Contacts of the strand formed by residues 225 - 235 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C ILE 4.1 2.9 - - - +
84C TYR* 5.7 2.8 + - - +
221C PHE* 3.2 4.5 - - - -
222C VAL 3.0 29.1 + - - +
223C ASP* 2.9 12.3 + - + +
224C ASP* 1.3 83.1 - - - +
226C LEU* 1.3 67.5 + - - +
227C VAL* 3.2 8.1 + - + +
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Residues in contact with LEU 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ILE* 3.3 36.9 + - + +
76C LEU* 3.7 44.0 - - + +
77C CYS* 4.0 12.4 - - + +
81C GLU* 4.5 16.7 - - - +
219C PHE* 3.9 20.2 - - + -
220C TYR 3.4 16.2 - - - +
221C PHE* 3.5 12.0 - - + -
225C ARG* 1.3 74.4 - - - +
227C VAL* 1.3 61.4 + - - +
228C MET 3.3 24.7 - - - +
229C HIS* 4.7 2.0 - - + -
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Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C CYS* 4.0 9.2 - - - -
78C SER 4.7 1.4 - - - +
79C PRO* 6.0 0.2 - - - +
81C GLU 3.6 15.3 - - - +
82C ASN* 3.4 24.0 + - - +
83C ILE* 5.9 0.4 - - + -
84C TYR* 3.6 31.9 - - + -
86C ILE* 4.1 15.3 - - + -
220C TYR* 2.8 22.9 + - + +
222C VAL* 3.7 26.2 - - + +
225C ARG* 3.4 17.5 - - + +
226C LEU* 1.3 75.5 - - - +
228C MET* 1.3 70.4 + - + +
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Residues in contact with MET 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C CYS* 3.7 6.9 - - - -
82C ASN* 3.9 18.6 - - + +
86C ILE* 3.9 41.5 - - - +
87C ASP* 5.8 0.4 - - - -
88C PHE* 3.6 32.8 - - + +
127C ARG* 5.4 0.4 - - - +
159C PHE* 5.4 0.4 - - - -
220C TYR* 2.9 46.3 + - + -
226C LEU* 3.3 8.5 - - - +
227C VAL* 1.3 85.2 - - + +
229C HIS* 1.3 60.3 + - - +
230C ASN* 4.2 19.3 - - - +
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Residues in contact with HIS 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C THR* 3.2 24.7 - - - -
74C ASP 3.8 3.6 - - - -
75C TYR* 3.4 13.8 - + - -
76C LEU* 3.0 31.3 + - + +
77C CYS* 3.7 16.6 - - - +
127C ARG* 3.2 23.0 + - - +
217C ASP* 2.9 24.6 + - - -
218C SER 3.3 10.5 - - - -
219C PHE* 3.5 25.2 - + + -
226C LEU* 4.7 2.2 - - + -
228C MET* 1.3 78.1 - - - +
230C ASN* 1.4 79.8 + - - +
231C LYS* 3.8 8.9 - - + +
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Residues in contact with ASN 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C PHE* 4.5 4.0 - - - -
126C GLY 4.0 5.6 + - - +
127C ARG* 3.3 25.6 + - - +
216C SER 4.2 0.2 - - - +
217C ASP* 3.7 0.5 - - - -
218C SER* 2.8 40.2 + - - -
220C TYR* 4.2 8.8 + - - -
228C MET* 4.2 22.3 - - - +
229C HIS* 1.4 85.1 + - - +
231C LYS* 1.4 62.6 + - - +
501I GLY* 2.8 39.7 + - - +
502I ALA* 4.2 5.1 + - - +
504I ALA* 4.2 6.5 - - - +
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Residues in contact with LYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ILE* 3.7 10.5 - - + +
72C THR* 2.8 36.8 + - - -
74C ASP 3.8 10.3 - - - -
75C TYR* 3.5 28.7 - - + +
127C ARG 2.9 6.6 + - - +
128C PHE* 3.3 14.0 - - + -
129C VAL* 2.9 26.2 + - - +
216C SER 3.6 4.5 - - - +
217C ASP* 2.7 32.4 + - - +
229C HIS* 3.8 6.7 - - - +
230C ASN* 1.4 74.9 - - - +
232C ALA* 1.3 61.3 + - - +
181E PHE* 3.6 42.2 - - + -
501I GLY* 5.1 1.1 - - - -
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Residues in contact with ALA 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C PHE* 4.1 4.7 - - - -
129C VAL* 3.1 25.4 - - + +
131C TYR* 4.1 4.3 - - + -
215C GLN* 3.4 4.2 - - - +
216C SER* 3.0 46.7 + - - +
231C LYS* 1.3 77.1 - - - +
233C ASP* 1.3 63.9 + - - +
234C TYR* 3.5 15.3 - - + +
501I GLY* 4.7 6.1 - - - -
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Residues in contact with ASP 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C PHE* 3.4 18.5 - - + -
129C VAL 3.0 8.1 + - - +
130C ARG* 2.7 48.3 + - - +
131C TYR* 2.9 25.8 + - - +
212C TYR* 3.5 22.9 - - - +
214C THR 3.4 13.9 - - - +
215C GLN* 3.8 8.9 + - + +
232C ALA* 1.3 75.5 - - - +
234C TYR* 1.3 67.8 + - - +
179E PHE 4.7 0.3 - - - +
180E GLY* 5.2 0.7 - - - -
181E PHE 5.3 0.7 + - - -
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Residues in contact with TYR 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C TYR* 3.4 26.2 - + + -
133C PHE* 3.7 26.7 - + - -
137C PHE* 5.7 1.3 - + - -
165C HIS* 3.2 22.2 - + - -
210C HIS 5.0 0.2 - - - +
211C PRO* 4.0 0.9 - - - +
212C TYR* 2.8 30.0 + - - -
214C THR* 3.1 25.9 + - + +
215C GLN 4.0 1.6 - - - -
216C SER* 2.6 42.9 + - - -
232C ALA* 3.5 15.9 - - + +
233C ASP* 1.3 79.5 + - - +
235C SER* 1.3 57.1 + - - +
236C TYR* 3.2 35.5 - - + +
500I DAO 3.6 22.4 - - + +
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Residues in contact with SER 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C TYR 2.8 7.6 + - - +
132C GLN* 3.7 12.6 + - - -
133C PHE* 2.7 35.7 + - - +
211C PRO* 3.7 12.0 - - - +
212C TYR* 3.5 30.6 + - - -
234C TYR* 1.3 74.2 - - - +
236C TYR* 1.3 61.7 + - - +
237C SER* 3.1 26.9 + - - -
238C GLY 4.8 0.5 + - - -
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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