Contacts of the strand formed by residues 210 - 218 (chain A) in PDB entry 3O4U
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 TYR 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A LYS* 5.9 0.4 - - - -
207A CYS* 2.9 53.2 + - + +
209A GLU* 1.3 95.8 - - + +
211A THR* 1.3 62.3 + - - +
212A VAL* 3.7 29.2 - - + -
229A ILE* 3.8 14.8 - - + -
230A LEU 3.2 15.3 - - - +
231A PHE* 3.9 16.4 - + + -
232A SER* 4.1 4.3 - - - -
248A ARG* 4.2 19.4 + - + +
249A LEU* 4.3 13.5 - - + -
252A GLU* 2.7 36.6 + - + +
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Residues in contact with THR 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A MET* 3.8 31.2 - - + -
205A LYS 3.6 12.3 - - - +
206A GLU* 3.6 15.9 - - + +
207A CYS 4.9 1.2 + - - -
210A TYR* 1.3 74.3 - - - +
212A VAL* 1.3 64.9 + - - +
213A ARG* 3.7 26.1 + - - +
228A HIS 3.6 1.6 - - - +
229A ILE* 3.6 1.2 - - - -
230A LEU* 2.9 40.9 + - - +
232A SER* 5.0 3.7 + - - -
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ASP* 4.3 1.5 - - - +
204A MET* 3.5 3.8 - - - +
205A LYS* 3.0 58.3 + - + +
207A CYS* 5.3 0.4 - - - -
210A TYR* 3.7 31.8 - - + -
211A THR* 1.3 71.9 - - - +
213A ARG* 1.3 64.8 + - - +
214A GLN* 4.2 12.2 + - + +
227A LYS* 3.8 27.8 - - + -
228A HIS 3.4 6.3 - - - +
229A ILE* 4.1 13.5 - - + -
252A GLU* 4.2 9.9 - - - +
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Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A TRP* 3.1 44.0 - - - +
201A ILE* 3.9 13.2 - - + +
203A ASP 3.8 3.4 - - - +
204A MET* 4.0 42.3 - - + +
211A THR* 3.7 18.7 + - - +
212A VAL* 1.3 78.9 - - - +
214A GLN* 1.3 61.4 + - - +
215A LEU* 3.8 14.1 + - + -
227A LYS* 3.7 1.6 - - - -
228A HIS* 2.7 56.4 + - + +
230A LEU* 3.8 28.9 - - - +
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Residues in contact with GLN 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ILE* 3.7 3.1 - - - +
202A GLN* 2.8 35.5 + - + -
203A ASP* 3.0 46.0 + - - +
212A VAL* 4.2 9.3 - - + +
213A ARG* 1.3 71.9 - - - +
215A LEU* 1.3 57.0 + - - +
225A SER* 3.8 18.7 + - - +
226A VAL 3.9 0.4 - - - +
227A LYS* 3.5 46.2 + - - +
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Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A TRP* 3.7 32.5 - - + -
187A TRP* 4.7 8.5 - - + -
199A ILE* 4.3 17.7 - - + -
200A ARG 3.4 4.3 - - - +
201A ILE* 3.4 34.1 - - + -
202A GLN* 4.8 1.4 - - - +
213A ARG* 3.9 15.9 - - + +
214A GLN* 1.3 75.6 - - - +
216A THR* 1.3 62.9 + - - +
217A ILE* 4.1 0.4 - - + -
225A SER* 3.4 8.7 + - - -
226A VAL* 2.8 45.9 + - + +
228A HIS* 3.9 28.3 - - + -
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Residues in contact with THR 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLN 3.3 2.1 - - - +
199A ILE* 3.3 7.1 - - - +
200A ARG* 2.7 46.3 + - + +
202A GLN* 3.0 25.8 - - - +
215A LEU* 1.3 75.1 + - - +
217A ILE* 1.3 63.5 + - - +
218A GLN* 4.9 3.1 - - + +
223A ARG* 4.0 33.7 - - + -
224A ARG 3.3 10.7 + - - +
225A SER* 5.2 1.9 + - - -
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A TRP* 3.8 35.0 - - + +
162A VAL* 4.4 5.4 - - + -
163A TRP* 3.6 25.3 - - + -
197A PHE* 3.9 21.8 - - + -
198A GLN 3.5 2.5 - - - -
199A ILE* 3.7 25.6 - - + -
215A LEU* 4.1 1.2 - - + +
216A THR* 1.3 73.9 - - - +
218A GLN* 1.3 61.9 + - - +
223A ARG* 3.5 1.4 - - - -
224A ARG* 2.8 58.2 + - + +
226A VAL* 3.8 22.0 - - + -
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Residues in contact with GLN 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TRP* 4.5 0.7 - - - -
196A PRO 3.7 2.1 - - - +
197A PHE* 3.5 6.6 - - - -
198A GLN* 2.8 61.9 + - + +
216A THR* 5.2 3.7 - - + +
217A ILE* 1.3 77.4 - - - +
219A TYR* 1.3 62.7 + - - +
220A GLN* 2.7 28.6 + - - +
221A GLU* 4.6 0.8 - - - +
222A GLU 3.3 11.4 - - - +
223A ARG* 3.2 43.5 + - + +
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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