Contacts of the helix formed by residues 236 - 247 (chain A) in PDB entry 2P02
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 CYS 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A GLU 3.7 2.7 + - - +
235A VAL* 1.3 76.9 - - - +
237A LEU* 1.3 67.8 + - - +
238A ASP* 3.8 13.0 - - - +
239A GLU* 3.3 30.1 + - - +
240A MET* 3.1 25.9 + - - +
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Residues in contact with LEU 237 (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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236A CYS* 1.3 75.9 - - - +
238A ASP* 1.3 60.7 + - - +
240A MET* 3.2 14.4 + - + +
241A ARG* 2.9 84.4 + - - +
267A GLN* 3.7 22.9 - - + +
270A GLY* 3.9 28.5 - - - +
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Residues in contact with ASP 238 (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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236A CYS* 3.3 11.7 - - - +
237A LEU* 1.3 76.9 - - - +
239A GLU* 1.3 66.4 + - - +
241A ARG* 4.1 8.6 + - - +
242A ASP* 3.0 27.0 + - - +
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Residues in contact with GLU 239 (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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197A TRP* 4.1 15.6 + - - +
235A VAL* 3.7 23.7 - - + +
236A CYS* 3.3 22.1 + - - +
238A ASP* 1.3 78.5 - - - +
240A MET* 1.3 62.6 + - - +
242A ASP* 3.9 5.9 - - - +
243A ALA* 3.1 24.3 + - + +
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Residues in contact with MET 240 (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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197A TRP* 3.6 25.4 - - + -
231A HIS* 3.3 55.9 - - + +
235A VAL* 3.6 17.9 - - + +
236A CYS 3.1 21.6 + - - +
237A LEU* 3.2 25.5 + - + +
239A GLU* 1.3 77.1 - - - +
241A ARG* 1.3 57.3 + - - +
243A ALA* 3.3 2.1 + - - +
244A LEU* 2.9 35.6 + - + +
267A GLN* 3.4 26.0 - - + +
270A GLY 5.4 1.6 - - - +
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Residues in contact with ARG 241 (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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237A LEU* 2.9 60.0 + - + +
238A ASP* 4.1 8.9 + - - +
240A MET* 1.3 72.7 - - - +
242A ASP* 1.3 62.5 + - - +
244A LEU* 3.4 1.1 + - - -
245A LYS* 3.1 21.0 + - - +
266A LEU* 2.7 48.2 + - + +
267A GLN* 3.0 26.0 + - + -
268A PRO* 4.3 6.7 + - - +
270A GLY* 4.5 3.6 - - - -
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Residues in contact with ASP 242 (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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238A ASP 3.0 18.1 + - - +
239A GLU* 3.9 5.2 - - - +
241A ARG* 1.3 77.8 - - - +
243A ALA* 1.3 58.9 + - - +
245A LYS* 3.3 4.3 + - - +
246A GLU* 2.9 48.2 + - - +
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Residues in contact with ALA 243 (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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195A LEU* 4.0 21.3 - - + -
197A TRP* 3.9 19.7 - - + +
239A GLU* 3.1 20.1 + - + +
240A MET 3.7 3.1 - - - +
242A ASP* 1.3 81.1 + - - +
244A LEU* 1.3 58.7 + - - +
246A GLU* 4.9 0.7 - - - -
247A LYS* 2.8 41.4 + - + +
248A VAL* 3.4 4.7 + - - +
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Residues in contact with LEU 244 (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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186A LEU* 3.6 31.2 - - + -
195A LEU* 5.7 0.9 - - + -
197A TRP* 4.5 10.1 - - + -
227A ILE* 4.1 25.8 - - + -
229A VAL* 4.2 7.9 - - + -
240A MET* 2.9 22.5 + - + +
241A ARG 3.9 4.0 - - - +
243A ALA* 1.3 76.5 - - - +
245A LYS* 1.3 58.4 + - - +
248A VAL* 3.3 13.1 - - + +
249A ILE* 2.9 32.1 + - - +
266A LEU* 4.2 22.9 - - + -
267A GLN* 3.8 34.1 - - + +
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Residues in contact with LYS 245 (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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241A ARG 3.1 17.2 + - - +
242A ASP* 3.8 4.5 - - - +
244A LEU* 1.3 77.8 - - - +
246A GLU* 1.3 74.0 + - - +
249A ILE* 3.6 9.9 - - + +
250A LYS* 3.0 43.0 + - + +
264A TYR* 3.6 54.0 - - + +
266A LEU* 4.0 9.5 - - + +
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Residues in contact with GLU 246 (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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242A ASP* 2.9 37.2 + - - +
243A ALA* 4.9 0.4 - - - -
245A LYS* 1.3 98.8 - - - +
247A LYS* 1.3 74.8 + - + +
250A LYS* 2.8 55.1 + - - +
251A ALA* 4.4 2.3 + - - +
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Residues in contact with LYS 247 (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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185A LYS* 4.0 1.7 - - - +
189A LEU* 3.5 27.2 - - + +
194A THR* 5.5 9.4 - - + -
195A LEU* 4.7 10.8 - - + -
243A ALA* 2.8 25.8 + - + +
246A GLU* 1.3 86.5 - - + +
248A VAL* 1.3 61.7 + - - +
251A ALA* 3.4 18.8 - - - +
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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