Contacts of the helix formed by residues 253 - 261 (chain A) in PDB entry 1OFD
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 THR 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A TRP* 1.3 77.2 - - - +
254A LYS* 1.3 64.8 + - - +
255A ALA* 3.7 8.0 + - - +
256A GLU* 3.1 39.2 + - - +
257A LEU* 3.1 24.3 + - - +
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Residues in contact with LYS 254 (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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245A LYS 6.0 2.5 - - - +
247A LEU 5.3 7.9 - - - +
252A TRP 4.1 0.2 + - - -
253A THR* 1.3 72.5 - - - +
255A ALA* 1.3 56.9 + - - +
257A LEU* 3.4 10.1 + - + +
258A GLU* 2.9 31.2 + - + +
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Residues in contact with ALA 255 (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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253A THR* 3.2 7.9 + - - +
254A LYS* 1.3 76.7 - - - +
256A GLU* 1.3 65.3 + - + +
258A GLU* 3.4 8.7 + - - +
259A ALA* 3.0 21.7 + - - +
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Residues in contact with GLU 256 (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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100A GLU* 5.1 4.6 - - - +
146A ARG* 2.3 45.2 + - - -
147A ARG* 6.0 0.3 - - - +
150A ILE* 3.8 17.8 - - + +
251A GLY 4.4 0.3 - - - +
252A TRP* 3.7 15.3 - - + -
253A THR* 3.1 38.5 + - - +
255A ALA* 1.3 76.6 - - + +
257A LEU* 1.3 62.5 + - - +
259A ALA* 3.2 20.9 + - - +
260A LEU* 3.4 13.2 + - - +
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Residues in contact with LEU 257 (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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244A GLU 6.1 0.2 - - - -
247A LEU* 3.5 57.4 - - + +
248A GLU* 3.9 10.1 - - - -
249A VAL* 4.1 15.9 - - + +
252A TRP* 3.7 36.3 - - + +
253A THR 3.1 22.3 + - - +
254A LYS* 3.7 9.4 - - + +
256A GLU* 1.3 71.7 - - - +
258A GLU* 1.3 64.8 + - - +
260A LEU* 3.1 32.7 + - + +
261A THR* 3.4 4.3 + - - -
280A LEU* 5.0 0.9 - - + -
284A THR* 4.6 4.7 - - + -
529A LEU* 4.8 2.0 - - + -
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Residues in contact with GLU 258 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A LYS* 4.3 0.2 + - - -
244A GLU 5.7 1.0 - - - +
245A LYS* 5.6 6.1 - - - +
254A LYS* 2.9 20.2 + - + +
255A ALA* 3.5 10.1 - - - +
257A LEU* 1.3 78.0 - - - +
259A ALA* 1.3 54.2 + - - +
261A THR* 2.5 63.5 + - + +
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Residues in contact with ALA 259 (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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150A ILE* 4.0 15.7 - - + -
153A SER* 3.9 8.5 - - - -
154A ILE* 4.0 28.0 - - + +
157A LYS* 3.1 13.0 + - - +
255A ALA 3.0 13.4 + - - +
256A GLU* 3.3 12.6 - - - +
257A LEU 3.2 0.2 - - - -
258A GLU* 1.3 76.5 - - - +
260A LEU* 1.3 59.1 + - - +
261A THR* 2.9 11.5 + - - -
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Residues in contact with LEU 260 (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 TYR* 3.5 41.7 - - + +
150A ILE* 4.1 16.4 - - + -
153A SER* 3.6 30.5 - - - +
157A LYS* 4.7 2.0 - - - -
247A LEU* 5.7 0.7 - - + -
252A TRP* 3.7 15.9 - - + -
256A GLU 3.6 13.5 - - - +
257A LEU* 3.1 17.5 + - + +
259A ALA* 1.3 76.0 - - - +
261A THR* 1.3 69.3 + - - +
262A PRO* 3.5 10.7 - - - +
263A ILE* 3.8 16.5 - - + +
280A LEU* 3.7 20.0 - - + -
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Residues in contact with THR 261 (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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157A LYS* 2.0 39.4 + - - +
244A GLU* 3.8 10.3 - - - +
247A LEU* 5.5 1.7 - - - +
257A LEU 3.4 4.5 + - - -
258A GLU* 2.5 48.3 + - + +
259A ALA 2.9 2.6 + - - -
260A LEU* 1.3 78.5 - - - +
262A PRO* 1.3 71.4 - - + -
263A ILE* 2.5 30.8 + - - +
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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