Contacts of the helix formed by residues 257 - 266 (chain C) in PDB entry 2BP1
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 TRP 257 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C ARG* 4.9 27.6 - - - +
77C MET* 4.9 18.8 - - + +
80C ASP* 5.7 5.2 - - - -
251C ARG* 4.6 2.5 - - - +
255C ASN* 2.8 19.1 + - + +
256C SER* 1.3 96.6 - - - +
258C ALA* 1.3 65.6 + - - +
259C GLU 3.3 3.1 - - - -
260C THR* 3.2 14.1 + - - -
261C TYR* 3.1 36.3 + - + -
1362C FLC 3.1 40.8 + - + +
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Residues in contact with ALA 258 (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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251C ARG 3.5 13.5 - - - +
252C PHE 3.4 25.4 - - - +
253C PHE* 3.6 14.6 - - - +
254C GLY 4.0 0.9 - - - +
255C ASN* 2.8 22.0 + - - +
257C TRP* 1.3 76.5 - - - +
259C GLU* 1.3 59.2 + - - +
261C TYR* 3.1 4.2 + - - +
262C ARG* 2.8 40.8 + - - +
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Residues in contact with GLU 259 (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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255C ASN 4.7 0.8 + - - -
256C SER 5.0 3.7 + - - +
257C TRP 3.3 0.4 - - - -
258C ALA* 1.3 79.8 - - - +
260C THR* 1.3 63.3 + - - +
262C ARG* 3.3 27.9 + - - +
263C ASN* 3.0 42.2 + - - +
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Residues in contact with THR 260 (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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256C SER 5.1 1.9 + - - -
257C TRP* 3.2 20.6 + - - +
259C GLU* 1.3 79.5 - - - +
261C TYR* 1.3 61.7 + - + +
263C ASN* 3.5 8.2 + - - +
264C ARG* 3.0 53.2 + - - +
1362C FLC 4.2 18.8 + - - +
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Residues in contact with TYR 261 (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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46C MET* 4.5 2.5 - - + +
227C ASN* 3.1 23.2 + - - -
231C GLY* 4.1 7.6 - - - -
251C ARG* 3.0 62.7 + - + +
252C PHE* 3.4 21.7 - + + -
257C TRP* 3.1 29.1 + - + +
258C ALA 3.1 6.5 + - - +
260C THR* 1.3 77.2 - - + +
262C ARG* 1.3 60.9 + - - +
264C ARG* 3.2 19.4 + - - +
265C PHE* 2.9 45.0 + + - +
1361C NDP 3.7 4.2 - - - -
1362C FLC 2.6 33.8 + - + -
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Residues in contact with ARG 262 (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 LYS* 5.0 6.5 - - - -
252C PHE* 2.8 31.6 + - + +
253C PHE* 3.6 29.0 - - - +
254C GLY 5.4 1.2 - - - +
258C ALA* 2.8 27.7 + - - +
259C GLU* 3.6 40.5 + - - +
261C TYR* 1.3 76.3 - - - +
263C ASN* 1.3 61.9 + - - +
266C TRP* 2.9 53.8 + - + +
267C LYS* 4.9 1.6 - - - +
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Residues in contact with ASN 263 (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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259C GLU* 3.0 42.0 + - - +
260C THR* 3.8 7.1 - - - +
262C ARG* 1.3 78.3 - - - +
264C ARG* 1.3 61.1 + - - +
267C LYS* 3.3 18.4 + - - -
356C PRO* 5.5 0.3 - - - +
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Residues in contact with ARG 264 (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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200C MET* 3.9 20.0 - - - +
226C TYR* 4.0 2.6 - - - -
227C ASN* 2.8 21.2 + - - -
260C THR* 3.0 29.5 + - - +
261C TYR* 3.4 18.8 + - - +
262C ARG 3.1 0.2 - - - -
263C ASN* 1.3 78.7 - - - +
265C PHE* 1.3 85.0 + - + +
267C LYS* 2.8 23.1 + - - -
356C PRO* 3.5 33.9 - - + +
360C ARG* 3.8 8.7 - - - +
1362C FLC 3.1 49.1 + - - -
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Residues in contact with PHE 265 (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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200C MET* 4.2 3.6 - - - -
202C ASN* 3.9 8.5 - - - -
205C THR* 3.6 23.3 - - + -
227C ASN* 3.4 23.3 - - + -
230C ALA* 3.4 42.0 - - + +
231C GLY 4.0 0.4 - - - -
233C LEU* 3.5 7.8 - - + +
252C PHE* 4.1 10.3 - + + -
261C TYR* 2.9 21.3 + + - +
264C ARG* 1.3 111.4 - - + +
266C TRP* 1.3 62.9 + - - +
267C LYS* 2.9 15.4 + - - +
270C HIS* 2.9 39.2 + + + +
356C PRO* 4.3 8.3 - - + -
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Residues in contact with TRP 266 (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 LEU* 3.7 16.2 - - + -
238C TYR* 3.7 35.9 - + + -
239C LYS 3.1 26.9 - - - -
240C TYR* 3.0 43.4 + + - -
242C ASP* 3.7 9.4 - - + -
243C LYS* 3.8 22.7 - - + +
252C PHE* 3.7 20.6 - + + -
253C PHE* 3.6 28.5 - + - -
261C TYR 3.9 0.4 + - - -
262C ARG* 2.9 41.6 + - + +
265C PHE* 1.3 68.5 - - - +
267C LYS* 1.3 61.1 + - - +
271C PHE* 3.6 11.2 - + - -
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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