Contacts of the helix formed by residues 232 - 243 (chain D) in PDB entry 1OP8
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 LYS 232 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D GLY* 3.5 20.1 + - - +
232D SER* 1.3 75.6 - - - +
233D LYS* 1.3 63.2 + - - +
235D LEU* 3.7 4.6 - - - +
236D ASN* 2.7 53.6 + - - +
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Residues in contact with LYS 233 (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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93C CYS 5.7 1.0 + - - -
95C ASP* 2.8 40.4 + - + +
100C GLU* 4.8 9.5 + - - -
91D TYR* 3.3 27.9 + - + +
93D CYS* 6.0 1.8 - - - +
100D GLU* 5.8 3.2 + - - +
179D ASN* 4.0 23.2 - - - +
232D LYS* 1.3 88.2 + - - +
234D HIS* 1.3 73.7 + - - +
236D ASN* 3.3 6.2 + - - +
237D TRP* 3.0 21.8 + - + +
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Residues in contact with HIS 234 (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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91D TYR* 4.0 24.2 + + - -
100D GLU* 6.2 0.2 - - - +
101D GLY* 4.1 17.9 + - - -
103D LEU* 3.8 24.7 - - + -
179D ASN* 3.5 32.4 + - + +
229D ILE* 3.7 14.9 - - + +
230D LEU 2.5 30.3 + - - +
231D LEU* 4.3 4.0 - - - -
232D SER* 3.2 14.5 + - - +
233D LYS* 1.3 85.8 - - - +
235D LEU* 1.3 67.9 + - - +
237D TRP* 3.0 8.2 + - - +
238D ILE* 2.9 30.4 + - + +
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Residues in contact with LEU 235 (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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123D LEU* 4.2 20.2 - - + -
124D PRO* 3.7 46.2 - - + +
125D LYS 4.8 1.8 - - - +
126D LYS* 3.9 3.4 - - - +
127D GLY* 3.4 31.6 - - - +
231D LEU* 3.4 21.1 - - + +
232D SER* 2.9 21.0 + - - +
234D HIS* 1.3 77.1 - - - +
236D ASN* 1.3 67.2 + - - +
238D ILE* 3.0 7.5 + - + +
239D ILE* 2.8 35.4 + - + +
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Residues in contact with ASN 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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232D LYS* 2.7 52.3 + - - +
233D LYS* 3.5 6.4 - - - +
235D LEU* 1.3 76.9 - - - +
237D TRP* 1.3 57.0 + - - +
239D ILE* 3.9 8.3 - - - +
240D MET* 2.8 48.0 + - + +
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Residues in contact with TRP 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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53D LEU* 5.3 0.4 - - + -
89D PHE* 3.3 31.4 - + + -
90D PRO 3.6 2.7 - - - -
91D TYR* 3.4 47.6 - + + -
92D PRO* 3.3 27.6 - - + +
103D LEU* 3.9 22.9 - - + -
105D LEU* 4.2 19.7 - - + -
233D LYS* 3.0 11.9 + - + +
234D HIS 3.0 8.3 + - - +
236D ASN* 1.3 75.2 - - - +
238D ILE* 1.3 85.7 + - + +
240D MET* 3.3 7.7 + - + +
241D THR* 2.7 60.6 + - + +
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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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47D ILE* 4.0 20.9 - - + -
53D LEU* 4.1 14.6 - - + -
103D LEU* 4.7 4.0 - - + -
105D LEU* 4.0 11.8 - - + +
123D LEU* 3.5 30.7 - - + -
231D LEU* 4.0 27.1 - - + -
234D HIS* 2.9 23.2 + - + +
235D LEU* 3.3 9.6 - - - +
237D TRP* 1.3 101.0 - - + +
239D ILE* 1.3 62.6 + - - +
241D THR* 3.1 2.3 + - - -
242D ILE* 3.0 31.7 + - + +
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Residues in contact with ILE 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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123D LEU* 4.4 18.6 - - + -
124D PRO 6.0 1.3 - - - +
235D LEU* 2.8 36.3 + - + +
236D ASN* 3.9 7.6 - - - +
238D ILE* 1.3 73.9 - - - +
240D MET* 1.3 59.5 + - + +
242D ILE* 3.5 7.4 + - + +
243D LYS* 3.0 35.8 + - + +
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Residues in contact with MET 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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236D ASN* 2.8 40.1 + - + +
237D TRP* 3.8 6.3 - - + +
239D ILE* 1.3 75.5 - - + +
241D THR* 1.3 62.6 + - - +
243D LYS* 3.6 5.7 - - - +
244D GLY* 3.2 19.8 + - - -
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Residues in contact with THR 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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51D TRP* 4.2 5.9 - - + -
89D PHE* 3.6 43.5 - - + -
105D LEU* 3.9 15.5 - - + -
237D TRP* 2.7 47.7 + - + +
238D ILE 3.1 4.7 + - - -
240D MET* 1.3 74.7 - - - +
242D ILE* 1.3 66.7 + - - +
244D GLY* 3.3 9.4 + - - -
245D ALA 3.7 12.1 - - - +
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Residues in contact with ILE 242 (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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47D ILE* 3.9 31.0 - - + +
48D ALA* 5.0 7.4 - - + -
51D TRP* 4.1 43.5 + - + +
105D LEU* 4.4 6.5 - - + -
123D LEU* 5.4 2.9 - - + -
238D ILE* 3.0 23.1 + - + +
239D ILE* 3.8 7.6 - - + +
241D THR* 1.3 74.3 - - - +
243D LYS* 1.3 62.6 + - + +
244D GLY 2.9 9.8 + - - -
245D ALA* 3.5 10.4 + - - +
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Residues in contact with LYS 243 (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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239D ILE* 3.0 24.8 + - + +
240D MET* 3.6 6.6 - - - +
242D ILE* 1.3 77.7 - - + +
244D GLY* 1.3 55.4 + - - +
245D ALA 3.6 1.3 - - - -
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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