Contacts of the strand formed by residues 227 - 235 (chain A) in PDB entry 2ZB5
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 MET 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A THR* 3.3 5.5 - - - -
224A SER* 2.8 41.1 + - - +
225A GLN* 3.2 17.0 + - + +
226A GLY* 1.3 75.0 - - - +
228A TYR* 1.3 62.3 + - - +
257A VAL* 4.9 1.6 - - - -
258A GLY 3.2 16.2 - - - +
259A VAL* 4.6 3.8 - - + -
260A ILE* 4.0 5.7 - - - +
291A LEU* 3.8 19.0 - - + +
292A GLY* 3.7 23.3 - - - +
293A GLU 4.1 0.7 - - - +
294A LEU* 3.3 32.1 - - + +
295A LYS* 3.7 9.4 - - - +
326A VAL* 3.3 30.1 - - + -
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Residues in contact with TYR 228 (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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204A SER* 3.4 10.4 + - - -
206A LEU* 6.0 2.2 - - + -
221A THR* 4.9 9.2 - - + -
222A MET 3.4 11.7 - - - +
223A THR* 4.4 5.8 - - + -
227A MET* 1.3 74.6 - - - +
229A GLY* 1.3 67.1 + - - +
256A GLU* 2.5 36.4 + - + -
257A VAL* 3.2 9.5 - - - +
258A GLY* 2.9 62.9 + - - -
259A VAL 3.7 5.8 - - - -
260A ILE* 4.5 2.7 - - + -
270A PHE* 3.5 43.5 - + + -
271A HIS 3.7 15.7 - - - -
272A MET* 3.2 22.0 + - - +
291A LEU* 3.6 6.4 - - - +
569A GLU* 5.1 0.4 - - - +
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Residues in contact with GLY 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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221A THR* 3.2 8.6 - - - +
222A MET* 3.0 35.4 + - - +
228A TYR* 1.3 86.1 - - - +
230A GLY* 1.3 58.8 + - - -
256A GLU* 3.1 14.1 - - - -
257A VAL* 4.0 2.0 - - - -
289A VAL* 4.4 4.5 - - - -
291A LEU* 3.6 5.7 - - - +
296A LEU* 4.3 6.1 - - - -
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Residues in contact with GLY 230 (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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220A VAL 3.0 14.6 - - - -
221A THR* 4.2 4.0 - - - -
229A GLY* 1.3 74.8 - - - -
231A THR* 1.3 61.6 + - - -
232A TYR* 4.8 3.7 - - - -
255A PHE* 3.7 2.6 - - - -
256A GLU* 2.9 31.2 + - - +
289A VAL* 3.4 16.6 - - - -
296A LEU* 3.7 9.0 - - - +
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Residues in contact with THR 231 (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 SER 3.4 1.0 - - - +
219A ILE* 4.6 0.5 - - - +
220A VAL* 3.0 40.2 + - + +
221A THR* 5.4 0.2 - - - +
230A GLY* 1.3 73.3 - - - -
232A TYR* 1.3 64.1 + - - +
253A ARG* 2.7 37.1 + - - +
254A VAL 2.8 19.4 + - - -
255A PHE* 3.6 18.0 - - - -
287A CYS* 3.6 22.4 - - + +
289A VAL* 3.8 14.1 - - + +
298A ALA* 5.2 0.9 - - - -
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Residues in contact with TYR 232 (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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205A LEU* 3.7 10.7 - - - +
206A LEU* 3.3 34.7 + - + -
209A TYR* 3.7 20.4 - + - -
216A VAL* 3.9 10.5 - - + -
217A SER 4.0 5.6 - - - +
218A SER 3.6 8.7 - - - -
219A ILE* 4.0 18.2 - - + -
221A THR* 6.4 1.1 - - + -
230A GLY 4.8 1.3 - - - -
231A THR* 1.3 85.9 + - - +
233A LEU* 1.3 61.9 + - - +
234A VAL* 3.7 17.9 - - + -
253A ARG* 3.3 8.4 - - - +
254A VAL* 2.8 62.5 + - + +
256A GLU* 2.9 37.4 + - + -
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Residues in contact with LEU 233 (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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11A NAG 5.5 0.7 - - - -
215A ASN 4.6 0.7 - - - -
216A VAL* 3.3 7.1 - - - +
217A SER* 2.8 50.3 + - - +
218A SER* 3.8 18.6 - - - +
232A TYR* 1.3 72.8 - - - +
234A VAL* 1.3 63.7 + - - +
251A MET* 3.4 26.9 - - + -
252A TYR 3.2 6.7 - - - +
253A ARG* 3.6 38.1 - - + +
280A VAL* 3.5 31.4 - - + -
284A LEU 4.2 2.7 - - - +
285A SER* 4.6 6.3 - - - +
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Residues in contact with VAL 234 (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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209A TYR* 3.6 35.4 - - + -
214A TYR* 5.6 2.5 - - + -
215A ASN 3.7 3.4 - - - +
216A VAL* 3.8 14.8 - - + -
232A TYR* 3.7 11.4 - - + -
233A LEU* 1.3 79.2 - - - +
235A GLU* 1.3 63.5 + - - +
236A LYS* 3.7 19.6 + - + -
251A MET* 3.1 7.4 - - - +
252A TYR* 2.8 53.5 + - + +
254A VAL* 3.9 18.4 - - + -
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Residues in contact with GLU 235 (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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11A NAG 3.5 17.0 + - - +
214A TYR* 3.6 17.0 - - - -
215A ASN* 3.2 50.7 + - + +
234A VAL* 1.3 71.7 - - - +
236A LYS* 1.3 60.0 + - - +
237A PRO* 3.9 2.6 - - - +
249A LEU* 3.4 33.4 - - + +
250A SER 3.6 10.1 - - - +
251A MET* 4.2 13.8 - - + +
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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