Contacts of the strand formed by residues 221 - 229 (chain A) in PDB entry 2Z53
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 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ALA* 3.3 3.2 - - - -
218A LYS* 3.0 32.6 + - - +
219A ASN* 3.2 2.3 + - + +
220A GLY* 1.3 76.9 - - - +
222A LEU* 1.3 68.6 + - - +
223A THR* 3.4 1.2 + - - +
239A LEU 3.9 6.7 - - - +
240A ARG* 3.9 14.4 - - + +
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A ALA* 4.0 31.2 - - + +
214A ILE* 5.0 0.7 - - + -
217A ALA* 4.0 3.1 - - + -
221A ALA* 1.3 77.5 - - - +
223A THR* 1.3 65.7 + - - +
224A SER* 3.4 17.4 + - - +
226A LEU* 3.7 24.5 - - + -
238A VAL* 3.6 31.6 - - + +
239A LEU* 3.0 18.3 + - - +
240A ARG 3.9 4.0 - - - -
241A VAL* 3.8 37.9 - - + +
244A ILE* 5.4 3.6 - - + -
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Residues in contact with THR 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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213A ALA* 5.3 4.1 + - - +
216A ASN* 3.0 52.8 + - - +
217A ALA* 4.5 1.7 - - - +
218A LYS* 4.3 11.9 - - + +
221A ALA 4.4 1.8 - - - +
222A LEU* 1.3 73.6 - - - +
224A SER* 1.3 67.1 + - - +
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Residues in contact with SER 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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213A ALA* 5.6 1.6 - - - +
222A LEU* 3.4 21.6 - - - +
223A THR* 1.3 85.7 + - - +
225A PRO* 1.3 83.7 + - - +
226A LEU* 3.4 1.6 + - - +
239A LEU* 5.6 0.2 - - - -
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Residues in contact with PRO 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A SER* 1.3 95.6 + - - +
226A LEU* 1.3 59.3 + - - +
227A GLU* 4.0 2.1 + - + -
237A ILE* 3.6 25.4 - - + -
238A VAL 3.6 7.4 - - - +
239A LEU* 3.7 18.4 - - + -
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A ASN* 5.2 3.1 - - - +
209A LYS* 4.4 25.1 - - + +
210A ILE* 3.6 38.8 - - + -
213A ALA* 4.0 15.0 - - + -
214A ILE* 6.3 0.2 - - + -
222A LEU* 3.7 20.6 - - + -
224A SER 3.4 1.5 + - - +
225A PRO* 1.3 71.8 - - - +
227A GLU* 1.3 63.3 + - - +
228A LEU* 3.7 22.3 + - + -
236A TRP 3.5 2.4 - - - +
237A ILE* 4.6 1.1 - - - -
238A VAL* 2.7 42.0 + - + +
244A ILE* 5.3 4.9 - - + -
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Residues in contact with GLU 227 (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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206A ASN* 4.7 6.9 + - - +
225A PRO* 4.0 2.5 + - + +
226A LEU* 1.3 76.4 - - - +
228A LEU* 1.3 78.9 + - - +
235A LYS* 3.6 28.5 - - + +
236A TRP 3.6 2.2 - - - -
237A ILE* 4.1 26.7 - - + +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A SER* 3.4 18.4 - - - +
203A LEU* 4.1 9.2 - - + -
206A ASN* 3.5 33.0 - - + -
210A ILE* 4.2 14.1 - - + -
226A LEU* 4.2 16.2 - - + +
227A GLU* 1.3 87.2 - - - +
229A LYS* 1.3 65.9 + - - +
235A LYS* 3.7 6.2 - - - -
236A TRP* 2.8 57.5 + - + +
238A VAL* 4.1 9.2 - - + -
244A ILE* 4.0 17.7 - - + -
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Residues in contact with LYS 229 (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 PRO* 3.7 22.0 - - + +
199A LYS* 3.4 23.9 - - - +
202A SER* 3.3 16.4 + - - +
228A LEU* 1.3 79.7 - - - +
230A ASN* 1.3 63.7 - - - +
233A ASP* 2.8 50.2 + - - +
234A THR 3.3 9.2 - - - +
235A LYS* 4.7 2.2 - - - +
236A TRP* 3.8 12.7 - - - -
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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