Contacts of the helix formed by residues 230 - 245 (chain C) in PDB entry 1Z6Z
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 ASP 230 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199C ASP* 6.1 2.0 - - - -
228C LEU 3.6 4.2 + - - -
229C VAL* 1.3 76.0 - - - +
231C CYS* 1.3 66.2 + - - +
232C LYS* 2.8 39.3 + - - +
233C VAL* 3.0 31.5 + - + +
234C SER 3.1 10.2 + - - -
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Residues in contact with CYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLY 4.3 2.9 - - - -
16C PHE* 3.9 21.5 - - + -
19C THR* 3.6 24.2 - - + +
198C LEU* 4.0 20.9 - - - -
199C ASP* 4.9 6.5 - - - +
200C THR* 3.7 30.3 - - - -
229C VAL 3.3 3.8 + - - -
230C ASP* 1.3 73.6 + - - +
232C LYS* 1.3 57.3 + - - +
234C SER* 3.4 1.6 + - - -
235C ALA* 2.9 31.5 + - - +
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Residues in contact with LYS 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C THR* 3.6 16.2 - - + +
23C LEU* 3.9 27.8 - - + -
230C ASP* 2.8 20.7 + - - +
231C CYS* 1.3 73.6 - - - +
233C VAL* 1.3 57.5 + - + +
235C ALA* 3.3 3.0 + - - +
236C GLN* 2.9 58.8 + - - +
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C VAL* 4.8 2.2 - - + -
230C ASP* 3.0 27.7 + - + +
232C LYS* 1.3 77.1 - - + +
234C SER* 1.3 63.8 + - - +
236C GLN* 3.3 16.0 + - - +
237C LYS* 3.0 21.3 + - - +
255C PHE* 3.8 23.8 - - + -
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Residues in contact with SER 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PHE* 3.8 9.8 - - - -
193C TYR* 3.0 29.5 + - - -
195C PRO* 2.7 37.9 + - - +
198C LEU* 3.9 8.5 - - - -
229C VAL* 3.9 5.4 - - - -
230C ASP 3.1 11.7 + - - -
231C CYS 3.8 6.3 - - - -
233C VAL* 1.3 79.5 - - - +
235C ALA* 1.3 60.5 + - - +
237C LYS 3.2 1.2 + - - -
238C LEU* 3.0 11.6 + - - +
255C PHE* 3.8 10.2 - - - -
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Residues in contact with ALA 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PHE* 3.6 16.1 - - + -
19C THR* 4.6 2.2 - - + -
20C LEU* 3.8 24.9 - - + +
23C LEU* 3.7 18.8 - - + -
231C CYS 2.9 19.1 + - - +
232C LYS* 3.6 4.7 - - - +
234C SER* 1.3 72.5 - - - +
236C GLN* 1.3 65.1 + - - +
238C LEU* 3.3 3.7 + - - +
239C LEU* 3.0 31.3 + - - +
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Residues in contact with GLN 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU* 4.4 15.1 - - + +
232C LYS* 2.9 50.0 + - - +
233C VAL* 3.6 17.6 - - - +
235C ALA* 1.3 77.0 - - - +
237C LYS* 1.3 57.1 + - - +
239C LEU* 3.4 10.0 + - + +
240C SER* 2.9 30.5 + - - -
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Residues in contact with LYS 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C TYR* 3.5 17.9 - - + +
233C VAL 3.0 13.1 + - - +
234C SER 3.2 9.2 + - - +
236C GLN* 1.3 76.8 - - - +
238C LEU* 1.3 62.2 + - - +
240C SER* 3.2 13.0 + - - +
241C LEU* 2.9 39.6 + - + +
253C VAL* 5.2 2.8 - - - +
254C ASP 3.9 11.3 + - - -
255C PHE* 3.4 36.8 + - + +
257C ASP* 4.2 12.9 + - - +
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Residues in contact with LEU 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PHE* 4.2 7.6 - - + -
20C LEU* 4.1 29.8 - - + -
95C ILE* 4.8 7.4 - - + -
150C VAL* 4.2 9.9 - - + -
152C ILE* 4.1 20.6 - - + -
191C LEU* 3.7 28.5 - - + -
193C TYR* 3.7 32.0 + - + -
234C SER 3.0 8.2 + - - +
235C ALA* 3.6 8.3 - - - +
237C LYS* 1.3 74.7 - - - +
239C LEU* 1.3 64.6 + - + +
241C LEU* 3.2 8.6 + - - +
242C LEU* 3.0 37.0 + - + +
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Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LEU* 4.9 5.8 - - + +
20C LEU* 4.1 15.0 - - + -
23C LEU* 3.8 32.5 - - + -
24C LEU* 3.8 29.4 - - + -
27C LEU* 4.0 29.9 - - + +
95C ILE* 5.8 0.4 - - + -
235C ALA 3.0 22.6 + - - +
236C GLN* 3.8 8.5 - - + +
238C LEU* 1.3 76.8 - - + +
240C SER* 1.3 57.0 + - - +
242C LEU* 3.1 18.6 + - + +
243C GLU* 2.9 29.6 + - - +
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Residues in contact with SER 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C GLN 2.9 15.5 + - - -
237C LYS* 3.2 18.4 + - - +
239C LEU* 1.3 75.4 - - - +
241C LEU* 1.3 58.7 + - - +
243C GLU* 3.8 8.9 - - - +
244C LYS* 2.9 50.1 + - - +
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Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C LEU* 4.7 14.4 - - + -
193C TYR* 3.6 37.2 - - + -
237C LYS* 2.9 31.9 + - + +
238C LEU* 3.2 9.4 + - - +
240C SER* 1.3 78.8 + - - +
242C LEU* 1.3 56.2 + - - +
244C LYS* 4.0 6.1 - - + +
245C ASP* 3.0 26.0 + - - -
246C GLU 4.4 0.5 + - - -
247C PHE* 3.7 24.2 - - + +
253C VAL* 3.8 25.4 - - + -
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Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LEU* 4.6 7.9 - - + -
91C ARG* 3.7 24.4 + - - +
93C LEU* 4.1 27.6 - - + -
95C ILE* 4.9 4.7 - - + -
148C THR* 3.8 29.2 - - + -
150C VAL* 4.0 14.1 - - + -
191C LEU* 4.1 13.2 - - + -
238C LEU* 3.0 34.0 + - + +
239C LEU* 3.1 19.5 + - + +
241C LEU* 1.3 75.0 - - - +
243C GLU* 1.3 62.2 + - - +
245C ASP* 3.4 17.0 + - - +
247C PHE* 4.4 8.3 - - + -
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Residues in contact with GLU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0C HIS* 3.9 47.8 - - + +
1C MET 5.2 4.9 - - - +
2C LEU* 4.6 9.1 - - + +
27C LEU* 6.4 1.6 - - + -
91C ARG* 4.7 8.2 + - - +
239C LEU 2.9 16.3 + - - +
240C SER* 3.8 9.3 - - - +
242C LEU* 1.3 76.0 - - - +
244C LYS* 1.3 75.8 + - + +
245C ASP* 3.4 4.0 + - - +
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Residues in contact with LYS 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C SER* 2.9 34.4 + - - +
241C LEU* 4.2 4.9 - - + +
243C GLU* 1.3 88.0 - - - +
245C ASP* 1.3 68.7 + - - +
246C GLU* 3.2 35.2 + - + +
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Residues in contact with ASP 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ARG* 5.2 2.1 + - - +
146C ASN* 3.1 27.4 + - - -
148C THR* 4.8 2.1 + - - -
189C ARG* 2.8 46.0 + - - +
241C LEU 3.0 14.6 + - - -
242C LEU 3.6 13.0 - - - +
243C GLU 3.2 4.2 - - - +
244C LYS* 1.3 77.8 - - - +
246C GLU* 1.3 57.4 + - - +
247C PHE* 3.9 10.2 - - - -
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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