Contacts of the helix formed by residues 240 - 251 (chain B) in PDB entry 4OBZ
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 PRO 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B GLY* 1.3 84.6 - - - +
241B VAL* 1.3 56.5 + - - +
242B ASP* 3.3 2.2 - - + +
243B GLU* 3.1 26.3 + - + +
244B VAL* 2.8 31.7 + - - +
309B MET 3.9 2.5 - - - +
310B ASP* 3.3 17.7 - - - +
317B PRO* 4.8 18.2 - - + -
318B LEU 4.7 5.8 - - - +
319B TRP* 3.4 31.9 - - + +
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Residues in contact with VAL 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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239B GLY 3.4 1.2 + - - -
240B PRO* 1.3 69.3 - - - +
242B ASP* 1.3 61.4 + - - +
244B VAL* 3.6 1.7 + - - +
245B ARG* 3.0 55.9 + - - +
261B TYR* 4.8 4.6 + - - +
308B GLY* 3.8 14.5 - - - +
309B MET* 3.7 19.3 - - - +
310B ASP* 3.3 32.4 + - + +
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Residues in contact with ASP 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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240B PRO* 3.3 1.9 - - + +
241B VAL* 1.3 77.9 - - - +
243B GLU* 1.3 67.2 + - + +
245B ARG* 3.2 34.2 + - - +
246B GLU* 3.1 30.0 + - - +
310B ASP* 5.2 0.9 + - - +
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Residues in contact with GLU 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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221B LEU* 3.2 38.6 - - + +
222B CYS* 2.8 32.1 + - - +
223B LYS* 5.4 4.2 + - - -
226B CYS* 5.7 0.9 - - - +
240B PRO* 3.1 23.0 + - + +
242B ASP* 1.3 76.3 - - + +
244B VAL* 1.3 61.4 + - - +
246B GLU* 3.3 14.9 + - - +
247B LEU* 3.2 11.4 + - - +
319B TRP* 3.6 32.6 + - + -
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Residues in contact with VAL 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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238B VAL 4.8 0.2 - - - -
239B GLY* 3.6 19.1 - - - +
240B PRO 2.8 22.0 + - - +
241B VAL 4.1 0.7 - - - +
243B GLU* 1.3 69.9 - - - +
245B ARG* 1.3 57.8 + - - +
247B LEU* 3.3 8.0 - - + +
248B GLN* 2.8 54.2 + - - +
261B TYR* 4.4 3.8 - - + -
306B PHE* 4.1 15.7 - - + +
307B MET 3.5 20.9 - - - +
308B GLY* 3.5 26.9 - - - +
319B TRP* 4.4 12.8 - - + -
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Residues in contact with ARG 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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241B VAL* 3.0 43.2 + - - +
242B ASP* 3.3 38.0 + - - +
244B VAL* 1.3 74.3 - - - +
246B GLU* 1.4 63.7 + - - +
248B GLN* 3.4 3.1 + - - +
249B LYS* 3.2 40.9 + - + +
261B TYR* 4.0 25.2 + - + +
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Residues in contact with GLU 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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219B LEU* 3.6 27.3 - - + +
221B LEU* 3.8 13.1 - - + +
223B LYS* 4.5 12.2 + - - -
242B ASP* 3.1 22.3 + - - +
243B GLU* 3.3 19.6 + - - +
245B ARG* 1.4 74.4 - - - +
247B LEU* 1.4 60.5 + - - +
249B LYS* 3.1 13.2 + - + +
250B ALA* 3.1 22.3 + - - +
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Residues in contact with LEU 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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213B VAL* 4.6 6.3 - - + -
215B VAL* 4.6 4.3 - - + -
219B LEU* 3.6 11.1 - - - +
221B LEU* 3.9 21.3 - - + -
243B GLU 3.2 8.5 + - - +
244B VAL* 3.3 14.1 - - - +
246B GLU* 1.4 77.7 - - - +
248B GLN* 1.3 60.3 + - - +
250B ALA* 3.3 5.6 - - - +
251B ILE* 3.1 38.3 + - + +
274B ILE* 3.8 26.7 - - + -
306B PHE* 3.7 48.5 - - + -
319B TRP* 4.8 5.6 - - + -
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Residues in contact with GLN 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 VAL* 2.8 46.7 + - - +
245B ARG 3.4 3.1 + - - +
246B GLU 3.3 0.2 - - - -
247B LEU* 1.3 75.3 - - - +
249B LYS* 1.3 64.8 + - - +
251B ILE* 3.3 9.8 + - + -
252B GLY 3.2 3.8 + - - -
253B ALA* 3.0 55.3 + - + +
261B TYR* 3.2 36.5 - - + +
304B SER* 2.7 27.2 + - - -
306B PHE* 3.0 19.6 - - - +
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Residues in contact with LYS 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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245B ARG* 3.2 31.4 + - + +
246B GLU* 3.1 14.5 + - + +
248B GLN* 1.3 76.8 - - - +
250B ALA* 1.3 60.9 + - - +
252B GLY* 3.4 10.1 + - - -
253B ALA 5.0 2.2 - - - -
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Residues in contact with ALA 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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215B VAL* 5.0 3.4 - - + -
217B SER* 4.2 18.0 + - - +
219B LEU* 3.8 25.8 - - + -
246B GLU 3.1 11.7 + - - +
247B LEU 3.3 11.0 - - - +
249B LYS* 1.3 77.1 - - - +
251B ILE* 1.3 62.2 + - + +
252B GLY 3.5 0.6 + - - -
272B PRO* 4.7 2.8 - - - +
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Residues in contact with ILE 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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215B VAL* 4.3 11.4 - - + -
247B LEU* 3.1 32.9 + - + +
248B GLN* 3.3 24.8 + - + +
250B ALA* 1.3 77.7 - - - +
252B GLY* 1.3 61.0 + - - +
253B ALA* 3.3 2.6 + - + -
263B ILE* 3.8 33.4 - - + +
267B LYS* 5.9 1.6 - - - +
271B LEU* 3.2 27.9 - - + +
272B PRO* 3.8 27.4 - - + -
274B ILE* 4.5 0.9 - - + -
290B TYR* 4.0 24.2 - - + +
304B SER* 4.1 5.8 - - - +
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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