Contacts of the helix formed by residues 248 - 261 (chain A) in PDB entry 2PUA
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 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A GLY* 1.3 69.0 - - - -
249A ILE* 1.3 57.7 + - - +
251A ALA* 3.0 10.1 - - - +
252A MET* 2.6 35.5 + - - +
274A TYR 2.9 13.2 + - - +
275A ASP* 4.0 3.2 + - - -
276A ASN* 2.7 27.6 + - - -
277A VAL* 2.8 34.2 + - + -
280A ALA* 3.4 9.1 - - - +
283A PHE* 3.5 7.0 - - + -
287A LEU* 3.8 13.0 - - + +
289A THR* 2.7 24.3 + - - +
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Residues in contact with ILE 249 (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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71A ALA* 6.4 0.2 - - + -
72A ALA* 3.5 35.9 - - + +
73A TYR* 5.4 1.3 - - + +
221A PHE 4.0 11.2 - - - +
222A GLU* 5.7 0.2 - - - +
223A PRO* 3.4 37.4 - - + +
247A GLY 3.4 1.4 + - - -
248A ASP* 1.3 77.5 - - - +
250A MET* 1.3 57.9 + - - +
252A MET* 3.4 15.8 - - - +
253A GLY 3.0 17.7 + - - -
275A ASP* 5.6 0.8 + - - -
277A VAL* 4.6 14.4 - - + -
279A ASN* 6.3 1.8 - - + +
283A PHE* 4.7 9.0 - - + -
599A 6MP 6.1 3.1 - - - +
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Residues in contact with MET 250 (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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184A ILE* 3.4 30.3 - - + +
186A GLY* 4.2 10.5 - - - +
219A GLY* 3.4 17.7 - - - -
221A PHE* 3.3 42.5 + - + +
222A GLU 3.6 1.6 - - - +
223A PRO* 4.2 7.6 - - - -
225A SER* 3.2 25.1 - - - +
226A GLY* 3.3 12.7 - - - +
245A CYS* 3.6 7.0 - - - -
246A GLY* 3.9 5.6 - - - +
247A GLY* 3.3 27.7 + - - +
248A ASP 3.1 0.2 - - - -
249A ILE* 1.3 77.6 - - - +
251A ALA* 1.3 61.3 + - - +
253A GLY* 2.8 13.4 + - - +
254A ALA* 2.8 12.3 + - - +
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Residues in contact with ALA 251 (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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245A CYS* 3.3 21.7 - - + -
247A GLY 3.0 14.3 + - - +
248A ASP* 3.0 16.8 - - - +
250A MET* 1.3 75.6 - - - +
252A MET* 1.3 67.0 - - - +
253A GLY 2.8 1.3 - - - -
254A ALA* 2.8 5.9 + - - +
255A LEU* 2.8 29.0 + - - +
271A LEU* 4.4 4.4 - - + +
273A GLY* 4.5 3.4 - - - -
287A LEU* 4.4 22.0 - - + -
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Residues in contact with MET 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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223A PRO* 5.3 6.5 - - + -
248A ASP 2.6 9.0 + - - +
249A ILE* 3.4 19.7 - - - +
251A ALA* 1.3 77.2 - - - +
253A GLY* 1.3 68.2 + - - +
255A LEU* 3.0 17.1 + - + +
256A CYS* 3.2 13.7 + - + +
283A PHE* 3.2 47.3 - - + -
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Residues in contact with GLY 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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223A PRO* 3.4 25.8 - - - -
227A TYR* 3.4 20.8 - - - -
249A ILE 3.0 10.6 + - - -
250A MET 2.8 10.8 + - - -
251A ALA 2.8 0.8 - - - -
252A MET* 1.3 80.2 - - - +
254A ALA* 1.3 59.7 + - - +
256A CYS* 3.4 9.4 + - - +
257A ALA 3.4 8.7 + - - -
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Residues in contact with ALA 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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184A ILE* 4.7 9.0 - - + -
226A GLY* 4.3 4.9 - - - +
227A TYR* 3.8 2.2 - - - +
230A MET* 3.4 48.6 - - + +
245A CYS* 5.1 1.6 - - - -
250A MET 2.8 9.8 + - - +
251A ALA* 2.8 9.2 + - - +
253A GLY* 1.3 74.3 - - - +
255A LEU* 1.3 69.9 + - - +
257A ALA 3.4 0.9 + - - +
258A ALA* 3.2 18.9 + - - +
271A LEU* 4.0 7.6 - - + -
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Residues in contact with LEU 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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230A MET* 5.5 0.2 - - + -
251A ALA 2.8 15.3 + - - +
252A MET* 3.0 8.0 + - + +
254A ALA* 1.3 79.7 - - - +
256A CYS* 1.3 63.5 + - - +
258A ALA* 3.2 4.4 + - - +
259A ASP* 3.1 22.1 + - - +
265A VAL* 4.7 13.3 - - + +
271A LEU* 3.3 37.5 - - + -
283A PHE* 4.2 24.7 - - + -
284A THR 4.3 19.1 - - - +
285A PRO* 4.5 11.7 - - + +
287A LEU* 4.1 21.3 - - + -
330A SER* 6.0 0.7 - - - -
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Residues in contact with CYS 256 (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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227A TYR* 3.2 23.8 - - - -
252A MET* 3.2 10.0 + - + +
253A GLY 4.1 4.7 - - - +
254A ALA 3.3 0.2 - - - -
255A LEU* 1.3 79.5 - - - +
257A ALA* 1.3 62.7 + - - +
259A ASP* 3.4 6.4 + - - +
260A GLU* 2.9 54.6 + - - +
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Residues in contact with ALA 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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227A TYR* 3.5 55.5 - - + +
230A MET* 4.5 7.4 - - + -
231A GLN* 4.6 9.4 - - + +
253A GLY 3.4 5.3 + - - -
254A ALA 3.4 6.5 + - - +
255A LEU 3.3 1.0 - - - -
256A CYS* 1.3 77.4 - - - +
258A ALA* 1.3 58.1 + - - +
260A GLU* 3.2 3.3 + - - +
261A MET* 2.9 31.5 + - + +
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Residues in contact with ALA 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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230A MET* 4.6 6.8 - - + +
234A LEU* 4.5 14.6 - - + -
254A ALA 3.2 10.9 + - - +
255A LEU 3.2 8.0 + - - +
257A ALA* 1.3 72.9 - - - +
259A ASP* 1.3 63.7 + - - +
261A MET* 2.8 12.2 + - - -
263A LEU* 2.7 48.6 + - + +
265A VAL* 4.1 21.3 - - + -
269A VAL* 4.8 0.4 - - + -
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Residues in contact with ASP 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 LEU 3.1 12.9 + - - +
256A CYS* 3.7 10.5 - - - +
258A ALA* 1.3 76.1 - - - +
260A GLU* 1.3 60.4 + - + +
262A GLY* 2.7 24.5 + - - -
263A LEU 4.1 8.3 + - - +
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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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227A TYR* 2.4 28.9 + - - +
256A CYS* 2.9 37.5 + - - +
257A ALA 3.6 5.2 - - - +
258A ALA 3.0 0.4 - - - -
259A ASP* 1.3 84.0 - - + +
261A MET* 1.3 57.1 + - + +
262A GLY 3.3 2.6 + - - -
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Residues in contact with MET 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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231A GLN* 4.8 21.1 - - - +
234A LEU* 3.9 38.6 - - + +
235A SER* 4.8 10.8 - - - +
239A ARG* 4.7 4.0 - - - +
257A ALA* 2.9 20.6 - - + +
258A ALA* 2.8 11.0 + - - +
260A GLU* 1.3 72.8 - - + +
262A GLY* 1.3 64.7 + - - +
263A LEU* 3.0 17.4 + - + +
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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