Contacts of the helix formed by residues 224 - 242 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C GLU* 3.8 25.8 + - - -
230C ARG* 3.9 11.9 + - - +
248C GLY* 4.5 8.9 - - - +
131D PHE* 4.8 2.5 - - - -
223D ARG* 1.3 76.8 - - - +
225D VAL* 1.3 62.5 + - - +
226D ASP* 3.3 10.6 + - - +
227D GLU* 3.0 26.2 + - - +
228D THR* 2.8 27.0 + - - -
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Residues in contact with VAL 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ALA* 5.5 3.1 - - + +
248C GLY* 5.4 2.0 - - - +
130D ALA* 3.7 39.3 - - + +
131D PHE* 3.8 26.7 - - + +
134D ARG* 3.7 39.3 - - + +
138D PHE* 3.8 26.0 - - + -
223D ARG 4.2 0.8 - - - -
224D SER* 1.3 72.7 + - - +
226D ASP* 1.3 56.6 + - - +
228D THR* 3.3 2.1 + - - -
229D LEU* 3.0 29.3 + - + +
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Residues in contact with ASP 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C LYS* 6.1 0.5 - - - -
134D ARG* 2.7 39.8 + - - +
224D SER* 3.2 8.2 + - - +
225D VAL* 1.3 75.0 - - - +
227D GLU* 1.3 60.8 + - - +
229D LEU* 3.5 6.1 + - - +
230D ARG* 3.0 28.4 + - - +
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Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C THR* 6.0 1.7 - - - +
223C ARG* 5.3 0.5 - - - -
224C SER* 3.7 12.1 + - - -
227C GLU* 3.6 35.3 - - + +
224D SER* 3.0 24.6 + - - +
225D VAL 3.3 0.2 - - - -
226D ASP* 1.3 76.7 - - - +
228D THR* 1.3 62.3 + - - +
230D ARG* 3.0 45.1 + - - +
231D LEU* 3.1 41.6 + - + +
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Residues in contact with THR 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D VAL* 3.9 39.7 - - + -
131D PHE* 3.5 20.6 - - + -
138D PHE* 4.0 2.5 - - + -
202D LEU* 3.8 20.7 - - + +
204D ILE* 4.2 4.9 - - + +
223D ARG* 5.6 0.9 - - - +
224D SER 2.8 20.9 + - - -
225D VAL 3.6 7.4 - - - -
227D GLU* 1.3 78.8 - - - +
229D LEU* 1.3 56.9 + - - +
231D LEU* 3.3 10.1 + - - +
232D VAL* 2.9 29.6 + - - +
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Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ARG* 3.6 15.3 - - - +
137D GLU* 3.1 53.8 - - + +
138D PHE* 3.3 34.8 - - + -
141D ILE* 4.4 9.4 - - + -
225D VAL* 3.0 22.0 + - + +
226D ASP* 3.7 6.3 - - - +
228D THR* 1.3 75.3 - - - +
230D ARG* 1.3 65.0 + - - +
232D VAL* 3.2 2.6 + - - +
233D GLN* 3.0 41.0 + - - +
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Residues in contact with ARG 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C VAL* 4.9 5.1 - - - +
222C GLY 3.0 27.7 + - - -
223C ARG* 3.7 12.7 - - - +
224C SER* 3.8 9.3 - - - +
226D ASP 3.0 17.6 + - - +
227D GLU* 3.0 42.3 + - - +
228D THR 3.3 0.2 - - - -
229D LEU* 1.3 76.9 - - - +
231D LEU* 1.3 67.6 + - - +
233D GLN* 3.3 11.8 + - - +
234D ALA* 2.9 29.0 + - - +
245D ALA* 6.1 0.4 - - - +
246D PRO 4.6 1.0 + - - -
248D GLY* 3.8 9.8 - - - +
249D TRP* 3.0 52.2 + - + +
250D LYS* 4.1 26.5 - - + +
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Residues in contact with LEU 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C THR* 5.8 1.3 - - + -
217C ASN* 3.6 30.3 - - - +
221C VAL* 3.8 11.4 - - + -
202D LEU* 6.1 0.9 - - + -
204D ILE* 3.7 14.6 - - + -
213D GLN* 3.8 30.5 - - + +
215D THR* 4.8 3.1 - - - +
227D GLU* 3.1 43.4 + - + +
228D THR* 3.6 8.7 - - - +
229D LEU 3.3 0.2 - - - -
230D ARG* 1.3 89.7 - - - +
232D VAL* 1.3 65.9 + - - +
234D ALA* 3.3 4.3 + - - +
235D PHE* 3.0 33.5 + - + -
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Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D TYR* 4.4 6.7 - - + -
112D VAL* 4.0 25.8 - - + -
138D PHE* 4.6 4.3 - - + -
141D ILE* 3.8 15.5 - - + -
143D THR* 3.4 31.0 - - + +
204D ILE* 4.1 20.2 - - + -
228D THR 2.9 25.7 + - - +
229D LEU* 3.2 6.7 + - - +
231D LEU* 1.3 71.9 - - - +
233D GLN* 1.3 63.5 + - - +
235D PHE* 3.3 6.6 + - - +
236D GLN* 3.0 31.2 + - - +
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Residues in contact with GLN 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ILE* 3.9 27.2 - - + +
229D LEU* 3.0 31.0 + - - +
230D ARG* 3.7 11.8 + - - +
232D VAL* 1.3 77.5 - - - +
234D ALA* 1.3 50.7 + - - +
236D GLN* 3.2 9.7 + - - +
237D TYR* 2.7 35.3 + - - +
249D TRP* 3.8 15.0 - - + -
251D PRO* 3.5 30.5 - - + +
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Residues in contact with ALA 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C VAL* 3.7 28.3 - - + -
230D ARG* 2.9 20.3 + - - +
231D LEU* 3.7 3.4 - - - +
233D GLN* 1.3 76.8 - - - +
235D PHE* 1.3 57.5 + - - +
237D TYR* 3.8 0.8 - - - -
238D THR* 2.9 34.8 + - - +
245D ALA* 4.3 8.5 - - + -
249D TRP* 3.3 26.8 - - + -
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Residues in contact with PHE 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C ASN* 4.7 1.6 - - + -
218C ASP* 3.7 29.6 - - + -
220C PRO* 4.8 0.9 - - + -
221C VAL* 3.5 34.8 - - + -
110D TYR* 3.3 22.2 - - + +
204D ILE* 4.8 7.9 - - + -
212D ARG* 3.3 50.3 - - + -
213D GLN* 3.9 27.4 - - + -
231D LEU* 3.0 34.7 + - + +
232D VAL 3.9 3.6 - - - +
234D ALA* 1.3 75.3 - - - +
236D GLN* 1.3 57.5 + - - +
238D THR* 3.5 3.4 + - - -
239D ASP* 2.8 35.9 + - - +
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Residues in contact with GLN 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D TYR* 3.6 32.0 - - + +
141D ILE* 2.8 45.2 + - - +
142D ASN* 4.4 5.8 + - - +
143D THR* 3.3 13.1 + - - -
232D VAL* 3.0 20.4 + - - +
233D GLN* 3.5 9.9 - - - +
235D PHE* 1.3 73.2 - - - +
237D TYR* 1.3 66.0 + - - +
239D ASP* 3.4 8.0 + - - +
240D LYS* 3.1 23.9 + - - +
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Residues in contact with TYR 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D GLN 2.7 19.8 + - - +
234D ALA 3.3 4.0 + - - +
236D GLN* 1.3 73.0 - - - +
238D THR* 1.3 65.3 + - + +
240D LYS* 3.1 3.4 + - - -
241D HIS* 3.0 73.5 + + + -
243D GLU* 4.1 8.1 + - + -
249D TRP* 3.9 26.5 - + + -
251D PRO* 6.2 0.4 - - + -
253D SER 5.5 1.8 + - - -
255D THR* 3.6 40.2 + - + +
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Residues in contact with THR 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C PRO* 3.5 30.5 - - - +
221C VAL* 3.9 1.4 - - + +
212D ARG* 5.0 0.2 + - - -
234D ALA 2.9 22.9 + - - +
235D PHE* 3.5 9.5 + - - -
237D TYR* 1.3 82.7 - - + +
239D ASP* 1.3 67.0 + - - +
242D GLY* 3.0 22.7 + - - +
243D GLU 3.3 25.6 - - - +
244D VAL* 4.0 1.1 - - - -
245D ALA* 3.8 29.4 - - + +
255D THR* 5.6 0.2 - - + -
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Residues in contact with ASP 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D TYR* 2.6 32.3 + - - -
206D ASP* 4.5 2.2 - - - +
207D ASP* 4.3 6.6 - - - +
212D ARG* 2.9 28.2 + - - -
235D PHE 2.8 26.0 + - - +
236D GLN* 3.6 6.5 - - - +
238D THR* 1.3 73.5 + - - +
240D LYS* 1.3 61.3 + - + +
242D GLY* 4.5 1.6 + - - -
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Residues in contact with LYS 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D GLN 3.1 13.9 + - - +
237D TYR* 3.6 4.3 - - - +
239D ASP* 1.3 82.8 - - + +
241D HIS* 1.3 88.3 + - + +
242D GLY 3.6 0.2 - - - -
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Residues in contact with HIS 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D TYR* 3.0 69.9 + + + +
240D LYS* 1.3 111.4 + - + +
242D GLY* 1.3 66.2 + - - +
243D GLU* 3.1 16.7 + - - +
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Residues in contact with GLY 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D THR 3.0 18.3 + - - -
239D ASP 4.5 1.6 + - - -
240D LYS 3.6 1.0 - - - -
241D HIS* 1.3 78.7 - - - +
243D GLU* 1.3 60.8 + - - +
244D VAL* 5.6 0.4 - - - -
258D PRO* 3.4 22.3 - - - +
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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