Contacts of the helix formed by residues 219 - 223 (chain A) in PDB entry 2OHF
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 PHE 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ASP* 3.4 31.2 - - + +
159A MET* 5.0 6.3 - - + -
160A ILE* 3.9 28.9 - - + -
163A ILE* 4.5 7.6 - - + -
186A MET* 4.3 18.8 - - + -
189A VAL* 4.1 16.6 - - + -
200A VAL* 3.8 26.9 - - + -
213A VAL 5.5 0.4 - - - -
214A LEU* 4.4 25.3 + - + -
217A HIS* 3.9 28.7 - + + -
218A LEU* 1.3 76.6 - - - +
220A LEU* 1.3 66.6 + - - +
221A THR 3.2 0.2 - - - -
222A SER* 2.4 31.0 + - - +
223A LYS* 3.5 4.7 - - - +
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Residues in contact with LEU 220 (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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111A LEU* 3.9 12.3 - - + +
114A ILE* 3.4 29.8 - - + -
115A SER* 3.2 35.0 - - - +
120A ILE* 4.3 8.1 - - - +
152A LEU* 3.7 32.7 - - + +
155A LYS* 3.3 42.8 - - + -
156A ASP* 2.9 13.7 + - - +
218A LEU 3.7 0.2 + - - -
219A PHE* 1.3 71.6 - - - +
221A THR* 1.3 58.6 + - - +
222A SER 3.2 4.0 + - - -
223A LYS* 3.3 24.7 + - - +
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Residues in contact with THR 221 (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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149A HIS* 5.5 1.8 - - - +
152A LEU* 4.0 9.9 - - + +
153A GLN* 3.2 40.1 + - + +
156A ASP* 2.5 24.0 + - - +
193A VAL* 5.1 1.9 - - - +
198A LYS 5.0 0.3 + - - -
199A PRO* 3.5 13.0 - - + +
200A VAL* 3.0 28.1 + - - +
201A ARG* 3.1 32.7 + - - +
220A LEU* 1.3 75.5 - - - +
222A SER* 1.3 56.6 + - - +
223A LYS 3.5 2.7 - - - -
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Residues in contact with SER 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.1 29.4 - - - +
17A GLY* 5.6 1.4 + - - -
200A VAL* 3.7 28.0 - - - -
201A ARG* 4.1 12.0 - - - +
214A LEU* 5.9 0.4 - - - -
218A LEU* 4.0 4.9 - - - -
219A PHE* 2.4 34.5 + - - -
221A THR* 1.3 77.7 + - - +
223A LYS* 1.3 67.0 + - - +
224A PRO* 3.8 3.6 - - - +
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Residues in contact with LYS 223 (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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17A GLY* 6.1 2.4 - - - -
18A ARG* 4.7 4.4 - - - +
114A ILE* 3.3 29.8 - - + +
115A SER* 3.6 20.9 + - - +
117A CYS* 2.7 32.0 + - + +
118A ASP* 4.4 6.1 + - - +
119A GLY* 4.1 11.4 - - - +
120A ILE* 4.1 11.5 - - + +
201A ARG* 3.3 19.6 + - - -
218A LEU* 4.1 28.3 - - - +
219A PHE 3.5 6.3 - - - +
220A LEU* 3.3 22.1 + - - +
222A SER* 1.3 80.3 + - - +
224A PRO* 1.3 71.2 - - + +
225A MET* 4.8 0.7 - - - +
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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