Contacts of the strand formed by residues 222 - 226 (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 ARG 222 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D GLU* 4.5 5.7 + - - -
138D LEU* 4.9 3.2 - - - +
168D GLU* 2.9 38.6 + - - -
195D THR* 3.0 16.0 + - - +
196D VAL* 3.3 26.5 - - + +
197D TYR* 2.8 31.7 + - - +
216D LEU* 4.9 0.4 - - - -
220D GLY 4.1 1.2 + - - -
221D LEU* 1.3 73.4 - - - +
223D PHE* 1.3 54.9 + - - +
224D TYR* 2.9 33.5 + - + -
310D HIS* 3.2 25.1 - - - +
311D GLY* 3.4 25.3 + - - +
312D ASP* 3.8 5.6 - - - +
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Residues in contact with PHE 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D TYR* 3.2 18.4 - + - -
199D GLY* 3.5 37.0 - - - -
201D TYR* 3.7 20.0 - + + -
208D VAL* 4.3 4.7 - - + -
212D LEU* 3.8 7.6 - - + -
213D PHE* 3.4 34.1 - + + -
216D LEU* 3.7 22.4 - - + -
222D ARG* 1.3 71.8 - - - +
224D TYR* 1.3 63.8 + - - +
225D ALA* 3.6 23.1 - - + -
306D LEU* 3.4 19.1 - - + -
312D ASP* 3.1 22.1 + - - +
313D ALA 2.9 23.9 + - - +
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Residues in contact with TYR 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D VAL* 4.3 12.6 - - + -
71D GLU* 3.0 42.5 + - - -
73D ASP* 5.9 0.2 - - - -
138D LEU* 4.1 3.6 - - + -
140D TYR* 3.3 24.2 - - - +
196D VAL* 3.8 13.0 - - + -
197D TYR 2.9 10.2 + - - +
198D GLN* 3.2 5.2 - - - +
199D GLY 2.9 25.3 + - - -
222D ARG* 2.9 33.4 + - + -
223D PHE* 1.3 84.6 - - - +
225D ALA* 1.3 62.0 + - - +
226D TYR 3.7 0.2 + - - -
311D GLY 3.6 20.3 + - - -
313D ALA* 3.3 22.9 - - + +
315D ILE* 4.0 20.0 - - + -
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Residues in contact with ALA 225 (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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199D GLY 3.4 5.6 - - - -
201D TYR* 3.9 7.9 - - + +
223D PHE* 3.6 16.2 - - + -
224D TYR* 1.3 69.9 - - - +
226D TYR* 1.3 60.5 + - - +
228D PRO* 4.3 1.9 - - + +
300D MET* 3.4 32.8 - - + -
306D LEU* 4.2 4.3 - - + -
313D ALA 2.9 14.4 + - - +
314D VAL* 3.9 2.8 - - + +
315D ILE* 2.8 35.2 + - - +
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Residues in contact with TYR 226 (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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173D ASN* 2.6 25.0 + - - -
198D GLN* 3.9 8.7 - - + -
199D GLY* 2.8 28.3 + - - -
200D MET* 3.4 37.2 - - + +
201D TYR 3.1 24.4 + - - +
224D TYR 3.7 1.0 + - - -
225D ALA* 1.3 72.1 - - - +
227D ASN* 1.3 89.2 + - - +
228D PRO* 3.3 5.4 - - - -
264D ARG* 4.2 4.5 - - - -
315D ILE* 4.5 5.2 - - + -
358D TYR 4.5 0.3 + - - -
360D ARG* 3.1 12.5 + - - -
1361D NDP 3.2 79.0 - + + +
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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