Contacts of the strand formed by residues 219 - 226 (chain A) in PDB entry 3ONA
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 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A MET 3.3 12.6 - - - +
173A TYR* 4.1 8.3 - - + -
215A VAL* 3.1 1.7 - - - +
216A VAL* 2.6 43.0 + - + +
217A ASP* 3.3 1.5 - - + -
218A LYS* 1.3 79.0 - - - +
220A ALA* 1.3 75.3 + - - +
307A LEU* 3.4 28.0 - - + -
308A ASN 3.4 26.7 - - - +
309A VAL* 4.1 8.1 - - + -
312A ILE* 3.7 20.3 - - + +
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Residues in contact with ALA 220 (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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170A ILE 4.5 0.9 - - - -
171A ASN* 3.3 6.1 - - - +
172A MET* 2.9 52.1 + - + -
175A VAL* 4.1 15.5 - - + -
213A TYR* 4.2 9.9 - - + -
214A SER 3.2 12.1 - - - +
215A VAL* 3.7 13.9 - - + -
218A LYS 4.1 0.4 + - - -
219A LEU* 1.3 80.1 - - - +
221A THR* 1.3 61.0 + - - +
309A VAL* 4.8 1.6 - - - -
312A ILE* 4.8 0.9 - - - -
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Residues in contact with THR 221 (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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169A GLU* 3.9 12.6 + - - +
170A ILE 3.4 4.9 - - - -
171A ASN* 2.5 21.3 + - - -
212A TYR* 4.0 15.2 + - + -
213A TYR* 3.4 2.4 - - - -
214A SER* 3.0 36.1 + - - +
220A ALA* 1.3 75.3 - - - +
222A SER* 1.3 66.8 + - - +
309A VAL* 3.9 16.8 - - + +
312A ILE* 3.8 34.2 - - + +
313A PRO 4.6 2.5 - - - +
314A PRO* 4.9 0.4 - - + -
47B ARG* 4.9 5.3 + - - +
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Residues in contact with SER 222 (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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169A GLU* 3.5 0.3 - - - +
170A ILE* 2.7 50.5 + - - +
172A MET* 3.8 10.7 - - - +
190A ILE* 4.5 7.2 - - - -
197A ILE* 3.9 7.8 - - - +
212A TYR* 3.0 38.5 + - - -
213A TYR* 3.8 17.3 - - - -
221A THR* 1.3 78.8 + - - +
223A GLY* 1.3 54.6 + - - +
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Residues in contact with GLY 223 (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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168A VAL 2.9 14.6 - - - -
170A ILE* 4.5 4.9 - - - -
190A ILE* 3.7 4.1 - - - +
211A ASP* 2.9 28.6 - - - +
212A TYR* 2.9 20.7 + - - -
222A SER* 1.3 75.3 - - - +
224A PHE* 1.3 71.4 + - - -
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Residues in contact with PHE 224 (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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167A ASP* 3.4 1.9 - - - +
168A VAL* 2.7 43.3 + - + +
170A ILE* 5.3 0.7 - - + -
184A ILE* 5.0 3.6 - - + -
188A SER* 3.8 37.2 - - - -
189A THR 4.0 0.2 - - - -
190A ILE* 3.4 29.8 - - + -
197A ILE* 3.7 23.8 - - + -
199A LEU* 3.8 25.6 - - + -
208A PHE* 3.6 23.3 - + + -
210A GLY 3.4 8.1 - - - +
211A ASP* 3.5 30.5 - - + +
212A TYR* 5.3 1.0 - - - -
223A GLY* 1.3 76.6 - - - -
225A PHE* 1.3 64.6 + - - +
242A LEU* 4.5 4.0 - - + -
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Residues in contact with PHE 225 (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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166A ILE 3.5 5.6 - - - -
167A ASP* 3.6 19.1 - - - +
208A PHE* 3.2 8.4 - - - -
209A ILE* 2.8 40.3 + - + -
210A GLY* 2.9 40.3 + - - -
211A ASP* 3.4 13.9 - - - -
212A TYR* 4.1 8.1 - + + -
224A PHE* 1.3 79.3 - - - +
226A THR* 1.3 58.1 + - - +
20B PRO* 3.6 23.6 - - + -
22B ALA* 3.7 26.5 - - + -
23B LEU* 3.8 35.0 - - + -
44B ARG* 3.7 8.7 - - - +
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Residues in contact with THR 226 (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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165A SER* 3.5 1.7 - - - -
166A ILE* 2.9 33.2 + - + +
206A PRO* 3.8 10.7 - - + +
207A VAL 2.9 41.5 - - - +
208A PHE* 3.6 24.5 - - + +
209A ILE* 3.9 4.9 - - - +
225A PHE* 1.3 74.8 - - - +
227A ASN* 1.3 77.2 + - - +
44B ARG* 3.1 25.5 + - - -
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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