Contacts of the helix formed by residues 239 - 247 (chain C) in PDB entry 1DXO
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 LYS 239 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226C SER* 2.9 29.2 + - - +
227C LEU 2.9 15.8 + - - +
228C PHE 3.5 15.9 + - - -
229C ASP* 3.7 34.5 - - - +
237C LEU 3.5 1.0 + - - -
238C MET* 1.3 74.4 - - - +
240C LYS* 1.3 54.8 + - - +
241C GLU* 3.4 28.5 - - - +
242C VAL* 3.1 15.2 + - + +
243C GLN* 2.7 31.9 + - - +
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Residues in contact with LYS 240 (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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229C ASP* 4.8 10.1 - - - +
238C MET 3.5 2.1 + - - +
239C LYS* 1.3 72.0 - - - +
241C GLU* 1.3 73.1 + - + +
243C GLN* 3.1 16.3 + - - +
244C ASP* 2.9 34.1 + - - +
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Residues in contact with GLU 241 (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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229C ASP* 5.5 0.2 - - - +
239C LYS* 3.4 30.9 - - - +
240C LYS* 1.3 92.6 + - + +
242C VAL* 1.3 59.8 + - + +
244C ASP* 3.3 5.8 + - - +
245C GLU* 2.9 48.0 + - + +
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Residues in contact with VAL 242 (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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226C SER 5.2 0.2 - - - +
227C LEU* 3.8 49.6 - - + +
238C MET* 3.8 18.8 - - + -
239C LYS* 3.1 28.4 + - + +
241C GLU* 1.3 76.8 - - + +
243C GLN* 1.3 65.7 + - - +
245C GLU* 3.9 9.7 - - - +
246C GLU* 3.0 36.6 + - - +
253C LEU* 5.4 0.2 - - + -
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Residues in contact with GLN 243 (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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158A GLN* 3.7 28.6 + - - +
237C LEU* 5.3 4.0 - - - +
238C MET* 3.1 47.4 + - + +
239C LYS 2.7 21.1 + - - +
240C LYS* 3.1 17.1 + - - +
242C VAL* 1.3 73.8 - - - +
244C ASP* 1.3 62.4 + - - +
246C GLU* 3.5 2.9 + - - +
247C LYS* 2.8 30.2 + - + +
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Residues in contact with ASP 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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240C LYS* 2.9 25.3 + - - +
241C GLU* 3.8 5.5 - - - +
243C GLN* 1.3 76.8 - - - +
245C GLU* 1.3 66.7 + - + +
246C GLU 3.0 1.8 - - - -
247C LYS* 2.9 35.3 + - - +
248C ASN* 3.6 9.6 + - - -
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Residues in contact with GLU 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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241C GLU* 2.9 41.5 + - - +
242C VAL* 3.9 10.2 + - - +
244C ASP* 1.3 76.5 - - + +
246C GLU* 1.3 65.5 + - - +
248C ASN* 4.0 14.7 + - - +
249C LYS* 3.9 20.9 + - - +
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Residues in contact with GLU 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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227C LEU* 5.6 0.7 - - - +
238C MET* 5.3 1.8 - - + -
242C VAL* 3.0 31.3 + - + +
243C GLN* 3.9 5.8 - - - +
245C GLU* 1.3 79.8 - - - +
247C LYS* 1.3 52.5 + - - +
248C ASN 3.0 5.8 - - - -
249C LYS* 2.9 43.9 + - + +
251C PHE 5.0 3.6 - - - +
252C GLY 5.9 0.3 - - - -
253C LEU* 4.0 27.5 - - + +
259C LEU* 3.7 29.2 - - + -
261C LYS* 2.4 31.9 + - - +
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Residues in contact with LYS 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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243C GLN* 2.8 26.8 + - + +
244C ASP* 2.9 27.8 + - - +
246C GLU* 1.3 76.1 - - - +
248C ASN* 1.3 62.1 + - - +
249C LYS 3.4 2.6 + - - +
261C LYS* 4.0 10.6 + - - +
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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