Contacts of the strand formed by residues 225 - 235 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D ILE 3.7 12.8 + - - +
61D GLY* 5.5 1.6 - - - -
63D GLU* 5.9 1.4 + - - -
221D PHE* 3.2 4.6 - - - -
222D VAL 2.9 31.3 + - - +
223D ASP* 3.8 14.3 + - + +
224D ASP* 1.3 96.4 + - - +
226D LEU* 1.3 69.3 + - - +
227D VAL* 3.2 7.1 + - + +
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Residues in contact with LEU 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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60D ILE* 3.0 37.2 + - + +
76D LEU* 3.7 39.9 - - + +
77D CYS* 3.9 16.8 - - + +
81D GLU* 4.4 14.9 - - - +
219D PHE* 3.7 29.8 - - + -
220D TYR 3.6 9.2 - - - +
221D PHE* 3.5 12.3 - - + -
225D ARG* 1.3 74.2 - - - +
227D VAL* 1.3 60.9 + - - +
228D MET 3.5 23.1 - - - +
229D HIS* 4.7 1.6 - - + -
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Residues in contact with VAL 227 (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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77D CYS* 3.9 10.8 - - - -
78D SER 4.6 1.4 - - - +
81D GLU* 3.5 17.5 - - - +
82D ASN* 3.4 23.8 + - - +
83D ILE* 5.2 0.7 - - + -
84D TYR* 3.8 32.3 - - + -
86D ILE* 4.5 4.7 - - + -
159D PHE* 4.9 0.2 - - + -
220D TYR* 2.8 23.5 + - + +
222D VAL* 3.8 25.6 - - + +
225D ARG* 3.2 16.6 + - + +
226D LEU* 1.3 74.5 - - - +
228D MET* 1.3 81.4 + - + +
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Residues in contact with MET 228 (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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77D CYS* 3.7 7.3 - - - -
82D ASN* 3.5 32.3 - - + +
86D ILE* 3.7 38.4 - - + +
88D PHE* 4.0 15.9 - - + -
127D ARG* 5.4 0.4 - - - +
159D PHE* 3.9 12.1 - - + -
220D TYR* 2.9 59.1 + - + -
226D LEU* 3.5 6.1 - - - +
227D VAL* 1.3 86.2 - - + +
229D HIS* 1.3 64.4 + - - +
230D ASN* 5.0 6.3 - - - +
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Residues in contact with HIS 229 (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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72D THR* 3.3 24.0 - - - -
74D ASP 3.7 3.4 - - - -
75D TYR* 3.4 13.8 - + - -
76D LEU* 2.9 27.7 + - + +
77D CYS* 3.7 17.8 - - - +
127D ARG* 3.2 22.4 + - - +
217D ASP* 2.8 24.0 + - - -
218D SER 3.2 11.0 - - - +
219D PHE* 3.5 28.5 - + + -
226D LEU* 4.7 2.5 - - + -
228D MET* 1.3 78.4 - - - +
230D ASN* 1.3 81.4 + - - +
231D LYS* 3.8 7.1 - - + +
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Residues in contact with ASN 230 (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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75D TYR* 4.5 0.2 - - - -
88D PHE* 4.5 11.1 - - - -
126D GLY 3.9 5.6 + - - +
127D ARG* 3.2 27.9 - - - +
217D ASP* 3.7 1.0 - - - -
218D SER* 2.8 38.4 + - - -
220D TYR* 4.1 13.7 + - + -
228D MET* 5.0 5.5 - - - +
229D HIS* 1.3 87.6 + - - +
231D LYS* 1.4 62.0 + - - +
501J GLY* 3.0 38.7 + - - +
502J ALA* 4.4 3.4 + - - +
504J ALA* 4.0 6.6 - - - +
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Residues in contact with LYS 231 (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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181A PHE* 3.7 42.4 - - + -
71D ILE* 3.8 9.5 - - - +
72D THR* 2.8 39.1 + - - +
74D ASP 3.7 10.1 - - - -
75D TYR* 3.7 21.3 - - + +
127D ARG 2.7 7.2 + - - +
128D PHE* 3.2 19.1 - - + -
129D VAL* 2.9 25.8 + - - +
216D SER* 3.5 5.6 - - - +
217D ASP* 2.8 31.2 + - - +
229D HIS* 3.8 6.3 - - - +
230D ASN* 1.4 76.8 - - - +
232D ALA* 1.3 63.4 + - - +
501J GLY* 5.1 1.3 - - - -
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Residues in contact with ALA 232 (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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128D PHE* 3.9 6.4 - - - -
129D VAL* 3.0 26.2 - - + +
131D TYR* 4.0 4.7 - - + -
215D GLN* 3.3 6.9 - - - +
216D SER* 3.0 44.9 + - - +
231D LYS* 1.3 77.8 - - - +
233D ASP* 1.3 64.2 + - - +
234D TYR* 3.6 15.7 - - + +
500J DAO 4.7 4.7 - - - +
501J GLY* 4.8 0.7 - - - -
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Residues in contact with ASP 233 (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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179A PHE 4.6 1.7 - - - +
180A GLY* 4.7 1.4 - - - -
128D PHE* 3.4 19.0 - - + -
129D VAL 3.0 7.7 + - - +
130D ARG* 2.9 47.0 + - - +
131D TYR* 2.8 27.4 + - - +
212D TYR* 3.4 22.7 - - - +
214D THR 3.4 13.5 - - - +
215D GLN* 3.9 9.8 + - + +
232D ALA* 1.3 75.0 - - - +
234D TYR* 1.3 68.3 + - - +
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Residues in contact with TYR 234 (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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131D TYR* 3.4 25.1 - + + +
133D PHE* 3.7 25.8 - + - -
137D PHE* 5.8 1.3 - + - -
165D HIS* 3.2 22.4 - + - -
207D MET 5.5 0.2 - - - +
210D HIS 5.0 0.2 - - - +
211D PRO* 4.1 0.7 - - - +
212D TYR* 2.8 25.8 + - - -
214D THR* 3.1 32.1 + - + +
215D GLN 4.0 0.9 - - - -
216D SER* 2.8 42.7 + - - -
232D ALA* 3.6 16.2 - - + +
233D ASP* 1.3 76.3 + - - +
235D SER* 1.3 61.5 + - - +
236D TYR* 3.3 34.3 - - + +
500J DAO 3.6 24.0 - - + +
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Residues in contact with SER 235 (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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131D TYR 2.8 10.9 + - - +
132D GLN* 4.1 10.0 - - - +
133D PHE* 2.7 34.0 + - - +
211D PRO* 3.8 12.5 - - - +
212D TYR* 3.4 31.9 + - - -
234D TYR* 1.3 74.7 - - - +
236D TYR* 1.3 61.5 + - - +
237D SER* 3.1 25.2 + - - -
238D GLY 4.7 1.2 + - - -
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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