Contacts of the helix formed by residues 233 - 241 (chain A) in PDB entry 6ABP
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 GLY 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ASP* 3.1 2.6 + - - -
232A ASN* 1.3 70.8 - - - +
234A VAL* 1.3 63.3 + - - -
235A ASP 3.1 1.3 - - - -
236A ALA* 3.0 20.0 + - - +
237A VAL* 3.9 4.4 + - - +
251A SER* 3.0 19.5 + - - -
252A LEU 3.5 0.8 + - - -
253A LEU* 4.0 15.5 - - - -
289A ILE* 3.7 27.2 - - - +
298A LEU* 5.1 0.9 - - - -
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Residues in contact with VAL 234 (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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15A PRO* 3.6 18.4 - - + +
16A TRP* 3.5 35.7 - - + +
19A THR* 4.2 13.2 - - - +
232A ASN 2.9 15.9 + - - +
233A GLY* 1.3 71.0 - - - -
235A ASP* 1.4 65.9 + - - +
236A ALA 3.4 0.7 + - - -
237A VAL* 3.7 21.4 + - - +
253A LEU* 4.3 6.0 - - + +
256A PRO* 4.4 10.3 - - + -
298A LEU* 4.3 11.2 - - + -
303A LEU* 4.2 30.3 - - + -
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Residues in contact with ASP 235 (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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14A GLU* 3.5 17.5 - - - +
15A PRO* 3.2 21.2 - - + +
16A TRP* 2.7 32.8 + - - +
206A ASP* 3.2 24.3 + - + +
207A SER* 4.9 7.4 + - - +
210A LEU* 4.5 10.8 - - + +
232A ASN* 3.0 28.8 + - - -
233A GLY 3.1 1.6 - - - +
234A VAL* 1.4 79.6 - - - +
236A ALA* 1.3 58.1 + - - +
237A VAL 3.4 1.0 + - - -
238A SER* 4.9 5.2 + - - -
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Residues in contact with ALA 236 (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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206A ASP* 3.5 4.4 + - - +
210A LEU* 5.1 2.7 - - - -
233A GLY 3.0 12.7 + - - +
235A ASP* 1.3 76.2 - - - +
237A VAL* 1.3 64.2 + - - +
238A SER 3.3 2.9 - - - -
239A GLU* 3.1 8.8 + - - +
240A LEU* 3.0 28.8 + - + +
248A PHE* 3.4 37.0 - - + -
251A SER* 3.8 12.6 - - - -
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Residues in contact with VAL 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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233A GLY 4.0 9.4 - - - +
234A VAL* 3.7 19.0 + - + +
235A ASP 3.4 3.0 - - - -
236A ALA* 1.3 77.0 - - - +
238A SER* 1.3 65.4 + - - +
240A LEU* 3.2 5.8 + - - +
241A SER* 2.9 38.0 + - - +
289A ILE* 5.3 2.5 - - + -
294A PHE* 4.0 15.0 - - + -
298A LEU* 3.5 28.9 - - + -
305A GLY 5.2 0.9 - - - +
306A LYS* 4.3 15.3 - - - -
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Residues in contact with SER 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ASP 4.9 4.9 + - - -
236A ALA 3.3 0.6 - - - -
237A VAL* 1.3 81.3 - - - +
239A GLU* 1.4 65.2 + - - +
241A SER* 3.7 7.1 - - - -
242A LYS* 3.5 24.4 + - - +
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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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210A LEU* 3.5 25.7 - - + +
214A ARG* 2.7 38.9 + - - -
236A ALA* 3.1 11.9 + - - +
237A VAL 3.1 0.8 - - - -
238A SER* 1.4 84.0 + - - +
240A LEU* 1.3 64.0 + - + +
241A SER 3.3 0.7 + - - -
242A LYS* 2.9 45.8 + - - +
244A GLN 5.3 0.3 - - - +
246A THR* 2.8 22.4 + - - +
248A PHE* 3.9 24.8 - - + +
291A ARG* 4.9 2.4 + - - -
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Residues in contact with LEU 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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236A ALA* 3.0 29.4 + - + +
237A VAL 3.2 2.7 + - - +
239A GLU* 1.3 80.8 - - - +
241A SER* 1.3 56.0 + - - +
242A LYS 3.4 0.9 + - - +
248A PHE* 4.4 15.5 - - + +
249A TYR 4.1 13.0 - - - +
250A GLY* 4.4 7.2 - - - -
251A SER 4.9 0.4 - - - +
289A ILE* 3.9 38.6 - - + +
290A THR* 4.0 3.1 - - - -
291A ARG* 3.8 48.6 + - + +
294A PHE* 3.5 40.6 - - + -
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Residues in contact with SER 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A VAL* 2.9 25.5 + - - +
238A SER* 3.7 9.4 - - - -
239A GLU 3.2 0.2 - - - -
240A LEU* 1.3 73.4 - - - +
242A LYS* 1.3 65.4 + - - +
243A ALA* 3.7 0.5 + - - -
294A PHE* 3.5 21.7 - - - -
306A LYS 4.6 7.1 - - - -
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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