Contacts of the helix formed by residues 235 - 242 (chain C) in PDB entry 2B5F
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 SER 235 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230C ALA 4.7 0.4 + - - -
233C PHE* 3.6 31.4 - - - -
234C ASN* 1.3 75.7 - - - +
236C ASN* 1.3 61.7 + - - +
237C LYS* 3.5 8.7 + - - +
238C VAL* 3.3 23.5 + - - +
239C TRP* 3.0 33.1 + - - -
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Residues in contact with ASN 236 (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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234C ASN* 5.6 1.4 - - - +
235C SER* 1.3 72.6 + - - +
237C LYS* 1.3 63.7 + - - +
239C TRP* 3.3 10.4 + - - +
240C ASP* 3.0 30.0 + - - +
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Residues in contact with LYS 237 (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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154C SER* 4.9 8.7 - - - -
155C VAL* 4.2 21.2 + - - +
157C LEU 6.2 0.2 - - - +
235C SER* 3.4 7.6 + - - +
236C ASN* 1.3 78.2 - - - +
238C VAL* 1.3 62.5 + - + +
240C ASP* 3.3 11.7 + - + +
241C ASP* 3.2 34.2 + - - +
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Residues in contact with VAL 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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149C GLY 5.4 0.7 - - - +
152C ALA* 3.9 17.3 - - + +
153C ASN 3.5 23.6 - - - +
154C SER* 4.5 14.6 - - - +
230C ALA* 3.8 28.9 - - + +
233C PHE* 4.0 20.2 - - + -
235C SER* 3.3 22.7 + - - +
236C ASN 3.3 0.4 - - - -
237C LYS* 1.3 79.5 - - + +
239C TRP* 1.3 64.1 + - - +
241C ASP* 3.3 5.4 + - - +
242C GLN* 3.1 21.7 + - - +
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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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227C PHE* 4.1 16.8 - + - -
230C ALA* 3.4 36.6 + - + -
231C VAL* 3.7 32.1 - - + -
234C ASN* 3.3 25.9 + - - +
235C SER 3.0 27.6 + - - +
236C ASN* 3.3 10.3 + - - +
238C VAL* 1.3 77.7 - - + +
240C ASP* 1.3 60.5 + - - +
242C GLN* 3.3 36.8 + - + +
243C TRP* 4.7 1.2 + - - -
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Residues in contact with ASP 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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161C LYS* 5.6 2.9 - - - +
236C ASN* 3.0 18.5 + - - +
237C LYS* 3.3 15.0 - - + +
238C VAL 3.2 0.2 - - - -
239C TRP* 1.3 79.6 - - - +
241C ASP* 1.3 63.4 + - - +
243C TRP* 3.4 22.2 + - - -
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Residues in contact with ASP 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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154C SER* 3.8 7.1 - - - -
155C VAL* 2.8 44.2 + - + +
161C LYS* 3.3 28.0 + - - +
237C LYS* 3.2 24.0 + - - +
238C VAL 3.3 4.0 + - - +
240C ASP* 1.3 82.8 - - - +
242C GLN* 1.3 64.2 + - - +
243C TRP* 3.1 4.9 + - - -
244C ILE* 3.2 26.6 + - + +
245C PHE* 3.5 14.5 - - + -
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Residues in contact with GLN 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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153C ASN 4.8 4.8 + - - -
226C SER* 3.5 27.3 + - - -
227C PHE* 3.2 23.6 + - + +
230C ALA* 3.6 16.5 - - - +
238C VAL 3.1 11.0 + - - +
239C TRP* 3.3 37.8 + - + +
241C ASP* 1.3 77.4 - - - +
243C TRP* 1.3 63.5 + - - +
245C PHE* 3.0 21.5 + - - +
246C TRP* 3.0 36.8 + - + +
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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