Contacts of the helix formed by residues 224 - 242 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C PHE* 4.9 1.8 - - - -
223C ARG* 1.3 77.0 - - - +
225C VAL* 1.3 62.0 + - - +
226C ASP* 3.4 9.4 + - - +
227C GLU* 3.0 24.6 + - - +
228C THR* 2.8 28.9 + - - -
227D GLU* 3.7 25.1 + - - -
230D ARG* 3.8 13.0 - - - +
248D GLY* 4.4 8.4 - - - +
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Residues in contact with VAL 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ALA* 3.8 31.4 - - + +
131C PHE* 3.8 31.6 - - + +
134C ARG* 3.7 36.6 - - + +
138C PHE* 3.8 26.4 - - + -
223C ARG 4.2 1.2 + - - -
224C SER* 1.3 68.5 + - - +
226C ASP* 1.3 66.7 + - - +
228C THR* 3.2 5.7 + - - -
229C LEU* 2.9 23.6 + - + +
247D ALA* 5.6 2.2 - - + +
248D GLY* 5.3 2.4 - - - +
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Residues in contact with ASP 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ARG* 2.8 38.8 + - - +
224C SER* 3.4 7.3 + - - +
225C VAL* 1.3 78.1 - - - +
227C GLU* 1.3 58.0 + - - +
229C LEU* 3.2 8.6 + - - +
230C ARG* 2.8 28.7 + - - +
250D LYS* 5.1 8.8 + - - -
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Residues in contact with GLU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C SER* 3.0 25.3 + - - +
226C ASP* 1.3 76.6 - - - +
228C THR* 1.3 57.4 + - - +
230C ARG* 3.0 43.5 + - - +
231C LEU* 3.0 44.6 + - + +
223D ARG* 5.5 0.3 - - - -
224D SER* 3.8 13.6 + - - -
227D GLU* 3.6 34.3 - - + +
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Residues in contact with THR 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C VAL* 3.7 34.3 - - + -
131C PHE* 3.6 27.0 - - + -
138C PHE* 4.1 3.6 - - + -
202C LEU* 3.7 15.7 - - + +
204C ILE* 4.4 8.7 - - + -
223C ARG* 5.6 0.2 - - - +
224C SER 2.8 22.8 + - - -
225C VAL 3.5 4.3 - - - -
227C GLU* 1.3 75.8 - - - +
229C LEU* 1.3 57.9 + - - +
231C LEU* 3.3 11.6 + - - +
232C VAL* 3.0 28.6 + - - +
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Residues in contact with LEU 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ARG* 3.6 17.3 - - - +
137C GLU* 3.1 47.6 - - + +
138C PHE* 3.3 39.0 - - + -
141C ILE* 4.2 10.1 - - + -
225C VAL* 2.9 14.9 + - + +
226C ASP* 3.3 10.5 - - - +
228C THR* 1.3 75.3 - - - +
230C ARG* 1.3 65.3 + - - +
231C LEU 3.2 0.2 + - - -
232C VAL* 3.3 3.1 + - - +
233C GLN* 3.0 43.4 + - - +
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Residues in contact with ARG 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ASP 2.8 14.2 + - - +
227C GLU* 3.0 42.6 + - - +
229C LEU* 1.3 76.5 - - - +
231C LEU* 1.3 71.7 + - - +
233C GLN* 3.4 12.1 + - - +
234C ALA* 2.9 33.4 + - - +
245C ALA* 5.9 0.4 - - - +
246C PRO 4.6 0.8 + - - -
248C GLY* 3.7 8.1 - - - +
249C TRP* 3.0 55.8 + - + +
250C LYS* 4.0 30.1 - - + +
221D VAL* 4.9 1.0 - - - +
222D GLY 3.0 27.5 + - - -
223D ARG* 3.8 11.3 - - - +
224D SER* 4.1 10.4 - - - -
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Residues in contact with LEU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C LEU* 5.9 1.1 - - + -
204C ILE* 3.6 19.7 - - + -
213C GLN* 3.8 32.3 - - + +
215C THR* 4.9 3.1 - - - +
227C GLU* 3.0 39.0 + - + +
228C THR* 3.7 3.8 - - - +
229C LEU 3.2 0.2 - - - -
230C ARG* 1.3 96.7 - - - +
232C VAL* 1.3 59.7 + - - +
234C ALA* 3.3 5.3 + - - +
235C PHE* 2.9 39.4 + - + -
215D THR* 6.2 0.2 - - + -
217D ASN* 3.8 23.1 - - - +
221D VAL* 4.1 9.9 - - + -
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Residues in contact with VAL 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C TYR* 4.5 5.8 - - + -
112C VAL* 3.9 26.7 - - + -
138C PHE* 4.8 4.0 - - + -
141C ILE* 3.7 17.5 - - + -
143C THR* 3.4 31.2 - - + +
204C ILE* 4.1 18.2 - - + -
228C THR 3.0 21.4 + - - +
229C LEU* 3.8 4.9 - - - +
231C LEU* 1.3 75.5 - - - +
233C GLN* 1.3 63.1 + - - +
235C PHE* 3.4 6.2 + - - +
236C GLN* 3.0 38.5 + - + +
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Residues in contact with GLN 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ILE* 4.1 25.5 - - + +
229C LEU* 3.0 36.5 + - - +
230C ARG* 3.7 11.8 - - - +
232C VAL* 1.3 75.2 - - - +
234C ALA* 1.3 58.1 + - - +
236C GLN* 3.2 9.2 + - - +
237C TYR* 2.9 30.8 + - - +
249C TRP* 3.8 13.5 - - + -
251C PRO* 3.3 33.7 - - + +
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Residues in contact with ALA 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C ARG* 2.9 21.6 + - - +
231C LEU* 3.6 5.4 - - - +
233C GLN* 1.3 75.7 - - - +
235C PHE* 1.3 59.4 + - - +
237C TYR* 3.3 1.5 + - - +
238C THR* 2.9 31.2 + - - +
245C ALA* 4.4 6.7 - - + -
249C TRP* 3.5 26.4 - - + -
221D VAL* 3.6 29.2 - - + -
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Residues in contact with PHE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C TYR* 3.3 24.5 - - + +
204C ILE* 4.5 9.0 - - + -
212C ARG* 3.2 48.5 - - + -
213C GLN* 3.8 28.7 - - + -
231C LEU* 2.9 38.6 + - + +
232C VAL 3.9 0.2 - - - +
234C ALA* 1.3 72.4 - - - +
236C GLN* 1.3 59.3 + - - +
238C THR* 3.2 2.4 + - - -
239C ASP* 2.9 35.5 + - - +
217D ASN* 4.8 1.8 - - + -
218D ASP* 3.7 29.4 - - + -
220D PRO* 4.6 1.6 - - + -
221D VAL* 3.4 34.1 - - + -
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Residues in contact with GLN 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C TYR* 3.5 32.3 - - + +
141C ILE* 2.9 42.8 + - - +
142C ASN* 4.4 6.1 + - - +
143C THR* 3.4 11.9 + - - -
232C VAL* 3.0 26.0 + - - +
233C GLN* 3.7 7.0 - - - +
234C ALA 3.2 0.2 - - - -
235C PHE* 1.3 78.4 - - - +
237C TYR* 1.3 62.0 + - - +
239C ASP* 3.6 7.4 - - - +
240C LYS* 3.1 27.2 + - - +
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Residues in contact with TYR 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C GLN 2.9 17.0 + - - +
234C ALA 3.8 3.4 - - - +
236C GLN* 1.3 78.0 - - - +
238C THR* 1.3 66.5 + - + +
240C LYS* 3.3 2.6 + - - +
241C HIS* 2.8 74.3 + + + +
243C GLU* 4.8 6.6 + - + -
249C TRP* 3.9 25.4 - + + -
252C GLY 6.4 0.2 - - - -
253C SER 5.5 2.0 + - - -
255C THR* 3.6 41.6 + - + +
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Residues in contact with THR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C ARG* 5.1 0.3 + - - -
234C ALA 2.9 18.5 + - - +
235C PHE* 3.2 14.6 + - - -
237C TYR* 1.3 79.5 - - + +
239C ASP* 1.3 66.6 + - - +
242C GLY* 2.9 23.8 + - - +
243C GLU 3.2 25.1 - - - +
244C VAL 4.1 0.9 - - - -
245C ALA* 3.7 17.5 - - + +
220D PRO* 3.6 34.4 - - - +
221D VAL* 3.8 6.6 - - + +
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Residues in contact with ASP 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C TYR* 2.5 31.3 + - - -
206C ASP* 4.5 2.8 - - - +
207C ASP* 4.3 6.8 - - - +
212C ARG* 2.9 27.9 + - - -
235C PHE 2.9 22.1 + - - +
236C GLN* 3.6 5.4 - - - +
237C TYR 3.3 0.2 - - - -
238C THR* 1.3 77.1 + - - +
240C LYS* 1.3 64.3 + - + +
242C GLY* 4.1 3.1 + - - -
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Residues in contact with LYS 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C GLN 3.1 15.9 + - - +
237C TYR* 3.3 1.5 + - - +
239C ASP* 1.3 82.2 - - + +
241C HIS* 1.3 88.8 + - + +
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Residues in contact with HIS 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C TYR* 2.8 72.8 + + + +
240C LYS* 1.3 99.9 + - + +
242C GLY* 1.3 58.8 + - - +
243C GLU* 2.8 23.3 + - + +
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Residues in contact with GLY 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C THR 2.9 18.4 + - - -
239C ASP 4.1 2.5 + - - -
240C LYS 3.6 1.4 - - - -
241C HIS* 1.3 76.5 - - - +
243C GLU* 1.3 61.4 + - - +
244C VAL* 5.1 0.6 - - - +
258C PRO* 3.7 20.3 - - - +
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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
------------------------------------------------------------
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