Contacts of the helix formed by residues 246 - 256 (chain B) in PDB entry 5WWT
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 GLY 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B PHE* 4.6 3.2 - - - -
243B ALA 2.7 25.4 + - - -
245B PRO* 1.3 75.7 - - - +
247B GLY* 1.3 60.9 + - - +
248B LYS 3.6 0.7 - - - -
249B THR* 3.6 16.8 - - - -
250B THR* 2.9 33.7 + - - +
275B ILE* 4.2 9.6 - - - -
278B ASN* 4.8 0.8 - - - +
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Residues in contact with GLY 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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56B ARG* 3.3 6.8 + - - -
217B PHE* 3.4 33.0 - - - -
219B GLN* 4.1 8.7 - - - -
243B ALA 4.2 1.4 + - - -
245B PRO* 3.7 5.4 - - - +
246B GLY* 1.3 73.9 - - - +
248B LYS* 1.3 60.4 + - - +
250B THR* 3.0 5.3 + - - -
251B HIS* 2.9 24.9 + - - +
73D U 5.6 2.5 - - - -
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Residues in contact with LYS 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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219B GLN* 3.9 5.0 - - - +
223B SER* 3.7 36.9 + - - +
226B VAL* 3.9 22.4 - - + -
227B SER* 3.7 12.6 - - - +
240B ASP* 4.8 2.2 - - - +
243B ALA 5.3 1.9 + - - +
247B GLY* 1.3 74.3 - - - +
249B THR* 1.3 57.5 + - - +
251B HIS* 3.6 2.4 - - - +
252B ILE* 2.9 37.7 + - - +
321B LEU* 3.9 25.4 - - + -
323B ASP* 3.1 40.6 + - + +
458B PHE* 4.1 2.7 - - - -
72D C 3.5 18.2 + - - -
73D U 4.9 4.8 + - - -
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Residues in contact with THR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ASP* 2.5 25.3 + - - +
243B ALA* 3.3 13.7 + - - +
246B GLY* 3.6 16.9 - - - -
247B GLY 3.1 0.4 - - - -
248B LYS* 1.3 78.5 - - - +
250B THR* 1.3 58.4 + - - +
252B ILE* 3.2 10.5 + - - +
253B ALA* 2.9 26.9 + - - +
262B VAL* 3.8 23.9 - - + +
264B ALA* 3.8 20.0 - - + -
275B ILE* 4.9 2.0 - - + -
287B ILE* 3.8 19.1 - - + -
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Residues in contact with THR 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ARG* 2.9 24.8 + - - -
217B PHE* 4.5 1.4 - - - -
246B GLY* 2.9 19.4 + - - +
247B GLY* 3.0 2.3 + - - -
249B THR* 1.3 78.9 - - - +
251B HIS* 1.3 56.0 + - - +
253B ALA* 3.7 1.2 - - - +
254B ALA* 2.9 29.5 + - - +
275B ILE* 5.1 1.8 - - + +
278B ASN* 4.2 5.8 - - + -
279B ALA* 4.0 24.2 - - + +
282B LEU* 3.7 23.3 - - + +
284B LEU* 4.1 8.0 - - + +
287B ILE* 3.7 23.8 - - + -
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Residues in contact with HIS 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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56B ARG* 3.5 41.4 + - - +
94B ASP* 3.0 23.9 + - - -
219B GLN* 4.3 1.6 + - - +
224B ALA* 3.1 33.6 + - + -
227B SER* 3.2 23.9 + - - +
228B HIS* 3.5 17.8 + + - -
247B GLY 2.9 19.4 + - - +
248B LYS* 3.6 1.8 - - - +
249B THR 3.1 0.2 - - - -
250B THR* 1.3 75.1 + - - +
252B ILE* 1.3 60.4 + - - +
254B ALA* 3.1 4.3 + - + +
255B LEU* 2.9 38.3 + - + +
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Residues in contact with ILE 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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227B SER* 4.0 14.6 - - - -
230B LEU* 3.6 27.4 - - + -
232B PRO* 3.9 23.1 - - + -
238B ILE* 4.1 14.4 - - + -
240B ASP* 5.2 6.1 - - - +
248B LYS 2.9 24.0 + - - +
249B THR* 3.4 7.6 - - - +
251B HIS* 1.3 73.9 - - - +
253B ALA* 1.3 65.1 + - - +
255B LEU* 3.1 6.1 + - - +
256B MET* 3.1 36.6 + - - +
262B VAL* 4.1 13.7 - - + -
321B LEU* 3.9 20.4 - - + -
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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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249B THR 2.9 16.1 + - - +
250B THR 3.7 1.6 - - - +
252B ILE* 1.3 76.6 - - - +
254B ALA* 1.3 59.5 + - - +
256B MET* 3.3 7.6 + - - +
258B ASP* 2.9 27.7 + - - -
262B VAL* 4.2 11.0 - - + -
284B LEU* 3.7 18.8 - - + -
286B SER* 3.8 12.6 - - - +
287B ILE* 3.6 26.2 - - + -
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Residues in contact with ALA 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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257A HIS* 3.4 20.3 - - - -
56B ARG* 4.5 7.6 - - - +
57B VAL 6.0 0.2 - - - +
58B ASN* 4.2 18.4 - - - +
59B THR* 4.1 14.8 + - - +
60B HIS* 4.6 6.1 - - + -
250B THR 2.9 18.8 + - - +
251B HIS* 3.1 9.4 + - + +
253B ALA* 1.3 75.4 - - - +
255B LEU* 1.3 64.5 + - + +
257B HIS* 3.2 9.6 + - - +
258B ASP 4.8 0.2 - - - +
284B LEU* 4.0 11.2 - - + +
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Residues in contact with LEU 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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59A THR 4.9 1.2 - - - +
59B THR* 5.8 2.0 - - - +
94B ASP* 3.8 22.4 - - - +
227B SER* 3.5 43.3 - - - +
228B HIS* 4.1 17.7 - - + +
232B PRO* 4.0 23.3 - - + +
234B PRO* 4.8 4.0 - - - +
251B HIS* 2.9 22.6 + - + +
252B ILE* 3.1 8.0 + - - +
254B ALA* 1.3 78.2 - - + +
256B MET* 1.3 59.8 + - - +
257B HIS* 3.1 14.8 + - - -
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Residues in contact with MET 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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232B PRO* 3.7 20.6 - - + +
233B GLN 3.6 16.8 - - - +
234B PRO* 3.7 15.4 - - + +
236B GLU 3.6 23.1 - - - +
238B ILE* 3.6 26.2 - - + -
252B ILE* 3.1 18.0 + - - +
253B ALA* 3.3 5.6 + - - +
254B ALA 3.2 0.4 - - - -
255B LEU* 1.3 76.6 - - - +
257B HIS* 1.3 66.6 + - - +
258B ASP* 4.4 1.3 - - - +
259B GLN* 2.9 44.7 + - - +
260B GLY* 3.7 8.7 - - - -
261B GLU 4.0 4.0 - - - +
262B VAL* 3.9 15.3 - - + -
286B SER* 5.7 0.9 - - - +
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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