Contacts of the helix formed by residues 231 - 235 (chain B) in PDB entry 2AVN
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 ILE 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A TYR* 3.8 38.1 - - + -
233A TRP 3.4 32.5 - - - +
234A LYS 4.1 0.7 - - - +
203B VAL* 3.8 25.5 - - + +
225B LEU* 3.7 18.4 - - + +
228B ASP* 3.5 23.1 - - + +
229B ARG 3.3 0.2 - - - -
230B ASN* 1.3 77.6 - - - +
232B ILE* 1.3 66.6 + - + +
233B TRP 3.3 3.1 - - - -
234B LYS* 3.2 37.2 + - + +
235B ALA 4.2 0.9 + - - -
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Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ILE* 3.4 38.8 - - + +
199B ARG 4.0 0.7 - - - -
200B GLY* 3.2 31.0 - - - +
203B VAL* 4.8 1.3 - - + -
225B LEU 3.9 8.3 - - - +
226B SER 3.6 14.4 - - - +
228B ASP 3.0 23.8 - - - +
229B ARG* 3.6 28.9 + - + +
230B ASN 3.7 1.2 - - - -
231B ILE* 1.3 81.5 - - + +
233B TRP* 1.3 75.5 + - + +
234B LYS 3.1 0.2 - - - -
235B ALA* 3.0 27.4 + - - +
238B ILE* 3.5 9.6 - - + +
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Residues in contact with TRP 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ASN* 3.5 29.6 + - + +
231A ILE* 3.9 17.3 - - + -
234A LYS* 4.7 4.6 - - - +
142B ASN* 2.8 42.4 + - - +
144B TYR* 3.8 17.9 - + + +
145B THR* 4.9 0.2 + - - -
182B PHE* 3.3 26.0 - - + -
183B LYS* 3.5 19.5 - - - -
184B PRO* 3.6 38.9 - - + +
187B LEU* 4.2 17.7 - - + -
198B ILE* 4.6 10.0 - - + +
229B ARG 5.2 3.1 - - - -
231B ILE 3.3 1.2 - - - -
232B ILE* 1.3 93.9 - - + +
234B LYS* 1.3 55.6 + - - +
235B ALA 3.2 0.4 - - - -
238B ILE* 3.6 34.8 - - + -
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Residues in contact with LYS 234 (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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144A TYR* 4.7 6.3 - - + -
145A THR* 6.0 1.1 - - - +
148A GLN* 3.0 36.1 + - - +
233A TRP 5.8 0.2 - - - -
234A LYS* 4.2 42.4 - - + +
142B ASN* 4.3 0.7 - - - -
145B THR* 4.5 3.4 + - - -
202B GLY 4.5 0.3 - - - +
203B VAL* 3.1 28.5 + - + +
204B MSE 3.8 15.4 - - + +
205B GLU* 4.7 4.0 - - - +
231B ILE* 3.2 40.2 + - + +
232B ILE 3.1 0.2 - - - -
233B TRP* 1.3 76.8 - - - +
235B ALA* 1.3 63.5 + - - +
236B ASP 3.9 0.3 + - - -
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Residues in contact with ALA 235 (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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142B ASN* 2.8 11.6 + - - +
145B THR* 2.8 18.2 + - - -
200B GLY* 3.4 26.7 - - - -
201B ILE 3.5 11.7 - - - +
202B GLY 3.3 9.2 - - - +
203B VAL* 3.9 10.3 - - + +
231B ILE 4.2 0.2 + - - -
232B ILE 3.0 17.6 + - - +
233B TRP 3.2 0.2 - - - -
234B LYS* 1.3 79.0 - - - +
236B ASP* 1.3 62.2 + - - +
237B HIS 3.3 4.8 + - - +
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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