Contacts of the strand formed by residues 223 - 227 (chain B) in PDB entry 5B2G
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 LEU 223 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198A PHE* 3.6 43.1 - - + -
1203A ILE* 4.4 5.4 - - + -
1204A VAL 5.4 2.0 - - - +
1207A GLN* 3.8 19.7 - - - +
1209A ILE* 3.4 29.8 - - + +
215B LEU* 4.1 10.1 - - - +
218B ASN* 3.3 26.2 + - - +
221B GLY 3.9 0.6 - - - -
222B ASN* 1.3 80.2 + - - +
224B TYR* 1.3 71.5 + - - +
225B ASP 4.7 0.4 - - - +
315B LEU* 3.9 6.5 - - + -
316B PHE 3.4 7.9 - - - +
317B GLN* 3.2 33.9 - - + +
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Residues in contact with TYR 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1209A ILE* 6.0 0.2 - - - -
1211A GLU* 4.9 13.5 - - - -
1235A ALA* 5.3 9.8 + - + +
1237A PRO* 5.6 6.6 - - - +
209B LEU* 5.0 5.3 - - + +
211B LEU* 5.6 0.2 - - + -
214B ALA* 3.6 42.2 - - + +
215B LEU* 4.0 15.3 - - + -
217B SER* 3.7 13.7 - - - -
218B ASN* 6.1 0.4 - - + -
223B LEU* 1.3 80.8 - - - +
225B ASP* 1.3 71.0 + - - +
226B TRP* 3.7 41.3 + + + -
227B ARG 5.6 0.2 + - - -
314B ILE 4.1 0.2 - - - +
315B LEU* 3.6 4.7 - - - +
316B PHE* 3.0 36.4 + + - +
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Residues in contact with ASP 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196A THR* 5.8 1.5 - - + +
1198A PHE* 3.9 30.8 - - + -
1319A GLN* 5.5 7.3 - - - +
1321A ARG* 4.3 18.6 + - - +
223B LEU* 4.7 2.0 - - - +
224B TYR* 1.3 86.6 + - - +
226B TRP* 1.3 60.1 + - - +
227B ARG* 3.1 33.9 + - - +
313B SER* 3.5 11.3 + - - -
314B ILE 3.3 15.7 - - - +
315B LEU* 4.1 7.5 - - + +
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Residues in contact with TRP 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B GLU* 4.1 11.9 - - + -
208B ARG 5.4 1.8 + - - -
209B LEU* 3.3 40.1 - - + +
224B TYR* 3.7 22.7 + + + -
225B ASP* 1.3 72.5 - - - +
227B ARG* 1.3 79.0 + - - +
228B SER* 4.0 22.4 - - - +
238B LEU* 4.0 22.9 - - + -
240B LEU* 3.8 39.0 - - + -
300B MSE 4.0 18.2 - - + -
312B TYR* 4.6 5.8 - - + -
313B SER* 3.3 1.0 + - - -
314B ILE* 3.0 53.1 + - + +
316B PHE* 4.0 13.0 - + + -
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Residues in contact with ARG 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309A ASP* 2.4 45.1 + - - -
1312A ASN* 4.5 3.2 - - - +
1315A VAL* 3.2 28.7 - - - +
1319A GLN* 4.9 6.5 + - - +
1321A ARG* 3.0 50.1 - - - +
224B TYR* 5.6 0.8 + - - -
225B ASP* 3.1 24.3 + - - +
226B TRP* 1.3 95.2 + - - +
228B SER* 1.3 68.8 + - - +
229B SER* 3.8 1.0 + - - -
311B PRO* 5.2 3.4 - - + -
312B TYR 3.3 9.0 - - - +
313B SER* 3.3 16.1 + - - +
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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