Contacts of the helix formed by residues 225 - 239 (chain B) in PDB entry 1TUB
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 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLN* 5.4 1.7 - - - +
19B LYS* 3.1 24.6 + - - +
223B THR* 3.2 6.6 - - - -
224B TYR* 1.3 77.2 - - - +
226B ASP* 1.2 57.5 + - - +
228B ASN* 2.9 33.2 + - - +
229B HIS 3.6 0.7 + - - -
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Residues in contact with ASP 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS* 5.3 0.4 - - - +
213B CYS* 4.9 5.2 - - - -
217B LEU* 5.4 3.3 - - - +
219B LEU* 2.5 31.4 - - + +
222B PRO* 5.4 0.4 - - + -
223B THR* 2.5 27.9 + - - +
225B GLY* 1.2 73.4 - - - +
227B LEU* 1.3 64.8 + - + +
228B ASN 2.9 5.4 - - - -
229B HIS* 3.0 15.5 + - - +
230B LEU 3.4 3.3 + - - -
501B TXL 2.3 54.3 - - + -
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Residues in contact with LEU 227 (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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206B ASN* 4.5 9.0 - - + +
209B LEU* 3.1 44.7 - - + +
210B TYR* 4.2 29.8 - - + +
213B CYS* 2.8 43.1 - - + -
222B PRO* 5.3 4.3 - - + -
223B THR 3.0 18.6 + - - +
224B TYR* 4.0 12.6 - - + +
225B GLY 3.1 0.4 - - - -
226B ASP* 1.3 77.4 - - + +
228B ASN* 1.3 61.4 + - - +
230B LEU* 3.2 22.4 + - - +
231B VAL* 3.4 11.4 + - - +
500B GDP 5.2 6.5 - - - +
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Residues in contact with ASN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 4.3 24.2 - - - +
16B ILE* 3.3 29.0 - - - +
19B LYS* 2.0 66.4 - - + +
224B TYR 3.0 21.0 + - - +
225B GLY* 2.9 7.5 + - - +
227B LEU* 1.3 78.2 - - - +
229B HIS* 1.4 68.2 + - - +
231B VAL* 4.4 4.4 - - - +
232B SER* 3.5 15.2 + - - -
500B GDP 4.2 5.2 + - - -
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Residues in contact with HIS 229 (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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19B LYS* 3.7 7.6 - - + +
225B GLY 3.6 2.8 + - - -
226B ASP* 3.0 9.0 + - - +
228B ASN* 1.4 79.0 - - - +
230B LEU* 1.3 68.8 + - - +
231B VAL 2.7 0.2 + - - -
232B SER* 2.9 13.1 + - - -
233B ALA* 3.8 0.9 + - - +
501B TXL 1.9 163.3 + + + +
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 1.5 67.1 - - + -
212B ILE* 3.7 31.2 - - + -
213B CYS* 4.5 6.9 - - - -
217B LEU* 6.0 0.9 - - + -
226B ASP 3.4 4.0 + - - -
227B LEU* 3.2 12.6 + - - +
229B HIS* 1.3 76.4 - - - +
231B VAL* 1.3 58.0 + - - +
233B ALA* 2.8 31.7 - - + +
272B PHE* 5.3 5.2 - - + +
275B LEU* 4.7 10.3 - - + -
302B MET* 3.3 37.2 - - + +
501B TXL 6.2 0.7 - - - -
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 4.3 21.3 - - + -
19B LYS* 6.1 0.9 - - + -
20B PHE 5.9 0.4 - - - +
204B ILE* 3.5 46.7 - - + -
209B LEU* 4.5 5.4 - - + -
227B LEU 3.4 12.2 + - - +
228B ASN* 4.4 4.9 - - - +
229B HIS 2.7 4.2 + - - -
230B LEU* 1.3 73.4 - - - +
232B SER* 1.3 69.4 + - - +
233B ALA 2.7 3.1 + - - -
234B THR* 2.7 12.4 + - - -
235B MET* 3.1 37.8 + - + +
302B MET* 3.2 11.2 - - + -
500B GDP 6.0 0.2 - - - +
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Residues in contact with SER 232 (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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19B LYS 3.5 9.8 + - - -
20B PHE* 4.3 2.6 - - - +
23B VAL* 3.2 43.1 - - - +
228B ASN 3.5 3.7 + - - -
229B HIS* 2.9 18.8 + - - -
231B VAL* 1.3 78.1 - - - +
233B ALA* 1.3 58.5 + - - +
235B MET* 3.3 13.1 + - - +
236B SER* 2.8 35.1 + - - -
501B TXL 4.2 9.6 + - - +
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Residues in contact with ALA 233 (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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229B HIS 4.7 1.1 - - - +
230B LEU* 2.8 19.5 - - + +
231B VAL 2.7 0.2 + - - -
232B SER* 1.3 81.0 + - - +
234B THR* 1.3 59.6 + - - +
236B SER* 2.9 20.0 + - - -
237B GLY 3.4 5.9 + - - -
272B PHE* 2.8 58.6 - - + -
376B THR* 4.1 2.8 + - - -
501B TXL 4.2 7.6 - - + -
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Residues in contact with THR 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 5.1 2.8 - - + -
202B TYR* 4.7 11.7 - - + -
203B CYS 5.6 0.2 - - - +
204B ILE* 5.6 3.6 - - + -
231B VAL* 2.7 9.1 + - - -
233B ALA* 1.3 76.8 - - - +
235B MET* 1.2 57.1 + - + -
238B VAL* 3.4 22.1 + - + +
270B PRO* 3.3 38.9 + - + +
271B GLY 4.8 3.1 + - - -
272B PHE* 5.2 1.3 - - - -
302B MET* 1.9 52.3 - - + +
376B THR* 4.4 9.6 - - + +
378B ILE* 5.3 0.2 - - + -
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Residues in contact with MET 235 (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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16B ILE* 4.6 6.3 - - + +
20B PHE* 1.3 128.3 - - + -
138B THR* 5.4 2.0 - - - -
169B PHE* 2.2 54.5 - - + -
231B VAL* 3.1 31.9 + - + +
232B SER* 3.9 1.6 - - - +
234B THR* 1.2 75.3 - - - +
236B SER* 1.3 53.9 + - - +
237B GLY 3.1 2.0 - - - -
238B VAL* 2.9 3.6 + - - +
239B THR* 2.5 40.4 + - - -
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Residues in contact with SER 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 4.4 0.4 - - - -
23B VAL* 5.4 3.1 - - - -
28B HIS* 4.9 4.5 - - - -
232B SER 2.8 14.5 + - - -
233B ALA 2.9 14.4 + - - -
235B MET* 1.3 73.0 - - - +
237B GLY* 1.3 50.8 + - - +
239B THR* 3.6 7.4 - - - -
240B THR* 2.8 17.9 + - - +
241B CYS* 2.5 37.0 + - - -
320B ARG* 2.9 25.7 + - - -
501B TXL 3.0 19.2 - - - -
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Residues in contact with GLY 237 (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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233B ALA 3.4 4.8 + - - -
235B MET 3.1 0.8 - - - -
236B SER* 1.3 79.3 + - - +
238B VAL* 1.3 63.6 + - - +
241B CYS* 2.3 48.2 - - - +
242B LEU* 4.4 1.7 - - - +
318B VAL* 4.4 6.4 - - - +
320B ARG* 4.4 0.4 - - - -
376B THR* 3.4 26.9 - - - -
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Residues in contact with VAL 238 (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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167B ASN* 5.5 2.7 - - + +
169B PHE* 6.1 0.4 - - + -
202B TYR* 2.9 39.9 - - + +
234B THR 3.4 19.3 - - - +
235B MET* 2.9 7.2 + - - +
237B GLY* 1.3 82.5 - - - +
239B THR* 1.4 65.0 - - + +
241B CYS 3.3 12.7 - - - +
242B LEU* 4.8 4.3 - - - +
243B ARG* 3.7 1.9 + - - +
250B ALA 5.2 0.5 - - - +
252B LEU* 3.7 16.6 - - + +
255B LEU* 3.0 34.4 - - + +
318B VAL* 6.1 1.3 - - + -
376B THR* 4.6 6.1 - - + -
378B ILE* 4.3 15.0 - - + -
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Residues in contact with THR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 3.4 29.8 - - + -
28B HIS* 3.9 6.4 + - - -
30B ILE* 4.2 4.7 - - - -
136B GLN* 3.7 13.0 - - - +
169B PHE* 4.3 8.7 - - + -
235B MET* 2.5 31.6 + - - +
236B SER* 3.6 3.1 - - - -
238B VAL* 1.4 59.4 - - + +
240B THR* 1.3 61.4 + - - -
243B ARG* 1.6 70.6 + - - +
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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
------------------------------------------------------------
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