Contacts of the strand formed by residues 225 - 235 (chain E) in PDB entry 3RBQ
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 225 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60E ILE 3.6 7.2 - - - +
84E TYR* 6.1 1.1 - - - -
221E PHE* 3.6 2.9 - - - -
222E VAL 3.0 30.4 + - - +
223E ASP* 3.1 14.4 + - - +
224E ASP* 1.3 82.5 - - - +
226E LEU* 1.3 67.9 + - - +
227E VAL* 3.3 8.2 + - + +
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Residues in contact with LEU 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E ILE* 2.8 39.9 + - + +
76E LEU* 3.8 39.9 - - + +
77E CYS* 4.0 16.3 - - + +
81E GLU* 4.8 12.8 - - - +
219E PHE* 3.7 21.8 - - + -
220E TYR 3.3 24.5 - - - +
221E PHE* 3.4 14.1 - - + -
225E ARG* 1.3 73.3 - - - +
227E VAL* 1.3 61.8 + - - +
228E MET 3.4 16.4 - - - +
229E HIS* 4.8 0.9 - - + -
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Residues in contact with VAL 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E CYS* 3.9 9.1 - - - -
78E SER 4.7 1.2 - - - +
81E GLU* 3.5 17.5 - - - +
82E ASN* 3.3 25.3 + - - +
84E TYR* 3.9 28.5 - - + -
86E ILE* 4.6 10.8 - - + -
220E TYR* 2.8 19.8 + - + +
222E VAL* 3.8 25.6 - - + +
225E ARG* 3.4 18.4 - - + +
226E LEU* 1.3 74.6 - - - +
228E MET* 1.3 75.9 + - + +
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Residues in contact with MET 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E CYS* 3.7 7.9 - - - -
78E SER 5.8 0.2 - - - -
82E ASN* 3.5 31.2 - - + +
86E ILE* 3.8 34.3 - - - +
87E ASP* 5.7 0.2 - - - -
88E PHE* 3.6 30.5 - - + -
127E ARG* 5.4 0.7 - - - +
159E PHE* 5.4 0.2 - - - -
220E TYR* 2.8 47.6 + - + -
226E LEU* 3.4 7.6 - - - +
227E VAL* 1.3 86.4 - - + +
229E HIS* 1.3 62.0 + - - +
230E ASN* 4.2 17.5 - - - +
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Residues in contact with HIS 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E THR* 3.3 23.3 - - - -
74E ASP 3.8 4.3 - - - -
75E TYR* 3.2 27.7 - + + -
76E LEU* 3.0 27.7 + - + +
77E CYS* 3.8 17.3 - - - +
127E ARG* 3.6 11.5 + - - +
217E ASP* 2.8 22.2 + - - -
218E SER 3.2 11.2 - - - +
219E PHE* 3.4 32.1 - + + -
226E LEU* 4.8 2.2 - - + -
228E MET* 1.3 78.2 - - - +
230E ASN* 1.3 79.6 + - - +
231E LYS* 3.8 6.6 - - + +
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Residues in contact with ASN 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E PHE* 4.3 8.9 - - - -
126E GLY 4.2 7.6 + - - +
127E ARG* 3.6 29.0 + - - +
217E ASP* 3.6 0.2 - - - -
218E SER* 2.8 38.9 + - - -
220E TYR* 3.9 16.8 + - + -
228E MET* 4.2 20.1 - - - +
229E HIS* 1.3 86.2 + - - +
231E LYS* 1.3 63.5 + - - +
501K GLY* 3.0 38.3 + - - +
502K ALA 5.1 0.2 - - - -
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Residues in contact with LYS 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E ILE* 3.7 10.7 - - - +
72E THR* 3.1 35.9 + - - -
73E GLY 4.9 1.3 - - - -
74E ASP* 3.9 20.0 - - - +
75E TYR* 3.7 24.0 - - + +
127E ARG 2.9 9.1 + - - +
128E PHE* 3.3 22.2 - - + -
129E VAL* 3.1 23.9 + - - +
215E GLN* 5.4 0.8 + - - -
216E SER 3.4 5.2 - - - +
217E ASP* 2.6 36.3 + - - +
229E HIS* 3.8 5.2 - - - +
230E ASN* 1.3 77.9 - - - +
232E ALA* 1.3 63.7 + - - +
501K GLY* 4.8 4.0 - - - -
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Residues in contact with ALA 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E PHE* 4.1 4.3 - - - -
129E VAL* 3.1 13.2 - - + +
131E TYR* 3.9 18.6 - - + -
215E GLN* 3.3 3.5 - - - +
216E SER* 2.9 35.0 + - - +
231E LYS* 1.3 77.7 - - - +
233E ASP* 1.3 64.2 + - - +
234E TYR* 3.7 23.6 - - + +
501K GLY* 4.6 9.0 - - - +
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Residues in contact with ASP 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E PHE* 3.3 15.3 - - + -
129E VAL 3.0 8.3 + - - +
130E ARG* 2.8 44.4 + - - +
131E TYR* 2.9 26.9 + - - -
212E TYR* 3.3 20.8 - - - +
214E THR 3.4 13.9 - - - +
215E GLN* 3.6 18.1 + - + -
232E ALA* 1.3 76.3 - - - +
234E TYR* 1.3 64.9 + - - +
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Residues in contact with TYR 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E TYR* 3.5 25.4 - + + +
133E PHE* 3.7 26.7 - + + -
137E PHE* 5.8 1.3 - + - -
165E HIS* 3.2 23.2 - + - -
207E MET 5.6 0.2 - - - +
210E HIS 4.9 0.3 - - - +
211E PRO* 4.0 0.9 - - - +
212E TYR* 2.8 27.8 + - - -
214E THR* 3.0 34.2 + - + +
215E GLN 4.1 0.9 - - - -
216E SER* 2.7 41.2 + - - -
232E ALA* 3.7 14.7 - - + +
233E ASP* 1.3 75.1 - - - +
235E SER* 1.3 57.4 + - - +
236E TYR* 3.3 32.0 - - + +
500K DAO 3.6 25.9 - - + +
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Residues in contact with SER 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E TYR 2.8 14.3 + - - -
132E GLN* 3.7 15.3 + - - +
133E PHE* 2.9 26.0 + - - +
211E PRO* 3.6 15.9 - - - +
212E TYR* 3.6 21.1 - - - -
234E TYR* 1.3 73.1 - - - +
236E TYR* 1.3 69.9 + - - +
237E SER* 3.4 21.0 + - - -
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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