Contacts of the strand formed by residues 226 - 230 (chain M) in PDB entry 2BDI
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 GLY 226 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172M TYR* 4.3 1.1 - - - -
181M PHE 3.7 0.2 - - - +
182M CYS* 3.2 8.0 - - - +
183M ALA 3.1 31.8 + - - -
189M ASP* 3.9 20.4 + - - -
215M PHE 4.0 5.2 - - - -
216M GLY* 4.6 2.5 - - - -
225M PRO* 1.3 74.3 - - - +
227M VAL* 1.4 62.6 + - - -
228M TYR* 3.8 7.5 - - - -
713M PBZ 4.2 10.1 - - - -
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Residues in contact with VAL 227 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168M CYS* 5.6 0.9 - - - -
172M TYR* 3.6 28.0 - - + -
176M TYR* 6.1 0.4 - - + -
180M MET* 3.4 34.3 - - + -
181M PHE 3.4 8.1 - - - +
182M CYS* 4.6 4.5 - - - -
213M VAL* 4.4 0.7 - - - +
214M SER* 3.2 19.2 + - - -
215M PHE* 2.6 69.2 + - + +
226M GLY* 1.4 75.1 - - - -
228M TYR* 1.3 68.6 + - - +
713M PBZ 5.4 1.4 + - - -
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Residues in contact with TYR 228 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138M VAL* 4.1 11.7 - - + +
160M VAL* 4.4 5.4 - - - +
180M MET* 3.3 3.8 - - - -
181M PHE* 2.8 53.8 + + + +
183M ALA* 3.6 32.0 + - + -
189M ASP* 3.8 8.3 + - - -
190M SER* 2.6 23.0 + - - -
199M LEU* 3.8 32.8 - - + -
212M LEU 3.1 22.9 - - - +
213M VAL* 3.6 28.0 - - + -
214M SER* 4.2 3.4 - - - -
226M GLY* 3.8 20.0 - - - -
227M VAL* 1.3 76.8 - - - +
229M THR* 1.4 63.7 + - - +
713M PBZ 5.5 0.7 - - - -
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Residues in contact with THR 229 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M ALA* 5.4 0.2 - - - +
102M ASP* 3.1 32.4 + - - +
103M LEU* 3.9 24.2 - - + -
179M SER 3.7 8.7 - - - +
180M MET* 4.6 0.7 - - - +
181M PHE* 3.6 0.3 - - - -
211M GLY* 3.3 19.2 - - - -
212M LEU* 3.0 27.8 + - - +
214M SER* 3.9 7.1 - - - -
228M TYR* 1.4 68.5 - - - +
230M ASN* 1.3 61.7 + - - +
231M LEU* 2.9 16.0 + - + +
234M PHE* 3.9 22.4 - - + -
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Residues in contact with ASN 230 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M CYS* 4.4 2.2 - - - +
129M PRO* 3.3 18.3 - - - +
178M PRO 3.4 15.2 + - - +
179M SER 3.1 27.8 + - - -
180M MET* 3.6 8.8 + - - +
181M PHE* 3.3 21.6 - - + +
210M GLN 4.8 0.9 - - - +
228M TYR 3.4 1.0 + - - -
229M THR* 1.3 68.2 - - - +
231M LEU* 1.3 52.5 + - - +
232M CYS* 3.2 20.9 + - - -
233M LYS* 2.7 53.4 + - - +
234M PHE* 3.6 5.9 - - - -
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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