Contacts of the helix formed by residues 237 - 241 (chain C) in PDB entry 5DST
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 HIS 237 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229C ARG 5.5 0.4 - - - -
232C LYS* 3.1 41.6 + - + +
233C ASP* 3.6 33.7 - - - +
236C ILE* 1.3 91.4 - - + +
238C TRP* 1.3 64.2 + - - +
240C GLU* 2.8 55.3 + - - +
241C ASN 4.4 0.2 + - - -
251C ARG* 5.5 1.6 - - - -
255C MET* 5.4 1.3 - - + -
343C GLU 5.1 4.9 - - - -
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Residues in contact with TRP 238 (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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233C ASP 2.9 11.6 + - - +
234C PHE* 3.3 27.1 - + - +
236C ILE 4.8 1.8 - - - +
237C HIS* 1.3 75.5 - - - +
239C TRP* 1.3 119.7 + + - +
240C GLU 3.0 1.4 + - - -
241C ASN* 3.1 26.9 + - - +
242C VAL* 4.0 20.4 - - + +
243C TYR* 5.4 2.7 - + - -
87D GLU* 4.2 8.5 - - + -
90D LEU* 3.8 32.5 - - + -
91D LYS* 3.5 43.7 - - + +
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Residues in contact with TRP 239 (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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235C LYS 3.4 21.7 + - - -
236C ILE* 3.6 15.0 - - - +
237C HIS 3.2 0.8 - - - -
238C TRP* 1.3 112.2 - + - +
240C GLU* 1.3 58.0 + - - +
241C ASN 3.1 0.9 + - - -
242C VAL* 3.7 5.2 - - - +
247C MET* 3.0 55.3 + - + +
248C THR* 5.1 0.2 - - - -
250C ILE* 3.5 40.2 - - + -
251C ARG* 3.6 30.7 - - + -
254C ALA* 4.3 10.1 - - + +
83D PHE* 3.5 40.2 - + + -
86D HIS* 4.8 0.9 - - + -
87D GLU* 3.8 22.4 + - + -
90D LEU* 4.4 5.6 - - + -
122D THR* 5.0 0.9 - - + -
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Residues in contact with GLU 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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237C HIS* 2.8 50.1 + - - +
238C TRP 3.0 0.6 + - - -
239C TRP* 1.3 76.8 - - - +
241C ASN* 1.3 60.7 + - + +
245C PHE 3.6 1.0 - - - +
246C ASP* 3.6 22.8 - - - +
248C THR* 3.8 27.1 - - + -
251C ARG* 3.4 24.9 + - + +
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Residues in contact with ASN 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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238C TRP* 3.1 18.9 + - - +
239C TRP 3.1 0.4 - - - -
240C GLU* 1.3 83.5 - - + +
242C VAL* 1.3 57.0 + - - +
243C TYR 3.6 2.4 + - - -
244C GLY* 2.9 34.5 + - - +
245C PHE 3.3 2.7 - - - -
241F ASN* 5.4 8.1 - - - +
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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