Contacts of the helix formed by residues 231 - 238 (chain E) in PDB entry 3VBB
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 LYS 231 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230E ARG* 1.3 80.2 - - - +
232E GLU* 1.3 65.7 + - + +
233E VAL 3.4 0.9 - - - -
234E MET* 3.5 19.7 + - - +
235E GLN* 3.9 12.2 - - - +
264E ASP* 4.9 7.0 - - - +
265E GLU* 3.5 14.4 - - + +
267E TYR* 3.9 18.8 - - + -
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Residues in contact with GLU 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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230E ARG* 4.5 0.6 - - - +
231E LYS* 1.3 75.3 - - + +
233E VAL* 1.3 66.4 + - + +
234E MET 3.1 2.2 - - - -
235E GLN* 3.0 32.9 + - - +
236E GLU* 2.9 18.7 - - - +
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Residues in contact with VAL 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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229E MET* 3.7 10.1 - - + -
230E ARG* 3.4 26.5 - - + -
231E LYS 3.4 0.4 - - - -
232E GLU* 1.3 76.6 - - + +
234E MET* 1.3 62.4 + - - +
236E GLU* 3.4 21.7 + - - +
237E VAL* 4.0 6.9 - - - +
278E ALA* 3.6 28.6 - - + +
281E ARG* 4.9 19.7 - - - +
187F VAL* 3.7 22.4 - - + +
188F VAL* 4.2 10.1 - - + +
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Residues in contact with MET 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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229E MET* 4.0 34.3 + - + +
231E LYS 3.5 13.1 + - - +
232E GLU 3.1 0.4 - - - -
233E VAL* 1.3 74.6 - - - +
235E GLN* 1.3 62.2 + - + +
236E GLU 2.9 6.7 + - - -
237E VAL* 3.1 4.1 + - - -
238E ALA* 3.0 36.3 + - + -
247E LEU* 4.2 13.5 - - + -
267E TYR* 4.0 39.0 - - + +
269E ILE* 4.3 11.2 - - - -
274E GLN* 3.3 44.2 - - - +
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Residues in contact with GLN 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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133E ARG* 5.0 9.5 + - - +
231E LYS* 3.9 8.8 - - - +
232E GLU* 3.0 34.5 + - - +
234E MET* 1.3 77.0 - - + +
236E GLU* 1.3 64.6 + - - +
238E ALA* 4.0 15.9 - - - +
267E TYR* 5.9 3.6 - - + -
405E ARG* 3.5 19.2 + - - +
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Residues in contact with GLU 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 GLU* 2.9 27.5 - - - +
233E VAL* 3.6 11.0 - - - +
234E MET 2.9 1.4 + - - -
235E GLN* 1.3 83.3 + - - +
237E VAL* 1.3 59.2 + - - +
238E ALA 4.7 1.2 - - - +
281E ARG* 3.1 33.1 + - - +
402E GLN* 5.1 6.6 - - - +
405E ARG* 3.7 56.5 + - + +
406E LEU* 3.3 27.3 - - + +
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Residues in contact with VAL 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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229E MET* 4.4 4.3 - - + -
233E VAL 4.0 11.4 - - - +
234E MET 3.9 8.1 - - - +
236E GLU* 1.3 76.6 - - + +
238E ALA* 1.3 63.7 + - - +
239E GLN* 4.0 0.9 + - - +
273E GLU* 4.3 8.6 - - + +
274E GLN* 3.4 45.3 - - + +
277E ALA* 3.4 29.6 - - + -
278E ALA* 4.8 4.5 - - + +
402E GLN* 3.9 31.0 + - - +
406E LEU* 4.9 4.9 - - + -
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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 MET* 3.0 37.3 + - + +
235E GLN* 4.0 14.2 + - - +
236E GLU 3.6 1.2 - - - +
237E VAL* 1.3 81.8 - - - +
239E GLN* 1.3 64.4 + - - +
240E LEU* 5.0 5.2 - - + +
247E LEU* 5.6 5.6 - - + -
274E GLN* 5.2 4.9 - - + -
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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