Contacts of the helix formed by residues 223 - 233 (chain A) in PDB entry 3VAS
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 GLU 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A ASN* 1.3 76.2 - - - +
224A SER* 1.3 58.2 + - - +
226A ALA* 3.3 4.2 + - - +
227A GLU* 2.9 35.6 + - - +
240A VAL* 4.0 21.7 - - + +
264A ILE* 4.4 6.1 - - - -
265A THR 3.0 12.7 + - - +
266A ARG* 3.2 49.6 + - + +
269A ASN* 5.0 4.2 + - - -
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Residues in contact with SER 224 (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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36A ASP 5.4 3.1 + - - -
199A PRO* 3.9 20.7 - - - +
222A ASN* 3.0 18.8 + - - -
223A GLU* 1.3 77.7 - - - +
225A GLU* 1.3 57.1 + - - +
227A GLU* 3.5 7.1 + - - +
228A ALA* 3.0 28.8 + - - +
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Residues in contact with GLU 225 (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 ASN* 4.2 2.6 - - - +
196A LEU* 3.6 21.5 - - + +
197A SER* 2.9 35.2 + - - +
198A ALA* 3.7 24.9 - - - +
199A PRO* 3.8 11.1 - - + +
202A SER* 4.3 4.9 + - - +
221A GLY* 3.3 10.0 - - - -
222A ASN* 2.9 51.5 + - - +
224A SER* 1.3 73.5 - - - +
226A ALA* 1.3 61.1 + - - +
228A ALA* 3.4 1.4 + - - +
229A TYR* 2.9 31.3 + - - +
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Residues in contact with ALA 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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196A LEU* 4.6 3.7 - - - +
222A ASN 3.0 16.8 + - - +
223A GLU 3.6 4.3 - - - +
225A GLU* 1.3 76.6 - - - +
227A GLU* 1.3 54.9 + - - +
229A TYR* 3.6 0.4 - - - +
230A GLY* 2.8 30.0 + - - -
239A THR* 4.2 1.3 - - - +
240A VAL* 4.1 24.9 - - + +
243A THR* 3.0 32.7 + - + -
264A ILE* 4.1 13.5 - - + -
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Residues in contact with GLU 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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223A GLU* 2.9 23.1 + - - +
224A SER* 3.6 8.3 - - - +
225A GLU 3.2 0.2 - - - -
226A ALA* 1.3 77.2 - - - +
228A ALA* 1.3 57.5 + - - +
230A GLY* 3.4 1.0 + - - -
231A GLU* 3.0 30.1 + - - +
239A THR* 3.5 30.1 + - + +
240A VAL* 3.7 21.2 - - - +
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Residues in contact with ALA 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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199A PRO* 3.8 31.9 - - + +
202A SER* 4.4 1.8 - - - -
203A GLN* 3.8 20.6 - - + +
224A SER 3.0 17.8 + - - +
225A GLU 3.9 3.1 - - - +
227A GLU* 1.3 73.5 - - - +
229A TYR* 1.3 64.4 + - - +
231A GLU* 3.5 7.2 + - - +
232A VAL* 3.2 30.2 + - - +
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Residues in contact with TYR 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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196A LEU* 4.7 4.5 - - + -
202A SER* 3.5 27.0 - - - +
206A THR* 5.8 0.2 - - + -
209A VAL* 4.1 9.4 - - + -
210A ASP* 2.6 27.7 + - - -
213A ILE* 3.8 15.5 - - + +
225A GLU 2.9 19.2 + - - +
226A ALA* 3.6 3.8 - - - +
228A ALA* 1.3 77.0 - - - +
230A GLY* 1.3 62.6 + - - +
232A VAL* 3.4 3.4 + - - +
233A HIS* 2.7 54.1 + + + -
235A LEU* 5.1 0.7 - - + -
243A THR* 3.5 22.2 - - + -
246A TYR* 3.4 36.9 - + + -
247A ILE* 3.7 17.4 - - + +
250A LEU* 3.5 9.5 - - - +
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Residues in contact with GLY 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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226A ALA 2.8 16.3 + - - -
228A ALA 3.3 0.2 - - - -
229A TYR* 1.3 74.6 - - - +
231A GLU* 1.3 59.9 + - - +
233A HIS 3.0 7.4 + - - -
235A LEU* 2.9 39.0 + - - +
239A THR* 3.7 12.1 - - - -
243A THR* 3.3 19.5 + - - -
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Residues in contact with GLU 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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203A GLN* 5.0 7.4 + - - -
227A GLU 3.0 17.0 + - - +
228A ALA* 3.9 9.1 - - - +
230A GLY* 1.3 74.3 - - - +
232A VAL* 1.3 67.3 + - + +
234A GLY* 3.1 14.5 + - - +
235A LEU 4.9 4.9 - - - +
236A LEU* 6.3 0.2 - - - +
239A THR* 4.2 2.5 - - + +
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Residues in contact with VAL 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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202A SER 3.7 14.6 - - - +
203A GLN* 3.8 22.9 - - + +
206A THR* 3.6 37.5 - - + +
228A ALA 3.2 18.2 + - - +
229A TYR 3.8 4.9 - - - +
230A GLY 3.3 0.2 - - - -
231A GLU* 1.3 79.6 - - + +
233A HIS* 1.3 60.5 + - + +
234A GLY 3.7 0.3 + - - -
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Residues in contact with HIS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SER 5.3 0.2 - - - -
206A THR* 3.7 23.2 - - + +
210A ASP* 2.8 27.6 + - - -
229A TYR* 2.7 58.8 + + - +
230A GLY 3.0 5.7 + - - +
232A VAL* 1.3 81.1 - - + +
234A GLY* 1.3 61.1 + - - +
235A LEU* 3.2 21.9 + - + +
246A TYR* 3.7 32.2 - + + -
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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