Contacts of the helix formed by residues 225 - 234 (chain A) in PDB entry 3V30
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 THR 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A LEU* 3.9 2.2 - - - -
216A LEU 4.2 6.5 - - - +
217A THR* 4.0 13.7 - - - +
219A GLU* 3.7 26.2 - - + +
223A GLY 3.7 0.4 + - - -
224A TYR* 1.3 75.3 - - - +
226A PRO* 1.4 76.6 - - - +
227A MET* 3.6 6.8 + - - +
228A ASP* 2.9 39.4 + - - +
229A LEU* 3.0 22.0 + - - +
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Residues in contact with PRO 226 (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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192A THR* 5.6 0.4 - - - +
194A LEU* 3.7 26.9 - - + -
195A LEU* 3.7 21.5 - - + -
198A VAL* 3.5 30.6 - - + +
215A ASP 4.7 0.9 - - - +
216A LEU* 3.6 28.7 - - + +
218A THR 3.4 17.3 - - - +
225A THR* 1.4 87.4 - - - +
227A MET* 1.3 60.7 + - - +
229A LEU* 3.3 4.0 + - + -
230A ALA* 3.0 19.9 + - - +
242A ILE* 4.2 3.6 - - + -
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Residues in contact with MET 227 (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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216A LEU* 4.7 4.5 + - + +
225A THR* 3.2 6.7 + - - +
226A PRO* 1.3 76.4 - - - +
228A ASP* 1.3 68.7 - - - +
230A ALA* 3.7 1.4 - - - +
231A VAL* 2.9 32.5 + - + +
239A GLN* 3.4 39.0 - - + +
242A ILE* 3.8 36.8 - - + +
243A GLU* 3.6 24.9 - - + +
246A ILE* 5.3 9.0 - - + -
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Residues in contact with ASP 228 (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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223A GLY 3.9 4.5 - - - +
224A TYR* 3.7 21.4 - - + -
225A THR* 2.9 50.0 + - - +
227A MET* 1.3 75.8 - - - +
229A LEU* 1.3 57.6 + - - +
231A VAL* 3.5 5.0 + - - +
232A ALA* 2.9 32.1 + - - +
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Residues in contact with LEU 229 (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* 3.9 38.1 - - + +
198A VAL* 3.9 9.2 - - + -
199A ARG* 4.5 9.2 - - + -
224A TYR* 3.7 30.1 - - + -
225A THR 3.0 13.1 + - - +
226A PRO 3.5 7.0 - - - +
228A ASP* 1.3 73.6 - - - +
230A ALA* 1.3 59.7 - - - +
232A ALA* 3.3 1.9 + - - -
233A LEU* 2.9 45.3 + - + +
12B LEU* 3.8 32.3 - - + +
13B ASP* 4.6 3.1 - - - +
14B LEU* 4.2 15.5 - - + -
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Residues in contact with ALA 230 (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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198A VAL* 3.8 5.8 - - + +
226A PRO 3.0 15.7 + - - +
227A MET* 3.2 5.1 + - - +
229A LEU* 1.3 76.1 - - - +
231A VAL* 1.3 62.2 + - - +
234A GLY* 3.1 3.3 + - - -
235A TYR* 3.0 44.4 + - - +
238A VAL* 3.8 28.0 - - + -
239A GLN* 4.2 11.9 - - + +
242A ILE* 4.3 6.7 - - + -
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Residues in contact with VAL 231 (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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227A MET* 2.9 36.7 + - + +
228A ASP* 3.9 5.4 - - - +
230A ALA* 1.3 75.8 - - - +
232A ALA* 1.3 62.7 + - - +
234A GLY* 3.2 13.4 + - - -
239A GLN* 3.8 31.9 - - - +
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Residues in contact with ALA 232 (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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224A TYR* 4.4 7.0 - - + -
228A ASP 2.9 21.6 + - - +
229A LEU 4.0 0.4 - - - +
231A VAL* 1.3 74.9 - - - +
233A LEU* 1.3 61.8 + - - +
234A GLY 3.6 0.3 + - - -
14B LEU* 3.6 38.6 - - + +
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Residues in contact with LEU 233 (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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198A VAL 5.0 0.2 - - - +
199A ARG* 3.6 43.1 - - - +
229A LEU* 2.9 31.2 + - + +
232A ALA* 1.3 76.5 - - - +
234A GLY* 1.3 61.3 + - - +
235A TYR* 3.5 49.0 - - + +
14B LEU* 4.0 23.6 - - + -
17B SER* 4.3 20.6 - - - +
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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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230A ALA 3.1 6.4 + - - -
231A VAL 3.2 10.2 + - - -
232A ALA 3.3 1.0 + - - -
233A LEU* 1.3 79.9 - - - +
235A TYR* 1.3 62.1 + - - +
236A ARG* 3.1 23.8 + - - +
239A GLN* 6.0 0.4 - - - -
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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