Contacts of the helix formed by residues 224 - 242 (chain B) in PDB entry 3TJK
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 SER 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A GLU* 3.8 28.6 + - - -
230A ARG* 3.9 10.8 - - - +
248A GLY* 4.5 8.4 - - - +
131B PHE* 4.7 2.5 - - - -
223B ARG* 1.3 78.1 - - - +
225B VAL* 1.3 57.2 + - - +
226B ASP* 3.3 10.2 + - - +
227B GLU* 2.8 24.9 + - - +
228B THR* 2.7 32.4 + - - -
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ALA* 5.6 2.4 - - + +
248A GLY* 5.5 1.4 - - - +
130B ALA* 3.8 30.3 - - + +
131B PHE* 3.7 36.1 - - + -
134B ARG* 3.7 31.6 - - + +
138B PHE* 3.7 16.6 - - + -
223B ARG 4.3 0.8 + - - -
224B SER* 1.3 69.2 + - - +
226B ASP* 1.3 66.1 + - - +
228B THR* 3.2 2.3 + - - -
229B LEU* 2.9 40.9 + - + +
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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
----------------------------------------------------------
250A LYS* 5.1 8.1 + - - -
134B ARG* 2.8 36.9 + - - +
224B SER* 3.3 7.2 + - - +
225B VAL* 1.3 79.0 - - - +
227B GLU* 1.3 62.2 + - - +
229B LEU* 3.3 6.2 + - - +
230B ARG* 3.0 24.3 + - - +
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ARG* 5.1 0.9 - - - -
224A SER* 3.6 15.2 + - - -
227A GLU* 3.7 34.3 - - + +
224B SER* 2.8 29.2 + - - +
226B ASP* 1.3 73.9 - - - +
228B THR* 1.3 64.3 + - - +
230B ARG* 3.1 44.5 + - - +
231B LEU* 3.0 41.9 + - + +
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Residues in contact with THR 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 3.9 33.9 - - + -
131B PHE* 3.6 26.8 - - + -
138B PHE* 4.0 3.6 - - + -
202B LEU* 3.6 19.9 - - + +
204B ILE* 4.4 4.5 - - + -
223B ARG* 5.5 0.5 - - - +
224B SER 2.7 23.0 + - - -
225B VAL 3.6 4.0 - - - -
227B GLU* 1.3 76.8 - - - +
229B LEU* 1.3 61.5 + - - +
231B LEU* 3.2 12.2 + - - +
232B VAL* 3.0 23.3 + - - +
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Residues in contact with LEU 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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134B ARG* 4.1 5.2 - - - +
137B GLU* 3.5 50.3 - - + +
138B PHE* 3.7 25.0 - - + -
141B ILE* 3.7 19.3 - - + -
225B VAL* 2.9 39.8 + - + +
226B ASP* 3.6 8.5 - - - +
228B THR* 1.3 75.5 - - - +
230B ARG* 1.3 64.4 + - - +
232B VAL* 3.2 3.0 + - - +
233B GLN* 2.9 41.6 + - - +
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Residues in contact with ARG 230 (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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221A VAL* 5.1 0.4 - - - +
222A GLY 3.0 28.5 + - - -
223A ARG* 3.7 11.6 - - - +
224A SER* 3.9 11.1 - - - -
226B ASP 3.0 13.4 + - - +
227B GLU* 3.1 44.4 + - - +
229B LEU* 1.3 77.2 - - - +
231B LEU* 1.3 64.0 + - - +
233B GLN* 3.4 11.7 + - - +
234B ALA* 2.8 38.9 + - - +
245B ALA* 6.1 0.2 - - - +
246B PRO 4.7 0.2 + - - -
248B GLY* 3.7 5.4 - - - -
249B TRP* 2.9 49.5 + - + +
250B LYS* 4.3 26.0 - - + +
251B PRO* 5.8 0.7 - - + -
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Residues in contact with LEU 231 (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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215A THR* 6.0 0.7 - - + -
217A ASN* 3.6 30.3 - - - +
221A VAL* 3.9 10.1 - - + -
202B LEU* 6.0 0.7 - - + -
204B ILE* 3.6 19.7 - - + -
213B GLN* 3.9 29.8 - - + +
215B THR* 4.8 3.1 - - - +
227B GLU* 3.0 42.3 + - + +
228B THR* 3.2 4.0 + - - +
230B ARG* 1.3 91.0 - - - +
232B VAL* 1.3 60.7 + - - +
234B ALA* 3.2 4.6 + - - +
235B PHE* 2.9 40.6 + - + -
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Residues in contact with VAL 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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110B TYR* 4.3 8.3 - - + -
112B VAL* 4.0 26.7 - - + -
138B PHE* 4.7 3.4 - - + -
141B ILE* 3.8 15.0 - - + -
143B THR* 3.4 28.9 - - + +
204B ILE* 4.1 17.9 - - + -
228B THR 3.0 19.2 + - - +
229B LEU* 3.8 7.2 - - + +
231B LEU* 1.3 74.5 - - - +
233B GLN* 1.3 64.1 + - - +
235B PHE* 3.2 7.1 + - - +
236B GLN* 2.9 37.3 + - - +
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Residues in contact with GLN 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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137B GLU 5.8 0.2 + - - -
141B ILE* 3.9 29.0 - - + +
229B LEU* 2.9 35.9 + - - +
230B ARG* 3.7 7.2 - - - +
232B VAL* 1.3 75.9 - - - +
234B ALA* 1.3 58.9 + - - +
236B GLN* 3.3 8.5 + - - +
237B TYR* 2.9 30.0 + - - +
249B TRP* 3.8 13.4 - - + -
251B PRO* 3.7 30.5 - - + +
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Residues in contact with ALA 234 (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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221A VAL* 3.6 28.9 - - + -
230B ARG* 2.8 23.4 + - - +
231B LEU* 3.6 4.3 - - - +
233B GLN* 1.3 76.1 - - - +
235B PHE* 1.4 55.9 + - - +
237B TYR* 3.4 1.8 + - - +
238B THR* 3.0 34.5 + - - +
245B ALA* 4.4 6.3 - - + -
249B TRP* 3.5 25.5 - - + -
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Residues in contact with PHE 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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217A ASN* 4.7 2.2 - - + -
218A ASP* 3.7 30.1 - - + -
220A PRO* 4.6 2.5 - - + -
221A VAL* 3.5 33.2 - - + -
110B TYR* 3.4 22.4 - - + +
204B ILE* 4.8 8.1 - - + -
212B ARG* 3.3 49.6 - - + +
213B GLN* 3.9 26.5 - - + -
231B LEU* 2.9 38.1 + - + +
232B VAL 3.9 2.7 - - - +
234B ALA* 1.4 68.7 - - - +
236B GLN* 1.3 60.1 + - - +
238B THR* 3.2 4.1 + - - -
239B ASP* 2.9 35.2 + - - +
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Residues in contact with GLN 236 (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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110B TYR* 3.7 28.8 - - + +
141B ILE* 2.8 46.2 + - - +
142B ASN* 4.4 1.8 + - - +
143B THR* 3.4 10.7 + - - -
232B VAL* 2.9 27.8 + - + +
233B GLN* 3.7 6.9 - - - +
235B PHE* 1.3 72.8 - - - +
237B TYR* 1.3 67.5 + - - +
239B ASP* 3.4 8.8 + - - +
240B LYS* 3.1 24.8 + - - +
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Residues in contact with TYR 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 GLN 2.9 17.2 + - - +
234B ALA 3.7 3.8 - - - +
236B GLN* 1.3 77.1 - - - +
238B THR* 1.3 64.6 + - + +
240B LYS* 3.2 6.6 + - + +
241B HIS* 2.9 65.0 + + + +
243B GLU* 5.2 4.8 + - + -
249B TRP* 3.7 28.0 - + + -
252B GLY 6.1 1.8 - - - -
253B SER 5.3 3.1 + - - -
255B THR* 3.4 39.9 + - + +
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Residues in contact with THR 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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220A PRO* 3.6 40.8 - - - +
221A VAL* 3.9 1.9 - - + +
212B ARG* 5.2 0.3 + - - -
234B ALA 3.0 21.4 + - - +
235B PHE* 3.2 14.4 + - - -
237B TYR* 1.3 82.9 - - + +
239B ASP* 1.3 62.8 + - - +
242B GLY* 3.0 23.4 + - - +
243B GLU 3.2 24.0 - - - +
244B VAL 4.1 0.7 - - - -
245B ALA* 3.8 17.3 - - + +
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Residues in contact with ASP 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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110B TYR* 2.6 31.4 + - - -
206B ASP* 4.6 1.8 - - - +
207B ASP* 4.3 5.0 - - - +
212B ARG* 3.0 27.1 + - - -
235B PHE 2.9 22.2 + - - +
236B GLN* 3.5 8.1 - - - +
237B TYR 3.3 0.2 - - - -
238B THR* 1.3 77.0 + - - +
240B LYS* 1.3 61.7 + - - +
242B GLY* 4.2 2.8 + - - -
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Residues in contact with LYS 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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236B GLN 3.1 14.8 + - - +
237B TYR* 3.7 4.5 - - + +
239B ASP* 1.3 81.6 - - - +
241B HIS* 1.3 92.8 + - + +
242B GLY 3.9 0.2 + - - -
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Residues in contact with HIS 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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237B TYR* 2.9 64.4 + + + +
240B LYS* 1.3 115.7 + - + +
242B GLY* 1.3 58.0 + - - +
243B GLU* 2.8 27.3 + - + +
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Residues in contact with GLY 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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238B THR 3.0 17.5 + - - -
239B ASP 4.2 2.7 + - - -
240B LYS 3.6 2.0 - - - -
241B HIS* 1.3 74.8 - - - +
243B GLU* 1.3 59.2 + - - +
244B VAL* 5.8 0.2 - - - -
258B PRO* 3.6 20.7 - - - +
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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