Contacts of the helix formed by residues 239 - 251 (chain B) in PDB entry 5Z7R
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 239 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A GLY 4.5 3.3 + - - -
205B VAL* 4.4 26.2 - - + +
235B GLU 3.9 5.6 - - - +
236B CYS* 3.0 23.5 + - - +
237B PHE 3.3 1.1 - - - +
238B SER* 1.3 94.5 - - - +
240B GLU* 1.3 67.1 + - - +
241B ASP* 3.8 8.6 + - - +
242B GLN* 3.2 24.3 + - - +
243B LYS* 3.6 11.3 + - - +
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Residues in contact with GLU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B SER 5.2 1.7 - - - +
239B THR* 1.3 71.4 - - - +
241B ASP* 1.3 66.3 + - - +
243B LYS* 3.0 6.8 + - - +
244B ASP* 2.8 50.8 + - - +
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Residues in contact with ASP 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU 4.2 0.3 - - - +
138A GLY* 4.3 3.5 - - - -
203B ALA* 4.2 17.3 - - + +
204B PRO* 3.4 28.8 - - - +
205B VAL* 5.5 2.7 + - + +
239B THR* 3.3 7.8 - - - +
240B GLU* 1.3 82.6 - - - +
242B GLN* 1.3 62.0 + - - +
244B ASP* 4.6 7.3 - - - +
245B ALA* 3.1 28.3 + - + +
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Residues in contact with GLN 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS 3.2 23.8 + - - -
74A MET 4.0 2.9 - - - +
137A LEU 3.7 7.7 - - - +
138A GLY* 3.7 8.4 - - - +
139A ILE* 4.2 13.9 - - + -
236B CYS 3.2 24.2 - - - +
237B PHE* 3.3 47.9 - - + +
239B THR* 3.2 11.9 + - - +
240B GLU 3.1 1.2 - - - -
241B ASP* 1.3 76.9 - - - +
243B LYS* 1.3 73.2 + - - +
246B MET* 3.1 49.3 + - + +
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Residues in contact with LYS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS* 3.2 24.1 - - + +
73A GLU* 3.8 30.9 + - - +
74A MET 5.7 1.6 - - - +
237B PHE 6.1 0.7 - - - +
239B THR 3.6 6.1 + - - +
240B GLU* 3.0 7.6 + - - +
242B GLN* 1.3 91.0 + - - +
244B ASP* 1.3 61.5 + - - +
246B MET* 3.5 1.6 + - - +
247B THR* 2.4 37.5 + - - +
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Residues in contact with ASP 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B GLU* 2.8 39.4 + - - +
241B ASP* 4.3 6.5 + - - +
243B LYS* 1.3 74.5 - - - +
245B ALA* 1.3 57.3 + - - +
247B THR* 3.2 6.2 + - - -
248B ALA* 2.9 32.1 + - - +
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLY 3.7 23.7 - - - +
137A LEU* 3.7 15.2 - - - +
138A GLY 4.2 0.7 - - - +
241B ASP* 3.1 21.7 + - + +
244B ASP* 1.3 73.3 - - - +
246B MET* 1.3 63.1 + - - +
247B THR 3.1 1.3 - - - -
248B ALA* 4.3 4.2 - - - +
249B PHE* 2.9 28.8 + - - +
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Residues in contact with MET 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 3.7 27.1 - - + +
71A MET* 4.0 11.0 - - + -
72A LYS* 3.9 27.8 - - + -
137A LEU* 3.7 17.5 - - + +
139A ILE* 3.7 47.8 - - + -
237B PHE* 3.9 13.7 - - + -
242B GLN* 3.1 31.6 + - - +
243B LYS 4.0 2.2 - - - +
245B ALA* 1.3 76.6 - - - +
247B THR* 1.3 64.5 + - - +
249B PHE* 3.6 4.4 - - - +
250B ILE* 3.3 27.0 + - - +
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Residues in contact with THR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS* 3.1 32.2 - - - -
243B LYS* 2.4 30.8 + - - +
244B ASP* 3.4 7.1 - - - -
245B ALA 3.1 0.2 - - - -
246B MET* 1.3 76.9 - - - +
248B ALA* 1.3 54.9 + - - +
250B ILE* 2.8 27.0 + - - +
251B GLU* 3.1 12.3 + - + +
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ASP 2.9 18.5 + - - +
245B ALA* 4.3 4.5 - - - +
247B THR* 1.3 70.2 - - - +
249B PHE* 1.3 65.2 + - - +
251B GLU* 3.2 28.3 + - + +
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Residues in contact with PHE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 3.5 39.9 - - + -
137A LEU* 3.8 21.3 - - + -
245B ALA 2.9 22.2 + - - +
246B MET 3.6 5.2 - - - +
248B ALA* 1.3 75.6 - - - +
250B ILE* 1.3 64.8 + - + +
252B LYS* 3.0 67.2 + - + +
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Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 3.8 29.6 - - + +
69A SER* 4.2 16.4 - - - +
72A LYS* 4.4 14.1 - - + -
246B MET 3.3 15.7 + - - +
247B THR* 2.8 9.8 + - - +
249B PHE* 1.3 85.1 - - + +
251B GLU* 1.3 56.3 + - - +
252B LYS* 2.8 13.8 + - + +
253B ARG* 3.9 34.7 + - - +
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Residues in contact with GLU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B THR* 3.1 10.0 + - + +
248B ALA* 3.2 25.1 + - + +
249B PHE 3.9 0.9 - - - -
250B ILE* 1.3 73.0 - - - +
252B LYS* 1.3 59.5 + - - +
253B ARG* 3.2 6.5 + - - +
254B LYS* 3.5 51.1 + - - +
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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