR* 3.3 6.3 + - - +
254B ILE* 3.4 32.4 + - + +
255B THR* 3.5 0.5 + - - -
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Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B SER 4.8 1.3 - - - -
250B THR 4.1 1.6 + - - -
251B ASP* 1.3 69.9 - - - +
253B THR* 1.3 68.1 + - + +
255B THR* 3.0 10.5 + - - -
256B LEU* 2.9 22.1 + - + +
298B LEU* 4.2 35.1 - - + +
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Residues in contact with THR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ASP* 4.1 6.5 + - + +
252B GLU* 1.3 79.1 - - + +
254B ILE* 1.3 82.7 + - - +
256B LEU* 3.2 5.3 + - + -
257B LYS* 2.7 54.4 + - - +
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Residues in contact with ILE 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B TRP* 4.7 10.3 - - + -
249B SER* 3.4 25.1 - - - +
251B ASP* 3.4 23.8 + - + +
252B GLU 3.2 0.4 - - - -
253B THR* 1.3 94.0 + - - +
255B THR* 1.3 56.0 + - - +
257B LYS* 3.4 7.3 + - + +
258B LYS* 2.9 43.0 + - + +
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Residues in contact with THR 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B LYS* 3.8 7.4 - - + +
249B SER* 3.3 32.0 + - - -
251B ASP 3.5 4.3 + - - -
252B GLU* 3.0 14.0 + - - -
254B ILE* 1.3 76.0 - - - +
256B LEU* 1.3 62.7 + - - +
258B LYS* 2.8 24.4 + - - +
259B LEU* 3.0 25.9 + - + +
262B TRP* 4.2 8.0 - - + -
298B LEU* 3.9 22.2 - - + +
301B GLY* 4.2 20.2 - - - -
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B GLU* 2.9 13.4 + - + +
253B THR* 3.5 10.1 - - + +
255B THR* 1.3 76.1 - - - +
257B LYS* 1.3 71.4 + - + +
259B LEU* 3.4 25.3 - - + +
260B GLU* 3.1 20.7 - - - +
298B LEU* 3.8 36.5 - - + +
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Residues in contact with LYS 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B THR* 2.7 55.5 + - - +
254B ILE* 3.6 6.5 - - + +
256B LEU* 1.3 89.8 - - + +
258B LYS* 1.3 56.8 + - - +
260B GLU* 2.9 23.8 - - - +
261B GLU* 4.0 17.8 + - - +
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Residues in contact with LYS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B TRP* 3.6 28.9 - - + -
254B ILE* 2.9 32.6 + - + +
255B THR* 2.8 8.3 + - - +
257B LYS* 1.3 75.9 - - - +
259B LEU* 1.3 64.7 + - - +
260B GLU 3.3 1.1 - - - -
261B GLU* 2.5 43.1 + - + +
262B TRP* 2.9 61.2 + - + +
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B THR* 3.0 33.2 + - + +
256B LEU* 3.4 27.8 - - + +
257B LYS 3.3 0.4 - - - -
258B LYS* 1.3 77.8 - - - +
260B GLU* 1.3 62.2 + - - +
262B TRP* 3.2 10.2 + - + +
263B LYS* 3.0 35.8 + - + +
296B ALA* 4.0 29.1 - - + +
297B ASP 3.7 20.9 - - - +
298B LEU* 4.4 10.8 - - + +
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Residues in contact with GLU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B LEU* 3.1 21.6 - - - +
257B LYS* 2.9 24.1 - - - +
259B LEU* 1.3 72.1 - - - +
261B GLU* 1.3 67.0 + - + +
263B LYS* 3.2 26.7 - - - +
264B ASN* 2.9 36.2 + - - +
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Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B LYS* 4.0 13.8 - - - +
258B LYS* 2.5 52.5 + - + +
260B GLU* 1.3 76.2 - - + +
262B TRP* 1.3 60.4 + - + +
264B ASN* 5.2 1.3 - - - -
265B GLY* 2.8 32.1 + - - -
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Residues in contact with TRP 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B TRP* 4.2 6.5 - + - -
247B GLU* 3.3 56.3 + - + -
248B LYS* 4.9 2.0 - - - -
255B THR* 4.2 20.0 - - + -
258B LYS* 2.9 56.9 + - + +
259B LEU* 3.6 11.2 - - + +
261B GLU* 1.3 81.5 - - + +
263B LYS* 1.3 62.8 + - - +
265B GLY* 3.7 2.9 + - - -
266B PRO 4.7 2.4 - - - +
267B GLN* 3.1 17.0 + - - -
269B ARG* 3.7 20.8 - - - +
293B PHE* 3.7 25.4 - + + -
296B ALA* 4.1 7.4 - - + -
301B GLY 4.3 3.8 - - - -
302B ALA* 3.6 24.9 - - + -
304B TRP* 4.1 11.6 - + - -
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Residues in contact with LYS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B LEU* 3.0 17.2 + - + +
260B GLU* 3.2 40.3 - - - +
262B TRP* 1.3 77.2 - - - +
264B ASN* 1.3 76.3 + - - +
265B GLY 4.4 0.2 - - - +
267B GLN* 3.3 17.3 + - - +
293B PHE* 4.6 13.9 - - + -
296B ALA* 5.9 1.8 - - + -
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Residues in contact with ASN 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B GLU* 2.9 26.5 + - - +
261B GLU* 3.7 1.3 - - - +
263B LYS* 1.3 98.7 - - - +
265B GLY* 1.3 64.3 + - - +
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Residues in contact with GLY 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ASP* 4.4 1.7 - - - +
261B GLU 2.8 20.0 + - - -
262B TRP 3.7 1.9 + - - -
263B LYS 3.4 2.0 - - - +
264B ASN* 1.3 82.1 - - - +
266B PRO* 1.3 77.1 - - - +
267B GLN* 3.1 15.1 + - - +
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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