Contacts of the helix formed by residues 225 - 232 (chain B) in PDB entry 1XV9
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B HIS* 6.1 1.6 - - + +
147B PRO* 6.0 0.3 - - - +
216B ASN* 3.2 37.5 - - - +
223B ARG* 4.3 10.8 - - + +
224B TYR* 1.3 75.0 - - - +
226B ILE* 1.3 63.9 + - - +
227B GLU* 3.6 26.6 + - - +
228B ASP* 3.3 31.2 + - - +
229B GLY 3.7 3.6 + - - -
243B PHE* 4.2 7.1 - - - -
1001D CI2 4.5 7.1 - - - +
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Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLN* 5.7 3.1 - - + +
216B ASN* 4.8 1.5 - - - +
225B THR* 1.3 73.9 - - - +
227B GLU* 1.3 77.4 + - + +
228B ASP 3.3 0.4 - - - -
229B GLY* 3.9 1.6 + - - -
230B ALA* 3.5 17.0 + - - +
239B LEU* 3.6 32.6 - - + +
240B GLU* 4.4 8.3 - - + +
243B PHE* 3.3 49.6 - - + -
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B PRO* 4.2 22.7 - - + +
225B THR* 3.6 21.6 + - - +
226B ILE* 1.3 94.8 - - + +
228B ASP* 1.3 56.9 + - - +
229B GLY 3.3 0.2 - - - -
230B ALA* 3.4 10.3 - - + +
231B ARG* 2.8 40.3 + - + +
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B HIS* 3.0 29.7 + - - -
141B LEU* 3.6 22.4 - - - +
148B LEU* 5.2 2.9 + - - +
157B LEU* 3.6 13.2 - - + +
223B ARG 4.3 1.7 - - - +
224B TYR* 3.9 3.5 - - - +
225B THR* 3.3 34.8 + - - +
226B ILE 3.3 0.4 - - - -
227B GLU* 1.3 77.8 - - - +
229B GLY* 1.3 62.7 + - - +
231B ARG* 3.0 8.9 + - - +
232B VAL* 2.9 28.4 + - - +
1001D CI2 4.8 13.0 - - + -
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Residues in contact with GLY 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B THR 3.7 7.0 + - - -
226B ILE 3.9 1.0 + - - -
227B GLU 3.3 0.2 - - - -
228B ASP* 1.3 78.3 - - - +
230B ALA* 1.3 61.8 + - - +
232B VAL* 3.2 19.6 + - - +
233B GLY 3.3 7.6 + - - -
234B PHE* 3.4 13.9 + - - -
239B LEU* 3.8 22.0 - - - -
1001D CI2 4.1 18.2 - - - +
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ILE 3.5 13.1 + - - +
227B GLU* 3.3 14.3 + - + +
229B GLY* 1.3 77.0 - - - +
231B ARG* 1.3 61.2 + - + +
233B GLY* 3.0 15.6 + - - -
234B PHE 4.1 5.0 - - - +
236B VAL* 6.3 0.7 - - - -
239B LEU* 3.4 19.9 - - + +
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Residues in contact with ARG 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B PRO* 5.8 0.8 - - - +
148B LEU* 3.0 61.0 + - + +
149B PRO 3.4 15.9 + - - -
150B THR* 4.3 10.7 + - - +
152B ALA 3.6 17.2 + - - -
154B VAL* 3.8 32.6 - - + +
157B LEU* 4.4 12.3 - - + -
227B GLU* 2.8 23.6 + - + +
228B ASP* 3.0 10.3 + - - +
230B ALA* 1.3 72.6 - - + +
232B VAL* 1.3 60.5 + - - +
233B GLY* 2.8 12.0 + - - -
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B LEU* 4.2 22.4 - - + -
158B VAL* 3.8 32.6 - - + +
161B PHE* 3.7 39.3 - - + -
228B ASP 2.9 20.4 + - - +
229B GLY* 3.2 11.6 + - - +
231B ARG* 1.3 74.8 - - - +
233B GLY* 1.3 56.8 + - - +
234B PHE* 3.7 8.2 + - + -
333B ILE* 4.3 16.5 - - - +
336B LEU* 4.9 3.5 - - + +
1001D CI2 5.1 5.6 - - + -
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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