Contacts of the strand formed by residues 213 - 220 (chain A) in PDB entry 2PZI
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 ILE 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A LEU* 4.2 18.3 + - + +
203A ALA* 4.2 20.1 - - + +
205A VAL 5.7 1.8 + - - +
211A VAL* 3.8 3.3 + - + +
212A GLN* 1.3 75.8 - - - +
214A PHE* 1.3 66.7 + - - +
215A ASN 4.1 4.7 - - - +
216A PHE* 3.9 21.8 - - + -
230A ILE* 3.5 36.6 - - + -
231A VAL 3.7 2.2 - - - +
232A MET* 3.4 28.9 - - + -
294A LEU* 3.7 35.9 - - + +
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Residues in contact with PHE 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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151A TYR* 4.9 2.2 + - - +
170A ASP* 5.5 0.2 - - - +
176A ARG* 3.6 47.3 - - - +
177A PRO 5.1 1.3 - - - -
178A VAL* 3.9 17.9 - - + -
203A ALA* 5.7 3.1 - - - -
212A GLN* 3.3 31.6 - - + -
213A ILE* 1.3 79.7 - - - +
215A ASN* 1.3 63.5 + - + +
231A VAL* 2.7 21.2 + - + +
232A MET 3.6 17.7 - - - -
233A GLU* 3.3 36.6 - - + -
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Residues in contact with ASN 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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150A GLN* 3.8 13.3 + - - +
151A TYR* 2.9 28.6 + - - +
200A GLN* 5.1 2.5 - - - +
203A ALA* 5.8 1.3 - - - +
213A ILE* 3.7 3.3 - - - +
214A PHE* 1.3 81.3 - - - +
216A PHE* 1.3 89.7 + - - +
217A VAL* 3.9 11.8 - - - +
230A ILE* 3.9 3.6 - - - +
231A VAL* 3.0 34.4 + - + +
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Residues in contact with PHE 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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183A LEU* 4.1 17.5 - - + -
196A MET* 3.9 30.9 - - + +
199A ARG* 3.4 41.1 - - + -
200A GLN* 3.3 40.8 + - - +
202A LEU* 4.5 4.7 - - + -
203A ALA* 4.9 5.2 - - + -
213A ILE* 3.9 16.8 - - + -
215A ASN* 1.3 89.1 + - - +
217A VAL* 1.3 64.8 + - - +
229A TYR 3.5 11.4 - - - -
230A ILE* 3.6 34.8 - - + -
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Residues in contact with VAL 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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147A VAL* 3.2 35.4 - - + -
148A ALA* 3.5 21.1 - - + -
150A GLN* 5.3 0.4 - - - +
151A TYR* 3.6 25.1 - - + -
180A LEU* 4.7 0.9 - - + -
196A MET* 3.7 7.0 - - - +
215A ASN* 3.9 11.0 - - - +
216A PHE* 1.3 80.0 - - - +
218A GLU* 1.3 60.4 + - - +
227A VAL 3.8 0.2 - - - +
228A GLY* 3.4 2.8 - - - -
229A TYR* 2.7 48.2 + - + +
231A VAL* 4.2 10.1 - - + -
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Residues in contact with GLU 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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148A ALA* 4.3 10.5 - - - +
189A ALA 5.2 1.2 - - - +
192A GLN* 5.1 2.4 - - + +
193A ALA* 4.6 18.7 + - - +
196A MET* 4.4 20.5 - - + +
217A VAL* 1.3 76.2 - - - +
219A HIS* 1.3 63.4 + - - +
220A THR* 4.4 1.0 + - - +
226A PRO* 3.4 35.4 - - + +
227A VAL 3.4 9.0 - - - +
228A GLY* 4.5 0.7 - - - -
751A CL 3.6 14.0 - - - +
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Residues in contact with HIS 219 (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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140A GLN 5.1 3.4 + - - -
141A LEU* 3.4 30.1 - - + +
145A ASP* 4.8 11.0 + - - -
146A ILE 4.4 12.3 - - - -
147A VAL* 3.9 17.5 - - + +
218A GLU* 1.3 74.1 - - - +
220A THR* 1.3 81.7 + - - +
221A ASP* 3.4 9.4 + - + -
225A ASP 3.3 0.7 - - - +
226A PRO* 4.2 1.3 - - - -
227A VAL* 2.6 42.7 + - + +
229A TYR* 3.7 21.8 - + + -
751A CL 3.3 19.2 - - + +
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Residues in contact with THR 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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218A GLU* 5.7 0.9 + - - +
219A HIS* 1.3 90.1 + - - +
221A ASP* 1.3 68.5 + - - +
224A GLY* 3.6 31.0 - - - +
225A ASP 3.3 5.8 - - - -
226A PRO* 4.2 9.4 - - - +
751A CL 4.4 4.0 - - - +
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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