Contacts of the helix formed by residues 233 - 244 (chain A) in PDB entry 2V40
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 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ASP* 3.8 14.1 + - - +
132A ARG* 2.9 31.0 + - - -
232A ARG* 1.3 77.2 - - - +
234A GLY* 1.3 57.5 + - - +
235A VAL* 3.2 8.1 + - - +
236A TYR* 3.0 40.9 + - + +
237A PHE* 3.1 26.6 + - - +
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Residues in contact with GLY 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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94A PHE* 3.7 30.7 - - - -
130A SER* 3.8 16.0 + - - -
131A ASP* 4.3 2.0 + - - -
132A ARG* 4.6 1.4 - - - +
232A ARG 3.1 8.4 + - - -
233A ASP* 1.3 72.8 + - - +
235A VAL* 1.3 61.4 - - - +
237A PHE* 3.8 2.5 - - - +
238A LEU* 3.0 31.0 + - - +
283A LEU 4.8 2.8 - - - +
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASN* 5.1 7.2 - - + +
130A SER* 4.9 1.7 + - - +
132A ARG* 4.0 25.6 - - - +
233A ASP* 3.2 6.8 + - - +
234A GLY* 1.3 76.1 - - - +
236A TYR* 1.3 60.2 + - - +
238A LEU* 3.9 1.7 - - - +
239A TYR* 2.9 35.2 + - + +
283A LEU 4.9 6.5 - - - +
284A GLY* 4.3 27.9 - - - +
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Residues in contact with TYR 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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233A ASP* 3.0 25.4 + - + +
235A VAL* 1.3 76.4 - - - +
237A PHE* 1.3 70.0 + - - +
239A TYR* 3.3 8.2 + + + +
240A GLU* 3.0 62.9 + - + +
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Residues in contact with PHE 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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56A ILE* 4.1 28.0 - - + -
92A THR* 4.3 20.2 - - + -
94A PHE* 3.8 43.1 - + + -
128A ILE* 4.3 15.3 - - + -
232A ARG* 4.0 31.9 - - + -
233A ASP 3.1 20.0 + - - +
234A GLY* 3.8 4.7 - - - +
236A TYR* 1.3 82.2 - - + +
238A LEU* 1.3 71.2 + - + +
240A GLU* 3.5 5.1 + - - +
241A ALA* 3.1 22.9 + - + +
247A LYS* 5.7 3.6 - - - -
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Residues in contact with LEU 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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30A VAL* 5.1 0.9 - - + -
56A ILE* 5.6 1.8 - - + -
58A CYS* 5.3 6.3 - - - -
94A PHE* 4.6 9.0 - - + -
234A GLY 3.0 17.4 + - - +
235A VAL 4.2 1.8 - - - +
237A PHE* 1.3 83.3 - - + +
239A TYR* 1.3 62.0 + - - +
241A ALA* 3.1 5.9 + - + -
242A LEU* 2.8 46.1 + - + +
249A ILE* 4.4 26.2 - - + -
283A LEU* 3.6 45.5 - - + +
284A GLY 5.1 1.3 - - - +
285A MET* 3.8 23.8 - - + -
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Residues in contact with TYR 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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235A VAL* 2.9 23.9 + - + +
236A TYR* 3.7 9.2 - + - +
238A LEU* 1.3 75.9 - - - +
240A GLU* 1.3 81.1 + - + +
242A LEU* 3.2 8.0 + - + -
243A HIS* 3.0 69.6 + + + +
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Residues in contact with GLU 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 TYR* 3.0 59.8 + - + +
237A PHE* 3.8 5.2 - - - +
239A TYR* 1.3 93.1 - - - +
241A ALA* 1.3 57.4 + - - +
243A HIS* 3.8 2.5 - - - +
244A GLY* 3.0 30.1 + - - -
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Residues in contact with ALA 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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28A ASN* 2.9 21.3 + - - -
56A ILE* 3.6 30.7 - - + -
237A PHE* 3.1 17.1 + - + +
238A LEU* 3.1 12.5 + - + +
240A GLU* 1.3 77.7 - - - +
242A LEU* 1.3 58.1 + - - +
243A HIS 3.5 0.2 + - - -
244A GLY* 4.0 2.5 + - - -
245A PRO 4.3 0.7 - - - +
247A LYS* 3.9 23.5 - - + +
249A ILE* 4.1 9.3 - - + +
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Residues in contact with LEU 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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27A GLY* 3.3 4.0 - - - -
28A ASN* 2.8 54.5 + - - +
30A VAL* 3.9 18.2 - - + -
238A LEU* 2.8 31.7 + - + +
239A TYR* 3.7 9.6 - - + +
241A ALA* 1.3 76.9 - - - +
243A HIS* 1.3 72.6 + - + +
244A GLY 3.5 0.7 - - - +
249A ILE* 3.9 18.8 - - + -
285A MET* 3.9 26.0 - - + -
286A PRO* 5.1 1.6 - - + -
289A ASN* 3.9 23.8 - - + +
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Residues in contact with HIS 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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26A GLY* 3.5 27.5 + - - -
27A GLY* 4.1 7.1 + - - -
239A TYR* 3.0 72.2 + + + +
240A GLU* 3.8 2.9 - - - +
242A LEU* 1.3 86.7 + - + +
244A GLY* 1.3 64.1 + - - +
286A PRO* 6.3 0.2 - - - +
289A ASN* 4.4 13.7 + - - -
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Residues in contact with GLY 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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28A ASN* 4.2 3.5 + - - -
240A GLU 3.0 15.8 + - - -
241A ALA 4.0 1.9 + - - -
242A LEU 3.5 1.7 - - - +
243A HIS* 1.3 82.9 - - - +
245A PRO* 1.3 79.5 - - - +
246A PRO* 4.5 0.5 - - - +
247A LYS* 6.5 0.2 - - - -
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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