Contacts of the helix formed by residues 257 - 266 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D ARG* 5.0 21.3 - - - +
77D MET* 4.7 20.0 - - + +
80D ASP* 5.7 4.9 - - - -
251D ARG* 4.5 1.6 - - - +
255D ASN* 3.1 12.2 + - + +
256D SER* 1.3 101.8 - - - +
258D ALA* 1.3 65.7 + - - +
259D GLU 3.3 2.5 - - - -
260D THR* 3.1 18.4 + - + +
261D TYR* 3.0 35.0 + - + -
1362D FLC 3.8 38.1 + - + +
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Residues in contact with ALA 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ARG 3.5 12.6 - - - +
252D PHE* 3.4 26.6 - - - +
253D PHE* 3.5 12.1 - - - +
254D GLY 4.0 0.4 - - - +
255D ASN* 3.1 25.3 + - - +
257D TRP* 1.3 77.1 - - - +
259D GLU* 1.3 57.7 + - - +
261D TYR* 3.1 3.6 + - - +
262D ARG* 2.8 43.3 + - - +
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Residues in contact with GLU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D ASN 4.7 0.8 + - - -
256D SER 5.0 3.9 + - - +
257D TRP 3.3 0.6 - - - -
258D ALA* 1.3 74.9 - - - +
260D THR* 1.3 60.3 + - - +
262D ARG* 3.6 28.3 + - + +
263D ASN* 2.9 52.2 + - - +
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Residues in contact with THR 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D SER 4.8 2.1 + - - -
257D TRP* 3.1 24.8 + - - -
259D GLU* 1.3 77.1 - - - +
261D TYR* 1.3 60.8 + - + +
263D ASN* 3.4 9.2 + - - +
264D ARG* 2.9 43.3 + - - +
1362D FLC 3.8 21.7 + - - +
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Residues in contact with TYR 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D MET* 4.8 1.8 - - - +
227D ASN* 3.1 28.7 + - - -
231D GLY* 4.2 2.7 - - - -
251D ARG* 3.2 53.3 + - + +
252D PHE* 3.5 24.8 - + + -
257D TRP* 3.0 28.5 + - + +
258D ALA 3.1 7.4 + - - +
260D THR* 1.3 78.0 - - + +
262D ARG* 1.3 60.4 + - - +
264D ARG* 3.2 20.5 + - - +
265D PHE* 3.0 45.0 + + - +
1361D NDP 3.6 3.3 - - - -
1362D FLC 2.4 33.9 + - + -
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Residues in contact with ARG 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D LYS* 5.1 7.9 - - - -
252D PHE* 2.9 29.8 + - + +
253D PHE* 3.8 25.6 - - + +
254D GLY 5.1 1.6 - - - +
255D ASN 5.5 0.4 + - - -
258D ALA* 2.8 30.6 + - - +
259D GLU* 3.6 37.1 + - - +
261D TYR* 1.3 76.7 - - - +
263D ASN* 1.3 63.1 + - - +
266D TRP* 2.8 54.3 + - + +
267D LYS* 5.0 0.9 - - - +
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Residues in contact with ASN 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D GLU* 2.9 40.9 + - - +
260D THR* 3.7 7.8 - - - +
262D ARG* 1.3 78.5 - - - +
264D ARG* 1.3 61.1 + - - +
267D LYS* 3.4 20.5 + - - +
356D PRO* 5.3 0.5 - - - +
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Residues in contact with ARG 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D MET* 4.0 15.5 - - - +
226D TYR* 4.2 4.4 - - - -
227D ASN* 3.0 19.5 + - - -
260D THR* 2.9 28.4 + - - +
261D TYR* 3.2 28.3 + - - +
262D ARG 3.2 0.2 - - - -
263D ASN* 1.3 78.5 - - - +
265D PHE* 1.3 88.4 + - + +
267D LYS* 3.0 19.1 + - - -
356D PRO* 3.4 40.2 - - + +
360D ARG* 3.6 13.1 - - - +
1362D FLC 3.0 43.4 + - - -
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Residues in contact with PHE 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D MET* 4.2 4.9 - - - -
202D ASN* 3.8 8.1 - - - -
205D THR* 3.4 28.5 - - + -
227D ASN* 3.4 27.4 - - + -
230D ALA* 3.5 39.3 - - + +
233D LEU* 3.4 12.1 - - + +
252D PHE* 4.2 9.2 - + + -
261D TYR* 3.0 22.8 + + - +
264D ARG* 1.3 111.7 - - + +
266D TRP* 1.3 62.6 + - - +
267D LYS* 2.9 14.5 + - - +
270D HIS* 3.0 36.7 + + - +
356D PRO* 4.4 2.9 - - + -
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Residues in contact with TRP 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D LEU* 3.6 17.5 - - + -
238D TYR* 3.6 44.2 - + + -
239D LYS 3.1 21.3 - - - -
240D TYR* 3.0 42.6 + + - -
242D ASP* 3.8 10.3 - - + -
243D LYS* 3.8 22.5 - - + +
252D PHE* 3.7 22.9 - + + -
253D PHE* 3.6 24.5 - + - -
261D TYR 3.9 0.4 + - - -
262D ARG* 2.8 41.8 + - + +
265D PHE* 1.3 67.9 - - - +
267D LYS* 1.3 62.6 + - - +
271D PHE* 3.5 12.1 - + - -
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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