Contacts of the strand formed by residues 219 - 226 (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 ALA 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ALA* 3.9 5.2 - - - +
150A LYS 3.1 15.5 - - - +
152A VAL* 3.9 13.2 - - + -
194A PHE* 3.5 30.7 - - + -
215A GLU* 3.7 0.9 - - - -
216A LEU* 2.7 41.3 + - + +
218A GLY* 1.3 81.5 - - - +
220A ARG* 1.3 61.2 + - - +
221A VAL* 3.9 7.2 - - + -
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Residues in contact with ARG 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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149A ALA* 4.1 33.6 + - - +
150A LYS 2.9 7.4 + - - +
151A ASP* 2.8 45.2 + - - +
152A VAL 2.9 25.1 + - - +
213A TYR* 3.3 29.2 - - + +
214A LEU 3.5 4.7 - - - -
215A GLU* 4.7 11.9 - - + -
219A ALA* 1.3 74.6 - - - +
221A VAL* 1.3 60.4 + - - +
222A ARG* 5.9 0.2 - - - -
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Residues in contact with VAL 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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152A VAL* 3.3 23.8 - - + +
154A LEU* 4.1 7.6 - - + -
190A LEU* 3.8 27.1 - - + -
213A TYR* 3.2 8.3 - - - -
214A LEU* 2.9 46.1 + - + +
216A LEU* 3.8 28.3 - - + -
219A ALA* 3.9 13.0 - - + -
220A ARG* 1.3 77.8 - - - +
222A ARG* 1.3 74.8 + - - +
223A TRP* 4.0 5.1 + - + -
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Residues in contact with ARG 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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152A VAL 3.0 9.7 + - - +
153A VAL* 3.4 30.6 - - + +
154A LEU 2.9 25.1 + - - +
212A GLY 3.6 5.2 - - - -
213A TYR* 4.0 8.7 - - + -
220A ARG 5.9 0.4 - - - +
221A VAL* 1.3 75.0 - - - +
223A TRP* 1.3 57.7 + - - +
302A PRO 4.9 4.0 + - - -
303A GLU* 3.6 22.4 + - - +
304A ASN 3.5 14.4 - - - +
305A ARG 2.9 28.2 + - - +
306A HIS* 3.6 20.8 - - + +
307A PRO* 3.7 18.8 - - - +
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Residues in contact with TRP 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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154A LEU* 3.2 15.5 - - + +
179A ALA* 5.2 0.2 - - + -
186A PHE* 3.7 32.1 - + + -
187A PHE* 3.8 24.6 - + - -
190A LEU* 5.3 0.2 - - + -
201A GLU 4.0 8.1 - - - -
202A VAL* 4.6 2.9 - - + -
210A ASN* 3.5 39.5 - - + -
211A ALA* 3.3 17.6 - - - +
212A GLY* 3.0 51.9 + - - +
213A TYR* 3.3 16.4 + - - +
214A LEU* 3.7 35.1 - - + +
221A VAL* 4.1 6.3 - - + -
222A ARG* 1.3 73.7 - - - +
224A PHE* 1.3 62.4 + - - +
225A LEU* 4.4 2.7 - - + -
292A LEU* 3.9 23.1 - - + -
306A HIS* 3.6 5.7 - - - +
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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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154A LEU* 3.0 6.7 + - - +
155A THR* 3.5 6.3 - - + -
156A TYR* 2.8 32.7 + - - +
157A VAL* 4.4 4.0 - - + -
186A PHE* 5.0 0.4 - - - -
209A VAL* 3.7 25.8 - - + -
210A ASN 3.7 3.6 - - - -
211A ALA* 4.0 5.8 - - + -
223A TRP* 1.3 76.6 - - - +
225A LEU* 1.3 57.9 - - - +
226A SER* 3.7 21.5 - - - -
231A PHE* 3.6 38.4 - + + -
306A HIS* 3.5 23.6 - - + +
308A PHE* 3.7 37.0 - + + -
309A LEU* 3.7 27.1 - - + -
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Residues in contact with LEU 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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156A TYR* 3.2 22.4 - - + +
178A LEU* 3.6 38.6 - - + +
179A ALA* 3.8 16.4 - - + +
182A ILE* 3.7 28.5 - - + -
183A GLY* 3.9 9.4 - - - +
186A PHE* 3.8 20.2 - - + -
209A VAL* 3.3 5.9 - - - +
210A ASN* 2.8 46.4 + - + +
223A TRP* 4.5 1.8 - - + -
224A PHE* 1.3 76.6 - - - +
226A SER* 1.3 66.7 - - - +
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Residues in contact with SER 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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156A TYR 2.9 8.4 + - - +
157A VAL* 3.2 7.8 - - - +
158A THR* 2.9 26.5 + - - +
178A LEU* 4.9 0.4 - - - -
208A THR 2.7 19.2 + - - -
209A VAL* 3.6 3.8 - - - +
224A PHE* 3.7 20.1 - - - -
225A LEU* 1.3 80.4 - - - +
227A ILE* 1.3 61.7 + - - +
228A ASP* 2.9 31.1 + - - +
231A PHE* 3.4 13.1 - - - -
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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