Contacts of the helix formed by residues 238 - 244 (chain B) in PDB entry 5COX
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 LEU 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A TYR* 6.1 0.4 - - - +
140A GLU* 3.8 26.5 - - + +
144A ASN* 6.1 0.2 - - - +
671A NAG 4.5 42.0 - - - +
237B THR* 1.3 70.3 - - - +
239B ASP* 1.3 67.1 + - - +
241B GLN* 3.9 17.9 - - + +
242B HIS* 3.1 75.9 + - + +
326B GLU* 5.4 2.7 - - - +
330B GLN* 6.1 0.9 - - - +
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B THR* 3.0 10.8 + - - +
238B LEU* 1.3 84.8 - - - +
240B ARG* 1.3 62.3 + - - +
242B HIS* 3.4 5.9 + - - +
243B LYS* 3.4 41.2 + - - +
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Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B GLY* 3.7 7.2 - - - -
236B GLU* 3.0 37.5 + - - +
237B THR* 2.8 21.9 + - - +
239B ASP* 1.3 76.3 + - - +
241B GLN* 1.3 57.9 + - - +
242B HIS 3.0 1.3 - - - -
243B LYS* 2.7 32.3 + - - +
244B LEU* 3.1 19.3 + - + +
271B VAL* 3.1 25.3 - - + +
272B GLU* 3.0 24.5 + - - +
273B MET* 3.3 30.9 - - - -
288B GLY* 3.4 29.2 + - - -
289B GLN 3.4 1.2 - - - +
290B GLU* 3.5 8.0 + - - +
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Residues in contact with GLN 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLU* 5.2 3.4 + - - +
234B TYR* 3.1 27.2 + - + +
235B GLY* 4.9 1.6 - - - +
237B THR 2.7 16.6 + - - +
238B LEU* 3.6 26.4 - - + +
240B ARG* 1.3 73.6 - - - +
242B HIS* 1.3 63.9 + - - +
244B LEU* 3.2 4.5 + - - +
245B ARG* 2.6 59.0 + - - +
252B LEU* 5.1 1.0 - - - +
329B PHE* 3.0 34.1 - - + -
330B GLN* 4.7 7.4 - - - +
333B LYS* 4.5 14.8 - - - +
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Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A NAG 6.0 0.6 - - - -
238B LEU* 3.1 54.8 + - + +
239B ASP* 3.7 6.7 - - - +
240B ARG 3.0 1.0 - - - -
241B GLN* 1.3 79.4 - - - +
243B LYS* 1.3 59.9 + - - +
244B LEU 3.1 5.2 + - - -
245B ARG* 3.0 41.8 + - - +
247B PHE* 3.3 39.2 - + + -
326B GLU* 4.2 6.7 - - - -
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Residues in contact with LYS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ASP* 3.4 31.5 + - - +
240B ARG* 2.7 15.6 + - - +
242B HIS* 1.3 72.3 - - - +
244B LEU* 1.3 53.9 - - - +
253B LYS* 2.6 24.2 + - - +
269B THR* 3.0 39.2 - - - +
270B GLN* 3.5 29.3 + - + +
271B VAL* 3.7 14.1 - - + +
272B GLU* 5.4 3.4 - - - +
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ILE 4.2 4.3 - - - +
234B TYR 3.2 31.6 - - - +
235B GLY* 4.1 4.7 - - - +
240B ARG* 3.1 16.8 + - + +
241B GLN* 3.5 6.7 - - - +
242B HIS 3.1 0.2 - - - -
243B LYS* 1.3 80.0 - - - +
245B ARG* 1.3 49.5 - - - +
252B LEU* 3.1 19.3 - - + +
253B LYS* 2.8 43.6 + - - +
264B PRO* 5.3 3.8 - - + +
269B THR* 4.8 1.6 - - + +
271B VAL* 3.5 31.0 - - + -
286B ALA* 4.2 14.4 - - + -
287B VAL* 4.3 9.9 - - - +
288B GLY* 3.7 17.7 - - - -
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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