Contacts of the strand formed by residues 286 - 292 (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 ASN 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A SER* 5.2 10.8 + - - +
220A VAL* 4.3 12.6 - - - +
253A ARG* 3.9 4.2 + - - +
285A SER* 1.3 84.2 + - - +
287A CYS* 1.3 77.5 + - - +
299A LEU 4.2 0.2 - - - +
300A CYS* 3.4 1.6 - - - +
301A HIS* 3.1 29.6 + - - +
302A GLY 5.9 0.7 - - - +
304A ASP* 5.6 12.5 + - + +
351A LEU* 6.1 2.2 - - + +
352A SER* 4.0 22.3 + - - +
353A SER* 5.6 0.3 - - - -
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Residues in contact with CYS 287 (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* 4.1 16.8 - - - +
231A THR* 3.6 18.0 - - + +
253A ARG* 3.3 35.5 - - - +
255A PHE* 4.2 1.1 - - - -
286A ASN* 1.3 85.6 + - - +
288A MET* 1.3 69.6 + - - +
289A VAL* 4.1 0.8 + - - -
298A ALA* 4.7 2.0 - - + -
299A LEU 3.3 5.4 - - - +
300A CYS* 2.0 47.8 - - - -
352A SER 5.0 3.3 - - - +
353A SER* 5.7 0.2 - - - -
354A HIS 4.7 4.2 + - - +
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Residues in contact with MET 288 (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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287A CYS* 1.3 75.8 - - - +
289A VAL* 1.3 62.0 + - - +
298A ALA* 3.1 8.7 - - - +
299A LEU* 2.9 71.4 + - + +
319A PHE* 4.7 2.9 - - + -
351A LEU* 4.4 13.2 - - + -
352A SER 6.0 0.2 - - - +
354A HIS* 3.5 37.2 - - + +
365A TRP* 3.5 42.2 - - + +
367A VAL* 4.0 9.9 - - - -
413A LEU* 3.8 16.2 - - + -
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Residues in contact with VAL 289 (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* 3.8 36.1 - - + +
222A MET* 3.9 10.8 - - + +
229A GLY 4.4 3.4 - - - +
230A GLY* 3.4 20.2 - - - +
231A THR* 3.8 23.1 - - + +
288A MET* 1.3 80.9 - - - +
290A ALA* 1.3 58.9 + - - +
296A LEU* 3.3 24.2 - - + -
297A ALA 3.7 2.5 - - - +
298A ALA* 4.5 4.0 - - + +
354A HIS 3.1 6.4 + - - +
355A ARG* 3.2 7.6 - - + -
356A GLY 2.6 29.6 + - - -
365A TRP* 3.0 3.4 + - - -
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Residues in contact with ALA 290 (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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222A MET* 3.9 2.2 - - - -
289A VAL* 1.3 79.3 - - - +
291A LEU* 1.3 60.7 + - - +
296A LEU* 3.1 7.0 - - - +
297A ALA 2.9 33.4 + - - +
356A GLY* 3.4 25.8 - - - -
357A VAL 3.7 4.0 - - - +
358A ILE* 3.4 15.2 - - + +
363A ALA* 4.7 1.8 - - + -
365A TRP* 3.5 21.8 - - + -
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Residues in contact with LEU 291 (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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222A MET* 3.2 58.4 - - + +
223A THR 3.8 6.1 - - - -
224A SER* 3.7 13.5 + - - +
227A MET* 3.8 27.8 - - + +
228A TYR* 3.6 17.9 - - - +
229A GLY* 3.6 12.6 - - - +
257A VAL* 4.3 1.3 - - + -
290A ALA* 1.3 76.1 - - - +
292A GLY* 1.3 57.7 + - - +
295A LYS 3.3 17.3 - - - +
296A LEU* 4.1 17.0 - - + -
356A GLY 3.9 1.1 + - - +
357A VAL* 3.8 7.6 - - - +
358A ILE* 3.2 19.1 + - - -
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Residues in contact with GLY 292 (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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224A SER* 4.6 1.8 - - - -
225A GLN* 4.1 10.1 - - - -
227A MET* 3.7 8.7 - - - +
291A LEU* 1.3 79.0 - - - +
293A GLU* 1.3 73.3 - - - +
294A LEU 3.4 2.5 - - - -
295A LYS* 3.2 23.8 + - - +
357A VAL* 5.9 0.2 - - - -
358A ILE* 3.6 20.6 - - - +
445A LYS* 6.4 0.4 - - - -
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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