Contacts of the helix formed by residues 243 - 250 (chain C) in PDB entry 6XHU
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 243 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C LEU* 4.6 4.5 - - - -
241C PRO* 4.4 7.6 - - + +
242C LEU* 1.3 78.5 - - - +
244C GLN* 1.3 64.8 + - - +
245C ASP* 3.4 18.6 + - - +
246C HIS* 3.0 38.9 + - + +
247C VAL* 3.1 15.6 + - - +
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Residues in contact with GLN 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C LEU* 4.6 14.0 - - + +
243C THR* 1.3 71.1 - - - +
245C ASP* 1.3 68.8 + - - +
247C VAL* 3.1 27.6 + - - +
248C ASP* 2.8 51.6 + - - +
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Residues in contact with ASP 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C THR* 3.2 11.3 + - - +
244C GLN* 1.3 78.1 - - - +
246C HIS* 1.3 64.6 + - + +
248C ASP* 3.2 13.7 + - - +
249C ILE* 3.1 34.5 + - + +
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Residues in contact with HIS 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C THR* 6.5 0.2 - - - -
202C VAL* 3.9 33.9 - - + +
240C GLU* 5.9 3.6 - - + -
241C PRO 3.6 17.9 - - - -
242C LEU* 3.5 25.9 - - + +
243C THR* 3.0 37.2 + - + +
245C ASP* 1.3 79.8 - - + +
247C VAL* 1.3 65.7 + - - +
249C ILE* 3.2 21.1 + - + +
250C LEU* 3.2 21.4 + - - +
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Residues in contact with VAL 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C LEU* 4.6 13.0 - - + -
242C LEU* 4.5 11.9 - - + -
243C THR 3.1 13.5 + - - +
244C GLN* 3.1 33.3 + - - +
246C HIS* 1.3 74.8 - - - +
248C ASP* 1.3 64.3 - - - +
250C LEU* 3.2 11.8 + - - +
251C GLY* 3.4 9.4 + - - -
261C VAL* 4.1 39.3 - - + +
262C LEU* 5.6 6.5 - - + -
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Residues in contact with ASP 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C GLN* 2.8 40.3 + - - +
245C ASP* 3.6 15.6 - - - +
246C HIS 3.2 0.2 - - - -
247C VAL* 1.3 78.5 - - - +
249C ILE* 1.3 62.9 + - + +
251C GLY* 3.1 14.4 + - - -
252C PRO* 4.1 4.3 - - - +
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Residues in contact with ILE 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL* 5.3 2.7 - - + -
245C ASP* 3.1 26.5 + - + +
246C HIS* 3.2 18.1 + - + +
248C ASP* 1.3 78.5 - - + +
250C LEU* 1.3 60.9 + - - +
251C GLY 3.5 0.5 + - - -
252C PRO* 3.6 11.9 - - - +
253C LEU* 5.8 0.7 - - - +
293C PRO* 3.8 32.6 - - + +
294C PHE* 4.0 31.1 - - + -
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Residues in contact with LEU 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL* 4.2 11.0 - - + +
205C LEU* 3.7 36.1 - - + -
206C ALA* 4.1 22.0 - - - +
209C TYR* 4.5 10.4 - - + -
242C LEU* 5.5 0.4 - - + -
246C HIS* 3.2 18.5 + - + +
247C VAL 3.2 6.8 + - - +
248C ASP 3.1 0.8 - - - -
249C ILE* 1.3 76.9 - - - +
251C GLY* 1.3 64.0 + - - +
252C PRO* 3.4 2.5 - - - -
253C LEU* 3.0 26.5 + - + +
254C SER* 3.0 10.4 + - - -
261C VAL* 4.0 24.2 - - + +
293C PRO* 3.8 27.4 - - + -
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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