Contacts of the helix formed by residues 235 - 241 (chain D) in PDB entry 1O97
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 SER 235 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207D SER* 4.0 0.4 + - - -
208D ILE 3.0 6.3 + - - -
209D GLY* 3.2 12.0 - - - -
234D CYS* 1.3 88.4 - - - +
236D ARG* 1.3 66.4 + - - +
237D PRO* 3.3 7.0 - - - +
238D ILE* 3.3 12.0 + - - +
239D ALA 3.7 0.2 + - - -
249D GLN* 4.3 2.0 - - - -
268D ILE* 4.2 8.7 - - - -
274D HIS* 3.6 17.3 - - - -
1319D FAD 2.6 46.2 + - - -
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Residues in contact with ARG 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ALA* 6.0 0.4 - - - +
163C GLU* 2.7 41.0 + - - -
183C GLN* 3.5 15.3 + - - +
184C LEU* 2.9 33.5 + - - +
185C GLY* 5.0 0.2 - - - -
235D SER* 1.3 74.0 - - - +
237D PRO* 1.3 65.5 - - + +
239D ALA* 3.0 3.8 + - - +
240D ASP* 2.8 47.4 + - - +
249D GLN* 3.7 23.4 + - - +
253D SER* 2.9 18.4 + - - -
1319D FAD 2.9 57.4 + - + +
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Residues in contact with PRO 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D ARG* 3.7 48.2 - - + +
235D SER* 3.3 13.5 - - - +
236D ARG* 1.3 93.9 - - + +
238D ILE* 1.3 56.8 + - + +
240D ASP* 3.8 8.5 - - + +
241D ALA* 3.0 30.0 + - - +
243D TRP* 6.0 0.2 - - - -
1319D FAD 3.3 32.3 - - - +
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Residues in contact with ILE 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D ILE* 3.6 28.5 - - + +
209D GLY* 3.4 28.0 - - - +
210D ARG* 4.1 6.3 - - - +
212D ILE* 3.9 17.5 - - + -
218D VAL* 5.1 0.2 - - + -
234D CYS* 3.6 16.2 - - + -
235D SER* 3.6 9.4 - - - +
236D ARG 3.1 0.6 - - - -
237D PRO* 1.3 77.1 - - + +
239D ALA* 1.3 60.4 + - - +
241D ALA* 3.4 8.0 + - - +
243D TRP* 3.1 57.4 + - + +
244D LEU* 3.8 20.4 - - + -
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Residues in contact with ALA 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D CYS* 4.1 14.8 - - - -
235D SER 3.7 1.6 + - - +
236D ARG 3.0 2.7 + - - +
238D ILE* 1.3 77.9 - - - +
240D ASP* 1.3 60.5 + - - +
241D ALA 3.1 1.3 - - - -
242D GLY* 2.9 19.4 + - - -
244D LEU 3.5 19.1 - - - +
246D LYS* 4.1 26.7 - - + +
249D GLN* 3.5 27.4 - - + +
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Residues in contact with ASP 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PHE* 5.4 3.6 - - + -
184C LEU* 3.6 15.8 - - - +
185C GLY* 3.7 25.8 + - - +
188C LYS* 3.4 17.0 + - - +
236D ARG* 2.8 60.8 + - - +
237D PRO* 3.8 8.8 - - + +
239D ALA* 1.3 76.9 - - - +
241D ALA* 1.3 60.9 + - - +
242D GLY* 3.3 0.9 + - - -
246D LYS* 4.8 6.6 - - - +
249D GLN* 4.7 3.1 + - - -
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Residues in contact with ALA 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C LYS* 3.7 20.6 + - - +
237D PRO 3.0 20.0 + - - +
238D ILE 3.8 2.7 - - - +
239D ALA 3.1 0.4 - - - -
240D ASP* 1.3 75.9 - - - +
242D GLY* 1.3 57.9 + - - +
243D TRP* 3.3 45.8 + - + +
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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