Contacts of the strand formed by residues 209 - 216 (chain A) in PDB entry 3O9Z
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 VAL 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A LEU* 3.8 1.7 - - - +
204A ALA* 4.4 14.8 - - + -
205A ARG* 3.5 1.7 + - - -
206A THR* 2.8 35.6 + - + +
208A THR* 1.3 92.9 - - - +
210A ASN* 1.3 81.4 + - - +
224A PHE* 3.7 27.4 - - + -
225A LEU 3.3 3.6 - - - +
226A SER* 3.6 4.3 - - - +
231A PHE* 3.6 34.3 - - + -
309A LEU* 5.6 0.4 - - + -
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Residues in contact with ASN 210 (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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178A LEU* 4.1 13.8 - - - +
179A ALA* 3.4 33.9 - - - +
202A VAL* 5.3 3.0 - - + +
204A ALA 3.2 9.6 - - - +
205A ARG* 3.6 24.7 - - - +
206A THR 3.7 6.4 - - - +
209A VAL* 1.3 93.0 - - - +
211A ALA* 1.3 61.6 + - - +
223A TRP* 3.5 19.6 - - + -
224A PHE* 3.7 0.2 - - - -
225A LEU* 2.8 41.8 + - + +
292A LEU* 5.8 2.8 + - - +
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Residues in contact with ALA 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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202A VAL* 3.5 6.8 - - - +
203A HIS* 2.7 23.0 + - - -
204A ALA* 3.1 15.7 + - + -
210A ASN* 1.3 74.8 - - - +
212A GLY* 1.3 59.7 + - - +
223A TRP* 3.3 21.8 - - - +
224A PHE* 4.0 8.5 - - + -
306A HIS* 5.0 0.9 - - + -
309A LEU* 3.8 38.8 - - + -
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Residues in contact with GLY 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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201A GLU 3.3 12.8 - - - -
203A HIS* 3.6 19.9 + - - -
211A ALA* 1.3 76.9 - - - +
213A TYR* 1.3 62.7 + - - +
222A ARG* 3.6 4.5 - - - +
223A TRP* 3.0 42.0 + - - +
304A ASN 4.2 1.2 - - - +
306A HIS* 4.9 2.5 - - - +
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Residues in contact with TYR 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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199A HIS* 4.2 10.8 - + - -
200A VAL* 3.7 1.4 - - - -
201A GLU* 2.9 48.3 + - + +
203A HIS* 3.7 9.1 - - + -
212A GLY* 1.3 74.1 - - - +
214A LEU* 1.3 82.6 + - - +
215A GLU* 4.0 11.3 - - + +
220A ARG* 3.3 33.2 - - + +
221A VAL 3.2 33.0 - - - -
222A ARG* 4.0 4.5 - - + -
223A TRP* 3.3 1.5 - - - +
303A GLU 4.9 1.3 - - - -
304A ASN* 3.4 61.2 + - + +
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Residues in contact with LEU 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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187A PHE* 4.0 17.0 - - + -
190A LEU* 3.8 29.4 - - + -
197A ALA* 4.6 4.5 - - + -
199A HIS 3.4 3.6 - - - +
200A VAL* 3.8 32.5 - - + -
213A TYR* 1.3 88.3 - - - +
215A GLU* 1.3 59.2 + - - +
216A LEU* 3.7 24.1 + - + -
220A ARG* 3.5 2.6 - - - -
221A VAL* 2.9 38.5 + - + +
223A TRP* 3.7 17.3 - - + +
288A VAL* 4.2 14.4 - - + -
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Residues in contact with GLU 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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197A ALA* 3.5 2.4 - - - -
198A LEU* 2.7 56.3 + - + +
199A HIS* 2.9 33.0 + - + +
213A TYR* 4.0 13.3 - - + +
214A LEU* 1.3 72.1 - - - +
216A LEU* 1.3 62.4 + - - +
219A ALA 3.8 4.5 - - - +
220A ARG* 4.6 12.6 - - + +
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Residues in contact with LEU 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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149A ALA* 5.4 0.9 - - - +
190A LEU* 3.8 26.0 - - + +
191A ALA 4.9 0.4 - - - +
194A PHE* 3.7 32.1 - - + +
195A GLY 4.2 4.9 - - - +
196A ARG 3.3 6.3 - - - +
197A ALA* 3.4 34.5 - - + +
198A LEU* 4.5 5.6 - - - +
214A LEU* 3.7 25.1 - - + -
215A GLU* 1.3 80.6 - - - +
217A GLU* 1.3 69.1 + - - +
218A GLY 3.1 0.9 + - - -
219A ALA 2.7 22.5 + - - +
221A VAL* 3.8 21.1 - - + -
288A VAL* 5.9 1.1 - - + -
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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