Contacts of the helix formed by residues 233 - 243 (chain A) in PDB entry 2ZB8
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 GLY 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A ASP* 2.9 14.8 + - - -
232A VAL* 1.3 84.5 - - - +
234A GLY* 1.3 68.2 + - - +
235A ASN 3.7 0.2 + - - -
236A ILE* 3.7 4.2 + - - +
237A SER* 3.2 23.6 + - - -
255A GLN* 3.3 27.1 - - - +
257A SER* 3.5 3.1 + - - -
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Residues in contact with GLY 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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233A GLY* 1.3 73.7 - - - -
235A ASN* 1.3 64.9 + - - -
237A SER* 3.1 11.9 + - - -
238A ASP* 3.2 20.1 + - - +
255A GLN* 4.4 2.8 + - - -
257A SER* 3.4 13.2 + - - -
258A GLN* 4.0 16.7 - - - +
267A PRO* 6.3 0.4 - - - +
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Residues in contact with ASN 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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233A GLY 3.7 0.2 + - - -
234A GLY* 1.3 68.1 - - - -
236A ILE* 1.3 66.2 + - + +
238A ASP* 3.3 16.4 + - - +
239A THR* 3.1 26.6 + - - -
257A SER* 5.9 0.2 - - - -
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Residues in contact with ILE 236 (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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161A SER* 4.2 3.1 - - - -
186A ILE* 4.2 31.0 - - + -
208A TYR* 3.4 50.5 - - + -
213A VAL* 5.5 6.0 - - + +
228A TYR* 3.9 13.2 - - - +
232A VAL* 3.9 18.2 - - + -
233A GLY 3.7 1.3 + - - +
234A GLY 3.2 0.8 - - - -
235A ASN* 1.3 75.7 - - + +
237A SER* 1.3 64.6 + - - +
239A THR* 3.2 9.1 + - - -
240A VAL* 3.0 20.0 + - + +
257A SER* 6.4 0.2 - - - -
700A NAP 3.9 21.8 - - + +
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Residues in contact with SER 237 (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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228A TYR* 2.8 25.4 + - - -
230A ASP* 2.5 32.0 + - - -
233A GLY* 3.2 14.2 + - - -
234A GLY 3.1 9.8 + - - -
236A ILE* 1.3 80.3 - - - +
238A ASP* 1.3 54.0 + - - +
240A VAL* 3.1 1.6 + - - +
241A ILE* 2.7 49.0 + - - +
255A GLN* 5.6 0.4 - - - -
269A LEU* 5.5 3.6 - - - -
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Residues in contact with ASP 238 (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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234A GLY 3.2 16.6 + - - +
235A ASN* 3.6 22.4 - - - +
236A ILE 3.3 0.2 - - - -
237A SER* 1.3 72.1 - - - +
239A THR* 1.3 66.0 + - - +
241A ILE* 3.4 1.9 + - - +
242A SER* 3.0 28.7 + - - -
269A LEU* 4.3 10.6 - - - +
270A SER* 4.2 11.0 + - - -
273A ILE* 3.4 44.9 - - + +
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Residues in contact with THR 239 (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 VAL* 3.9 17.4 - - + +
214A ALA* 3.7 40.2 - - + +
217A LEU* 4.1 5.0 - - + +
235A ASN* 3.1 12.6 + - - +
236A ILE* 3.5 9.5 - - - -
238A ASP* 1.3 81.3 - - - +
240A VAL* 1.3 65.7 + - - +
242A SER* 3.3 18.1 - - - -
243A GLN* 3.7 9.2 + - - +
601A SO4 4.1 15.2 + - - +
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Residues in contact with VAL 240 (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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159A VAL* 3.9 18.6 - - + -
186A ILE* 3.6 30.3 - - + -
217A LEU* 3.9 11.7 - - + -
225A VAL* 4.6 5.9 - - + +
228A TYR* 3.5 48.2 - - + +
236A ILE 3.0 17.9 + - - +
237A SER 3.1 6.7 + - - +
239A THR* 1.3 75.7 - - - +
241A ILE* 1.3 64.6 + - - +
243A GLN* 2.9 16.8 + - - +
244A MET* 3.3 14.8 + - + +
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Residues in contact with ILE 241 (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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228A TYR* 4.5 5.8 - - + -
230A ASP* 5.7 0.7 - - - +
237A SER* 2.7 31.8 + - - +
238A ASP 3.9 4.0 - - - +
240A VAL* 1.3 71.4 - - - +
242A SER* 1.3 60.7 + - - +
244A MET* 3.1 25.8 + - - +
250A ILE* 3.8 30.5 - - + -
269A LEU* 3.6 33.2 - - + -
273A ILE* 3.8 28.0 - - + +
276A ILE* 4.0 9.7 - - + +
277A GLN* 4.7 6.3 - - + +
280A ARG* 3.6 6.1 + - - -
282A ILE* 4.3 15.7 - - + +
284A ARG* 5.0 1.8 - - - +
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Residues in contact with SER 242 (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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238A ASP 3.0 18.4 + - - -
239A THR* 3.3 16.0 - - - -
241A ILE* 1.3 76.8 - - - +
243A GLN* 1.3 61.7 + - - +
273A ILE* 4.1 12.7 - - - +
276A ILE* 4.3 16.9 - - - +
280A ARG* 2.8 26.1 + - - +
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Residues in contact with GLN 243 (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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214A ALA* 2.8 39.0 + - - +
217A LEU* 3.3 20.5 - - + +
218A ARG* 3.2 44.7 + - - +
221A CYS* 5.0 3.3 - - - +
224A GLY* 3.5 10.9 - - - -
225A VAL* 3.1 29.2 + - + +
239A THR* 4.3 8.1 + - - +
240A VAL* 2.9 11.8 + - - +
242A SER* 1.3 83.4 - - - +
244A MET* 1.3 62.1 + - - +
245A ASN* 4.3 0.2 - - - +
280A ARG* 4.1 0.7 - - - -
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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