Contacts of the helix formed by residues 231 - 241 (chain E) in PDB entry 2ACL
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 PRO 231 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227E ASN* 2.8 15.7 - - - +
228E GLU* 3.6 13.7 - - + +
229E ASP 3.6 5.2 - - - +
230E MET* 1.3 84.2 - - - +
232E VAL* 1.3 53.4 + - - +
233E GLU* 2.6 31.9 + - + +
234E ARG* 2.7 45.6 + - + +
235E ILE* 3.4 4.9 + - - +
287E PRO* 4.3 12.4 - - + +
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Residues in contact with VAL 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E ASN* 3.0 31.1 - - - +
230E MET 2.7 7.9 + - - +
231E PRO* 1.3 70.3 - - - +
233E GLU* 1.3 75.7 + - + +
234E ARG 3.3 0.2 - - - -
235E ILE* 3.4 13.1 + - - +
236E LEU* 3.1 21.3 + - - +
365E THR* 4.0 19.3 - - + +
369E CYS* 4.5 10.3 - - - -
399E SER* 3.6 34.8 - - - +
403E TYR* 4.1 25.6 - - + -
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Residues in contact with GLU 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E ASN* 3.2 22.5 + - - +
231E PRO* 2.6 18.4 + - + +
232E VAL* 1.3 94.6 - - + +
234E ARG* 1.3 62.0 + - + +
236E LEU* 3.2 9.3 + - - +
237E GLU* 3.1 29.0 + - - +
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Residues in contact with ARG 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E PRO* 2.7 36.0 + - + +
233E GLU* 1.3 72.5 - - + +
235E ILE* 1.3 59.3 + - - +
237E GLU* 3.0 22.1 + - - +
238E ALA* 2.9 28.5 + - - +
284E LYS 4.3 6.7 + - - -
285E ARG* 3.2 37.9 + - - +
287E PRO* 4.1 29.5 - - + +
288E HIS 5.3 1.6 - - - +
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Residues in contact with ILE 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E MET* 3.1 37.2 - - + +
231E PRO 3.4 4.7 + - - +
232E VAL* 3.4 13.7 + - + +
233E GLU 3.3 0.2 - - - -
234E ARG* 1.3 76.4 - - - +
236E LEU* 1.3 57.9 + - - +
238E ALA* 3.2 8.4 - - - +
239E GLU* 3.1 25.4 + - + +
286E ILE* 4.1 13.2 - - + -
287E PRO* 4.0 11.4 - - + -
365E THR* 4.6 4.7 - - - +
368E GLY* 3.5 33.7 - - - +
369E CYS* 3.8 21.8 - - - +
372E ALA* 4.3 13.2 - - + -
396E VAL* 4.9 1.8 - - + -
399E SER* 6.1 0.9 - - - -
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Residues in contact with LEU 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E VAL 3.1 12.6 + - - +
233E GLU* 3.5 12.1 - - - +
234E ARG 3.1 0.6 - - - -
235E ILE* 1.3 76.7 - - - +
237E GLU* 1.3 65.8 + - - +
239E GLU* 3.3 4.7 + - + -
240E LEU* 2.8 50.6 + - + +
364E LYS* 3.8 30.3 - - + +
365E THR* 3.2 30.7 - - + +
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Residues in contact with GLU 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E GLU* 3.1 20.2 + - - +
234E ARG* 3.0 22.4 + - - +
236E LEU* 1.3 75.8 - - - +
238E ALA* 1.3 54.2 + - - +
240E LEU* 2.8 11.4 + - - +
241E ALA* 2.8 36.4 + - - +
285E ARG* 5.8 6.7 + - + -
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Residues in contact with ALA 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E ARG 2.9 13.4 + - - +
235E ILE 3.2 12.1 - - - +
237E GLU* 1.3 75.4 - - - +
239E GLU* 1.3 61.0 + - - +
241E ALA* 3.2 19.7 + - - +
242E VAL* 3.9 5.4 + - - +
282E TRP* 3.5 23.9 - - + +
285E ARG* 3.9 24.6 - - + +
286E ILE* 3.8 22.2 - - + -
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Residues in contact with GLU 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E ILE 3.1 10.7 + - - +
236E LEU* 3.7 10.5 - - + +
237E GLU 3.3 0.2 - - - -
238E ALA* 1.3 79.5 - - - +
240E LEU* 1.3 64.8 + - + +
241E ALA 3.4 0.3 + - - -
242E VAL* 3.5 19.9 + - - +
243E GLU* 4.5 3.3 + - - +
282E TRP* 2.8 20.7 + - - +
312E SER* 4.0 2.1 + - - -
364E LYS* 4.0 15.4 + - + +
367E LEU* 3.1 26.1 - - + +
368E GLY* 3.4 31.6 - - - +
371E ARG* 2.7 34.6 + - - -
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Residues in contact with LEU 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E LEU* 2.8 51.5 + - + +
237E GLU* 2.8 14.1 + - - +
239E GLU* 1.3 75.6 - - - +
241E ALA* 1.3 57.3 + - - +
242E VAL 3.2 4.5 + - - -
243E GLU* 4.0 11.8 + - - +
364E LYS* 3.3 38.6 - - + +
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Residues in contact with ALA 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E GLU* 2.8 15.6 + - + +
238E ALA* 3.2 10.2 + - - +
240E LEU* 1.3 76.5 - - - +
242E VAL* 1.3 66.5 + - + +
243E GLU 3.9 0.9 - - - -
285E ARG* 5.3 11.7 - - + -
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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