Contacts of the helix formed by residues 232 - 243 (chain A) in PDB entry 1OWK
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 ARG 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TYR* 6.1 3.2 - - - +
127A ASP* 3.2 20.4 + - - +
178A THR* 2.9 30.9 + - - -
179A LYS* 3.1 28.5 + - - +
180A MET 4.8 0.2 - - - -
181A LEU* 3.9 30.1 - - + -
212A THR* 3.9 5.6 - - + +
230A TYR 3.6 2.2 + - - -
231A THR* 1.3 68.6 - - - +
233A VAL* 1.3 66.4 + - - +
234A SER* 2.8 38.2 + - - +
235A HIS* 3.1 51.5 + - - +
236A PHE* 3.3 14.2 - - - -
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 5.2 1.8 - - + -
97A ILE* 5.5 2.0 - - + -
121A LEU* 3.7 21.1 - - + -
122A PRO* 3.3 28.7 - - + -
211A LEU* 3.6 22.0 - - + +
212A THR 3.5 15.5 + - - +
213A GLY 4.3 1.6 - - - +
214A ILE* 4.3 21.3 - - + -
231A THR* 3.0 11.2 + - - +
232A ARG* 1.3 69.6 - - - +
234A SER* 1.3 63.8 + - - +
236A PHE* 2.8 22.0 + - - +
237A LEU* 3.4 9.6 + - + +
240A ILE* 4.1 12.3 - - + -
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Residues in contact with SER 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PRO* 3.4 20.5 - - - +
123A SER 4.3 12.1 - - - -
124A MET* 4.4 9.2 - - - +
125A TYR* 4.8 9.0 + - - -
127A ASP* 3.2 29.9 + - - -
212A THR* 5.0 0.8 + - - +
232A ARG* 2.8 30.9 + - - +
233A VAL* 1.3 76.0 - - - +
235A HIS* 1.3 59.8 + - - +
237A LEU* 3.1 25.6 + - - +
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Residues in contact with HIS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A MET* 5.8 0.5 - - - +
179A LYS* 3.3 45.5 + - + +
232A ARG* 3.1 45.5 + - + +
233A VAL 2.9 0.2 + - - -
234A SER* 1.3 82.2 + - - +
236A PHE* 1.3 79.2 + + + +
237A LEU 3.5 1.0 + - - -
238A PRO* 3.6 10.9 - - - +
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Residues in contact with PHE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A HIS* 3.7 25.6 - + - -
95A ASN* 3.6 29.8 - - - -
97A ILE* 3.9 31.9 - - + -
179A LYS* 3.8 30.7 - - + -
231A THR* 3.7 24.5 - - + -
232A ARG 3.3 20.2 - - - -
233A VAL* 2.8 14.6 + - - +
235A HIS* 1.3 87.1 - + + +
237A LEU* 1.3 63.4 + - - -
238A PRO* 3.3 4.3 - - - -
239A TRP* 2.8 19.8 + - + +
240A ILE* 3.0 13.4 + - + +
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Residues in contact with LEU 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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121A LEU* 4.3 16.2 - - + -
122A PRO* 3.3 31.0 - - + +
123A SER* 3.7 2.7 - - - -
124A MET* 3.3 44.6 - - + +
233A VAL* 3.4 13.8 + - + +
234A SER* 3.1 19.1 - - - +
235A HIS 3.3 0.2 - - - -
236A PHE* 1.3 74.7 - - - +
238A PRO* 1.3 71.7 - - + +
239A TRP 3.1 0.3 + - - -
240A ILE* 3.2 8.3 + - + +
241A ARG* 2.9 27.0 + - - +
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Residues in contact with PRO 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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124A MET* 3.2 27.1 - - + -
235A HIS 3.6 12.3 - - - +
236A PHE* 3.4 4.5 - - - -
237A LEU* 1.3 93.4 - - + +
239A TRP* 1.3 47.5 + - - +
241A ARG* 4.0 9.2 - - + +
242A SER* 2.7 37.1 + - - -
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Residues in contact with TRP 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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81A ILE* 4.4 12.3 - - + -
82A LEU 4.4 3.6 - - - -
83A HIS* 3.2 51.3 + + + -
84A LYS* 4.1 11.2 - - + +
97A ILE* 3.4 47.8 - - + -
98A ALA* 4.2 4.9 - - - -
99A LEU* 3.8 31.4 - - + -
236A PHE* 2.8 17.8 + - + +
238A PRO* 1.3 79.0 - - - +
240A ILE* 1.3 80.4 + - + +
242A SER* 3.3 3.5 + - - -
243A HIS* 2.9 68.6 + + - +
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Residues in contact with ILE 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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35A MET* 5.1 7.2 - - + -
41A ILE* 3.6 26.5 - - + -
97A ILE* 4.0 7.2 - - + -
99A LEU* 4.5 10.8 - - + -
121A LEU* 4.0 28.9 - - + -
233A VAL* 4.1 11.4 - - + -
236A PHE 3.0 14.0 + - - +
237A LEU* 3.7 11.2 - - + +
239A TRP* 1.3 101.4 - - + +
241A ARG* 1.3 58.0 + - - +
243A HIS 3.2 1.0 + - - -
244A THR* 2.7 49.9 + - + +
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Residues in contact with ARG 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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237A LEU 2.9 17.5 + - - +
238A PRO* 4.0 7.6 + - - +
240A ILE* 1.3 78.2 - - - +
242A SER* 1.3 77.1 + - - +
243A HIS 3.2 0.7 + - - -
244A THR* 3.2 25.4 + - - +
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Residues in contact with SER 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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238A PRO 2.7 21.4 + - - -
239A TRP* 3.3 8.0 + - - -
241A ARG* 1.3 90.7 - - - +
243A HIS* 1.3 68.9 + - - +
244A THR* 3.5 1.0 + - - +
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Residues in contact with HIS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP* 3.7 14.9 - - - -
81A ILE* 3.7 34.0 - - + +
84A LYS* 3.7 32.9 + - - +
99A LEU* 3.9 16.4 - - + +
239A TRP* 2.9 52.2 + + + +
240A ILE 3.9 0.2 - - - +
241A ARG 3.1 0.4 - - - -
242A SER* 1.3 88.6 - - - +
244A THR* 1.3 62.5 + - - +
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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