Contacts of the strand formed by residues 234 - 241 (chain N) in PDB entry 1CZA
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 THR 234 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229N ILE 3.0 17.1 + - - -
230N ILE* 4.2 7.5 - - - +
233N GLY* 1.3 74.5 - - - -
235N ASN* 1.3 62.0 + - - +
261N TRP* 3.0 32.4 + - + +
262N GLY 4.0 5.5 + - - -
293N PHE* 4.8 1.3 - - + -
294N GLU* 2.7 37.2 + - + +
297N VAL* 3.6 34.8 - - + +
298N SER* 4.2 4.0 - - - -
386N VAL* 4.4 0.9 - - - +
918N GLC 3.2 12.6 + - - -
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Residues in contact with ASN 235 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208N ASN* 3.0 20.4 + - - -
210N THR* 3.5 7.0 - - + +
228N LEU* 3.7 3.5 - - - +
229N ILE* 2.9 28.5 + - - +
234N THR* 1.3 79.9 + - - +
236N ALA* 1.3 72.9 + - - +
258N ASN* 2.6 24.8 + - - +
259N THR* 3.5 0.3 + - - -
260N GLU* 2.9 41.8 + - - -
261N TRP* 3.3 13.2 + - - +
918N GLC 3.1 23.5 + - - +
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Residues in contact with ALA 236 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210N THR* 3.8 5.6 - - - -
226N VAL* 4.8 4.7 - - + -
227N GLY 3.1 12.6 - - - +
228N LEU* 4.2 5.2 - - + -
235N ASN* 1.3 81.8 + - - +
237N CYS* 1.3 60.5 + - - +
259N THR* 2.8 34.4 + - - +
261N TRP* 3.5 34.4 - - + -
390N LEU* 5.4 0.2 - - + -
393N ILE* 3.8 12.6 - - + -
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Residues in contact with CYS 237 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210N THR* 3.3 45.0 - - - +
211N VAL* 3.5 7.9 - - + -
214N MET* 4.0 6.1 - - - -
226N VAL* 3.3 7.4 - - - +
227N GLY 2.8 34.8 + - - -
236N ALA* 1.3 73.9 - - - +
238N TYR* 1.3 67.5 + - - +
256N CYS* 3.6 23.1 - - - -
257N ILE 3.1 18.4 - - - +
258N ASN* 4.0 2.0 - - - -
393N ILE* 5.3 0.2 - - - -
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Residues in contact with TYR 238 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N MET* 3.5 20.5 - - + +
51N LEU* 3.9 0.3 - - - +
63N MET* 3.2 20.6 - - + +
214N MET* 4.8 1.3 - - - -
225N GLU 3.2 13.0 - - - +
226N VAL* 3.8 4.0 - - + -
237N CYS* 1.3 80.9 - - - +
239N MET* 1.3 73.3 + - - +
240N GLU* 2.6 50.6 + - + +
256N CYS* 4.2 4.7 - - - -
257N ILE* 2.8 43.9 + - + +
259N THR* 3.9 17.0 - - + -
393N ILE* 3.5 31.6 - - + -
396N ARG* 4.3 10.3 - - + -
397N LEU* 4.2 11.4 - - + -
400N ASN* 5.1 0.4 - - - -
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Residues in contact with MET 239 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N VAL 4.8 0.7 - - - +
69N ARG 3.5 29.6 - - - +
70N SER* 4.1 8.5 - - - +
71N ILE* 5.1 5.4 - - + +
214N MET* 3.6 30.3 - - - -
224N CYS 5.0 2.0 - - - +
225N GLU* 3.1 24.3 + - + +
238N TYR* 1.3 72.8 - - - +
240N GLU* 1.3 59.9 + - - +
241N GLU* 4.7 1.4 - - - +
254N ARG* 3.7 44.3 + - + +
255N MET 3.9 4.5 - - - -
256N CYS* 3.7 25.4 - - - +
397N LEU* 3.4 22.1 - - - +
400N ASN* 4.8 1.0 + - - -
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Residues in contact with GLU 240 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N LEU* 3.7 3.7 - - + +
238N TYR* 2.6 31.9 + - + +
239N MET* 1.3 75.1 - - - +
241N GLU* 1.3 76.0 + - - +
244N HIS* 3.1 15.7 - - + -
245N ILE* 3.6 22.8 - - + +
254N ARG* 3.2 4.4 - - - +
255N MET 2.8 31.9 + - - +
257N ILE* 3.5 23.3 - - + -
396N ARG* 2.7 30.5 + - - -
400N ASN* 2.8 25.5 + - - +
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Residues in contact with GLU 241 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239N MET 4.7 0.2 - - - +
240N GLU* 1.3 84.1 + - - +
242N LEU* 1.3 65.0 + - - +
243N ARG* 3.5 40.2 + - + +
244N HIS* 3.0 22.3 + - + +
245N ILE* 3.5 12.3 + - - +
253N GLY* 3.6 7.0 - - - +
254N ARG* 3.1 40.4 + - - +
400N ASN* 3.7 37.4 + - + +
401N LYS* 5.9 1.0 - - - +
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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