Contacts of the helix formed by residues 232 - 244 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A LYS* 5.8 3.6 - - - +
127A GLY* 3.9 27.9 + - - +
128A ASP* 5.9 1.6 + - - -
232A SER* 1.3 71.9 - - - +
233A LYS* 1.3 59.4 + - - +
235A LEU* 3.2 5.9 + - - -
236A ASN* 2.7 49.5 + - - +
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Residues in contact with LYS 233 (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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91A TYR* 3.3 27.3 + - - +
179A ASN* 3.8 21.8 - - - +
232A LYS* 1.3 82.2 + - - +
234A HIS* 1.3 75.5 + - - +
236A ASN* 3.7 7.8 + - - +
237A TRP* 3.2 20.4 + - - +
94B TYR 6.1 0.2 - - - +
95B ASP* 2.5 35.4 + - + +
100B GLU* 5.4 3.6 + - - -
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Residues in contact with HIS 234 (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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91A TYR* 3.7 30.6 + + - -
101A GLY* 4.2 12.6 - - - -
103A LEU* 4.0 17.9 - - + -
179A ASN* 3.7 25.2 - - + +
229A ILE* 3.4 24.6 - - + +
230A LEU 2.7 23.0 + - - +
231A LEU* 4.5 3.4 - - - -
232A LYS* 3.2 17.8 + - - +
233A LYS* 1.3 89.4 + - - +
235A LEU* 1.3 65.9 + - - +
237A TRP* 3.0 18.1 + - - +
238A ILE* 3.0 19.3 + - + +
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Residues in contact with LEU 235 (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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123A LEU* 3.8 29.4 - - + -
124A PRO* 3.5 50.0 - - + +
125A LYS 4.8 2.9 - - - +
126A LYS 4.5 0.2 - - - -
127A GLY* 4.3 13.9 - - - +
231A LEU* 3.8 22.7 - - + +
232A SER* 2.8 24.8 + - - +
234A HIS* 1.3 72.6 - - - +
236A ASN* 1.3 66.8 + - - +
238A ILE* 3.1 12.7 + - + +
239A ILE* 2.8 36.5 + - + +
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Residues in contact with ASN 236 (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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232A LYS* 2.7 34.1 + - - +
233A LYS* 3.8 7.3 + - - +
235A LEU* 1.3 74.4 - - - +
237A TRP* 1.3 55.4 + - - +
238A ILE 3.1 0.3 + - - -
239A ILE* 3.1 12.3 + - - +
240A MET* 2.6 40.9 + - + +
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Residues in contact with TRP 237 (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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53A LEU* 5.1 2.0 - - + -
89A PHE* 3.0 32.5 - - + -
90A PRO 3.5 12.3 + - - -
91A TYR* 3.6 29.6 - + + -
92A PRO* 3.0 31.6 - - + +
103A LEU* 4.2 21.5 - - + -
104A LYS* 4.2 2.9 - - - -
105A LEU* 3.8 29.6 - - + -
233A LYS 3.2 11.7 + - - +
234A HIS 3.0 8.9 + - - +
236A ASN* 1.3 78.5 - - - +
238A ILE* 1.3 77.4 + - + +
240A MET* 4.0 16.7 - - + +
241A THR* 2.6 55.5 + - - -
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Residues in contact with ILE 238 (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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47A ILE* 3.7 28.5 - - + -
53A LEU* 4.1 24.7 - - + -
103A LEU* 5.4 2.7 - - + -
105A LEU* 3.8 14.8 - - + -
123A LEU* 4.0 17.0 - - + -
231A LEU* 4.7 10.3 - - + -
234A HIS* 3.0 18.1 + - + +
235A LEU* 3.1 26.4 + - + +
237A TRP* 1.3 93.8 - - + +
239A ILE* 1.3 64.9 + - - +
241A THR* 3.1 8.1 + - - -
242A ILE* 3.0 24.8 + - + +
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Residues in contact with ILE 239 (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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123A LEU* 4.1 23.1 - - + -
235A LEU* 2.8 33.9 + - + +
236A ASN* 3.9 11.7 - - - +
238A ILE* 1.3 72.8 - - - +
240A MET* 1.3 60.2 + - - +
241A THR 3.6 0.2 + - - -
242A ILE* 3.9 5.3 + - - +
243A LYS* 3.2 49.4 + - - +
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Residues in contact with MET 240 (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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236A ASN* 2.6 25.2 + - + +
237A TRP* 4.0 14.4 - - + +
239A ILE* 1.3 73.6 - - - +
241A THR* 1.3 79.6 + - - +
243A LYS* 4.0 7.2 + - - +
244A GLY* 3.5 14.7 + - - -
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Residues in contact with THR 241 (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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51A TRP* 4.2 8.7 - - + -
89A PHE* 3.9 34.5 - - + -
105A LEU* 3.7 19.5 - - + -
237A TRP* 2.6 45.2 + - - -
238A ILE 3.1 4.2 + - - -
240A MET* 1.3 84.6 - - - +
242A ILE* 1.3 69.3 + - - +
244A GLY* 3.2 15.9 + - - +
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Residues in contact with ILE 242 (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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47A ILE* 4.7 4.3 - - + -
48A ALA* 5.5 3.6 - - + -
51A TRP* 3.5 56.9 + - + +
105A LEU* 3.6 26.5 - - + -
238A ILE* 3.0 32.6 + - + +
239A ILE* 4.3 5.6 - - - +
241A THR* 1.3 73.2 - - - +
243A LYS* 1.3 70.9 + - + +
244A GLY 2.9 11.8 - - - +
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Residues in contact with LYS 243 (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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239A ILE* 3.2 41.5 + - - +
240A MET* 4.2 6.3 - - - +
241A THR 3.4 0.4 - - - -
242A ILE* 1.3 81.8 - - + +
244A GLY* 1.3 64.2 + - - +
245A ALA* 3.4 6.1 + - - +
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Residues in contact with GLY 244 (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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51A TRP* 5.2 3.5 - - - -
107A GLN* 5.7 1.7 + - - -
240A MET 3.5 8.4 + - - -
241A THR 3.2 13.3 + - - +
242A ILE 2.9 15.3 + - - +
243A LYS* 1.3 77.6 - - - +
245A ALA* 1.3 59.9 + - - +
246A VAL* 4.7 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