Contacts of the helix formed by residues 228 - 241 (chain F) in PDB entry 2ZXX
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 228 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226F THR* 3.2 27.4 + - + +
227F VAL* 1.3 76.2 - - - +
229F PHE* 1.3 68.3 + - - +
230F ALA* 4.5 1.0 - - - +
231F LYS* 3.0 39.3 + - - +
232F VAL* 3.1 11.4 + - - +
267F ASN* 6.2 4.7 - - + -
281F GLN* 3.5 27.5 + - + +
282F LEU 3.5 6.5 - - - -
283F THR* 4.1 11.2 - - + +
284F ILE* 4.3 2.5 - - - -
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Residues in contact with PHE 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228F THR* 1.3 69.7 - - - +
230F ALA* 1.3 72.3 + - - +
232F VAL* 2.9 12.6 + - + +
233F LYS* 3.0 45.3 + - + +
244F PHE* 4.0 13.7 - + - -
245F GLU* 3.9 6.1 - - - -
246F GLU* 3.6 36.8 - - + -
249F VAL* 3.7 30.3 - - + -
281F GLN* 3.7 3.9 + - + +
282F LEU* 2.8 46.2 + - + +
284F ILE* 4.1 8.9 - - + +
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Residues in contact with ALA 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228F THR* 3.4 2.2 - - - +
229F PHE* 1.3 83.3 - - - +
231F LYS* 1.3 66.8 + - + +
233F LYS* 3.4 7.2 + - - +
234F GLN* 2.9 27.6 + - - +
281F GLN* 3.7 19.4 + - - +
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Residues in contact with LYS 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216F ILE* 4.3 4.5 - - - +
220F LEU* 3.9 22.2 - - + +
225F GLU* 2.4 38.7 + - - +
226F THR* 3.2 22.4 + - - +
228F THR* 3.0 30.4 + - - +
230F ALA* 1.3 80.5 - - + +
232F VAL* 1.3 62.2 + - - +
234F GLN* 3.7 6.6 + - - +
235F GLY* 3.2 17.2 + - - -
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Residues in contact with VAL 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213F MSE 4.1 28.3 - - + +
216F ILE* 4.1 18.1 - - + +
217F VAL* 4.3 10.1 - - + -
220F LEU* 4.8 2.9 - - + -
227F VAL* 3.9 24.9 - - + -
228F THR 3.1 10.4 + - - +
229F PHE* 2.9 12.7 + - + +
231F LYS* 1.3 73.5 - - - +
233F LYS* 1.3 67.5 + - - +
234F GLN 3.1 0.7 - - - -
235F GLY* 2.7 14.2 + - - -
236F VAL* 2.8 27.0 + - + +
244F PHE* 4.5 6.1 - - + -
284F ILE* 4.4 9.2 - - + -
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Residues in contact with LYS 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229F PHE* 3.0 41.3 + - + +
230F ALA* 3.5 6.7 - - - +
232F VAL* 1.3 72.6 - - - +
234F GLN* 1.3 58.3 + - - +
236F VAL* 3.8 6.7 - - - +
237F GLN* 2.4 77.7 + - - +
243F ARG* 5.0 1.0 - - - +
244F PHE* 3.4 21.7 + - - +
245F GLU* 3.4 30.6 + - - -
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Residues in contact with GLN 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F ALA 2.9 19.8 + - - +
231F LYS* 4.0 6.4 - - - +
232F VAL 2.9 0.8 + - - -
233F LYS* 1.3 75.4 - - - +
235F GLY* 1.3 59.2 + - - +
237F GLN* 4.0 6.4 - - - +
238F GLU* 2.5 63.4 + - - +
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Residues in contact with GLY 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216F ILE* 3.5 26.9 - - - +
231F LYS 3.2 9.1 + - - -
232F VAL 2.7 12.2 + - - -
234F GLN* 1.3 76.6 - - - +
236F VAL* 1.3 56.2 + - - -
238F GLU* 3.6 8.6 + - - +
239F MSE 3.0 27.4 + - - +
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Residues in contact with VAL 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F MSE 5.0 0.7 - - - +
212F SER* 4.0 14.1 - - - +
213F MSE 4.4 9.6 - - - +
216F ILE* 3.8 4.8 - - + +
232F VAL* 2.8 29.2 + - + +
233F LYS 3.8 2.0 - - - +
235F GLY* 1.3 70.0 - - - -
237F GLN* 1.3 59.9 + - - +
239F MSE 4.0 6.3 - - - -
240F MSE 2.8 53.3 + - + +
244F PHE* 3.5 49.1 - - + -
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Residues in contact with GLN 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F LYS* 2.4 61.6 + - - +
234F GLN* 4.0 5.5 - - - +
236F VAL* 1.3 75.0 - - - +
238F GLU* 1.3 60.1 + - - +
241F ARG* 2.8 33.8 + - - -
242F LYS 3.2 22.7 - - - +
243F ARG* 3.6 5.4 - - - +
244F PHE* 2.9 26.2 + - + +
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Residues in contact with GLU 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 5.0 0.7 + - - -
234F GLN* 2.5 55.3 + - - +
235F GLY* 3.8 6.9 - - - +
237F GLN* 1.3 75.0 - - - +
239F MSE 1.3 59.5 + - + +
241F ARG* 2.8 30.0 + - - +
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Residues in contact with MSE 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F ARG* 3.4 33.9 - - - +
212F SER* 3.3 31.9 - - - +
215F THR* 4.0 26.7 - - + -
216F ILE* 4.0 15.7 - - + -
219F MSE 6.3 0.2 - - - -
235F GLY 3.0 19.1 + - - +
236F VAL 3.4 4.0 - - - +
237F GLN 3.1 0.2 - - - -
238F GLU* 1.3 75.8 - - - +
240F MSE 1.3 58.2 + - - +
241F ARG* 2.4 38.7 + - - +
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Residues in contact with MSE 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG* 4.9 2.8 + - - -
205F VAL* 5.4 1.6 - - + -
208F GLU* 3.6 40.6 - - + +
209F MSE 2.8 59.0 - - + -
212F SER* 4.5 4.9 - - - +
236F VAL* 2.8 40.7 + - + +
239F MSE 1.3 72.4 - - + +
241F ARG* 1.3 57.2 + - - +
242F LYS* 2.7 51.8 + - + +
243F ARG 3.7 14.8 - - - +
244F PHE* 4.2 1.3 - - + -
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Residues in contact with ARG 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLU* 4.9 7.0 + - - +
130A ARG* 3.0 47.0 - - - +
131A LEU* 4.7 4.4 - - - +
134A GLU* 4.1 18.2 + - - -
132B ARG* 5.3 22.3 - - - +
237F GLN 2.8 16.6 + - - +
238F GLU* 2.8 28.6 + - - +
239F MSE 2.4 31.3 + - - +
240F MSE 1.3 76.8 - - - +
242F LYS* 1.3 61.2 + - - +
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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