Contacts of the helix formed by residues 238 - 256 (chain B) in PDB entry 6YB9
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 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236B GLU* 3.5 34.6 + - + +
237B VAL* 1.3 76.0 - - - +
239B PRO* 1.4 74.6 - - - +
240B GLU* 3.6 8.4 + - - +
241B GLY* 3.0 21.8 + - - +
242B LEU* 3.1 24.2 + - - +
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Residues in contact with PRO 239 (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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237B VAL 4.8 0.7 - - - +
238B THR* 1.4 88.2 - - + +
240B GLU* 1.3 59.9 + - - +
242B LEU* 3.5 11.9 + - + +
243B GLN* 3.5 27.0 + - - +
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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
----------------------------------------------------------
238B THR* 3.3 8.1 + - - +
239B PRO* 1.3 78.6 - - - +
241B GLY* 1.3 64.2 + - - +
243B GLN* 3.5 9.1 + - + +
244B MET* 3.4 19.4 + - - +
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Residues in contact with GLY 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 4.0 24.5 - - - +
236B GLU 6.0 0.2 - - - -
238B THR* 3.0 21.3 + - - -
240B GLU* 1.3 77.4 + - - +
242B LEU* 1.3 59.3 + - - +
244B MET* 3.5 9.7 + - - +
245B VAL* 3.3 25.8 + - - +
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 4.6 4.5 - - + -
48B ASN* 3.9 32.1 - - + +
49B HIS 4.2 10.3 - - - +
50B LEU* 4.0 23.5 - - + +
231B TYR* 4.0 29.8 - - + -
234B LEU* 4.9 0.4 - - - +
237B VAL* 4.0 13.2 - - + -
238B THR 3.1 9.4 + - - +
239B PRO* 3.8 13.5 - - + +
240B GLU 3.4 0.4 - - - -
241B GLY* 1.3 73.1 - - - +
243B GLN* 1.3 65.3 + - - +
245B VAL* 3.5 7.4 + - + +
246B LYS* 2.9 27.0 + - - +
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Residues in contact with GLN 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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50B LEU* 5.3 4.2 - - - +
239B PRO 3.5 14.6 + - - +
240B GLU* 3.5 11.3 + - + +
241B GLY 3.4 0.8 - - - -
242B LEU* 1.3 80.5 + - - +
244B MET* 1.3 59.9 + - - +
246B LYS* 3.4 27.0 + - - +
247B LYS* 3.0 52.1 + - - +
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Residues in contact with MET 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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230B SER* 3.7 29.8 - - - +
234B LEU* 4.5 11.0 - - + -
240B GLU 3.4 10.1 + - - +
241B GLY* 3.6 11.0 - - - +
242B LEU 3.4 0.2 - - - -
243B GLN* 1.3 74.5 - - - +
245B VAL* 1.3 93.5 + - + +
247B LYS* 3.2 10.8 + - - +
248B ASN* 3.1 31.5 + - - +
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Residues in contact with VAL 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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39B ILE* 3.9 18.2 - - + -
50B LEU* 4.6 5.4 - - + -
230B SER* 4.1 5.8 - - - +
231B TYR* 3.7 41.7 - - + +
234B LEU* 4.2 3.1 - - + -
241B GLY 3.3 14.0 + - - +
242B LEU* 3.6 11.4 - - + +
243B GLN 3.4 0.2 - - - -
244B MET* 1.3 90.7 - - + +
246B LYS* 1.3 63.9 + - - +
248B ASN* 3.2 4.4 + - - +
249B PHE* 3.0 50.5 + - + -
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Residues in contact with LYS 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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50B LEU* 4.3 23.1 - - + -
51B GLU* 3.7 28.2 + - - +
52B GLY* 5.7 1.3 - - - -
56B ILE* 5.2 5.8 - - + -
242B LEU 2.9 17.2 + - - +
243B GLN* 3.6 27.2 + - - +
244B MET 3.3 0.2 - - - -
245B VAL* 1.3 78.5 - - - +
247B LYS* 1.3 51.3 + - + +
249B PHE* 3.2 8.6 + - - +
250B GLU* 2.9 59.4 + - + +
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Residues in contact with LYS 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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243B GLN* 3.0 40.3 + - - +
244B MET* 3.2 8.7 + - + +
246B LYS* 1.3 72.8 - - - +
248B ASN* 1.3 56.7 + - - +
250B GLU* 3.2 19.6 + - - +
251B TRP* 2.8 35.8 + - - +
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Residues in contact with ASN 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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225B GLN 3.8 13.4 + - - +
226B LYS* 3.3 44.0 + - - +
230B SER* 3.2 33.4 + - - +
244B MET* 3.1 32.5 + - - +
245B VAL 3.4 7.6 - - - +
247B LYS* 1.3 75.8 - - - +
249B PHE* 1.3 61.7 + - + +
251B TRP* 3.2 5.8 + - - +
252B VAL* 3.1 25.5 + - - +
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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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39B ILE* 3.7 17.3 - - + -
50B LEU* 5.5 3.6 - - + -
53B LYS* 3.8 26.5 - - + -
56B ILE* 3.7 29.1 - - + +
57B SER* 5.3 1.3 - - - -
211B ASN* 3.4 36.1 - - + +
212B ASP* 3.6 24.5 - - - -
226B LYS 4.6 1.1 - - - -
227B ASP 4.5 2.7 - - - -
228B LYS* 4.0 22.4 - - + -
230B SER* 4.9 0.2 - - - -
245B VAL* 3.0 46.0 + - + +
246B LYS* 3.5 10.8 - - - +
248B ASN* 1.3 75.5 - - + +
250B GLU* 1.3 57.2 + - - +
252B VAL* 3.3 3.3 + - - +
253B ALA* 2.9 27.9 + - - +
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Residues in contact with GLU 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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56B ILE* 4.2 14.9 - - + +
246B LYS* 2.9 43.6 + - - +
247B LYS* 3.2 29.9 + - + +
249B PHE* 1.3 72.3 - - - +
251B TRP* 1.3 61.5 + - - +
253B ALA* 3.3 7.8 + - + +
254B GLU* 2.9 31.4 + - - +
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Residues in contact with TRP 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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180B TRP* 4.9 3.6 - + - -
183B GLN 5.1 3.8 - - - -
185B CYS* 3.4 33.4 - - - -
216B LEU* 4.9 5.2 - - + -
218B PRO* 4.0 17.3 - - + -
226B LYS* 3.5 45.4 - - + +
247B LYS 2.8 13.5 + - - +
248B ASN 3.3 10.1 - - - +
250B GLU* 1.3 78.6 - - - +
252B VAL* 1.3 71.3 + - + +
254B GLU* 3.5 0.6 + - - -
255B ARG* 3.2 77.9 + - - +
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Residues in contact with VAL 252 (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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60B ILE* 3.9 17.3 - - + -
180B TRP* 4.0 21.1 - - + -
211B ASN* 3.5 28.9 - - - +
214B TRP* 4.1 11.7 - - + -
216B LEU* 4.1 7.0 - - + -
226B LYS* 3.8 23.6 - - + +
248B ASN 3.1 14.1 + - - +
249B PHE 3.8 5.2 - - - +
251B TRP* 1.3 82.1 - - + +
253B ALA* 1.3 65.4 + - - +
255B ARG* 3.1 2.1 + - - +
256B VAL* 2.9 25.2 + - + +
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Residues in contact with ALA 253 (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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56B ILE* 4.0 26.9 - - + -
59B LYS* 3.2 36.0 + - + +
60B ILE* 4.4 7.0 - - + +
249B PHE 2.9 17.9 + - - +
250B GLU* 3.6 7.6 - - - +
252B VAL* 1.3 77.3 - - - +
254B GLU* 1.3 62.0 + - - +
256B VAL* 3.5 13.5 - - - +
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Residues in contact with GLU 254 (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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59B LYS* 4.6 6.1 + - - +
250B GLU 2.9 16.7 + - - +
251B TRP* 3.8 5.4 - - - +
252B VAL 3.2 0.2 - - - -
253B ALA* 1.3 79.1 - - - +
255B ARG* 1.3 88.6 + - - +
256B VAL 3.5 0.2 + - - -
257B GLU* 4.0 13.5 + - - +
258B LEU* 4.7 7.3 - - - +
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Residues in contact with ARG 255 (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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180B TRP* 4.3 14.8 - - + -
183B GLN* 3.7 22.1 - - - +
251B TRP* 3.2 85.7 + - + +
252B VAL 3.1 3.8 + - - +
254B GLU* 1.3 102.2 + - - +
256B VAL* 1.3 64.7 + - - +
257B GLU 3.2 2.9 - - - -
258B LEU* 3.0 31.3 + - + +
259B LEU* 3.8 7.6 - - - +
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Residues in contact with VAL 256 (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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59B LYS* 4.5 4.5 - - + -
60B ILE* 4.1 28.0 - - + -
63B CYS* 4.0 27.8 - - + +
64B ILE* 3.8 34.5 - - + -
180B TRP* 4.2 18.4 - - + -
252B VAL* 2.9 13.8 + - + +
253B ALA* 3.5 16.4 - - - +
254B GLU 3.4 0.2 - - - -
255B ARG* 1.3 76.4 - - - +
257B GLU* 1.3 62.6 + - - +
259B LEU* 3.2 20.6 + - + +
260B LEU* 4.4 1.4 + - - +
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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