Contacts of the helix formed by residues 249 - 260 (chain E) in PDB entry 1TKK
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 THR 249 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97E MET* 4.4 20.9 - - + -
247E VAL* 4.0 1.0 - - - +
248E PHE* 1.3 91.7 - - + +
250E PRO* 1.3 68.8 - - - +
251E ARG* 3.3 10.7 + - - +
252E GLN* 3.2 26.3 + - - +
253E ALA* 2.9 28.4 + - - +
272E ALA* 4.9 0.7 - - - +
281E ILE* 3.8 5.2 - - - +
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Residues in contact with PRO 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E PHE 4.7 0.2 - - - +
249E THR* 1.3 86.9 - - - +
251E ARG* 1.3 55.5 + - - +
253E ALA* 3.2 3.9 + - + +
254E PHE* 2.9 25.3 + - - +
272E ALA* 5.2 3.4 - - + +
277E GLY* 4.0 28.7 - - - +
280E LYS* 4.0 23.3 - - + -
281E ILE* 3.6 17.9 - - + +
284E MET* 3.6 16.3 - - + +
283F ALA 5.9 0.4 - - - +
287F ALA* 4.3 17.3 - - + -
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Residues in contact with ARG 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D HIS* 5.2 7.0 - - - +
225D ASP* 3.2 46.3 + - + +
226D ASP* 3.5 24.2 + - - +
227D LEU 4.7 0.8 - - - +
249E THR* 3.2 10.1 + - - +
250E PRO* 1.3 75.7 - - - +
252E GLN* 1.3 67.5 + - + +
254E PHE* 3.3 14.4 + - - +
255E GLU* 3.3 46.4 + - - +
260F ARG* 4.6 9.2 - - - +
287F ALA* 3.1 31.5 + - + +
288F CYS* 5.0 7.0 - - - +
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Residues in contact with GLN 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E LYS* 5.8 3.8 + - - +
225E ASP* 5.7 2.6 + - - -
245E GLU 5.2 1.2 + - - -
246E SER 3.7 23.9 + - - +
247E VAL* 4.2 4.5 - - - -
248E PHE* 2.8 43.5 + - - +
249E THR* 3.2 17.3 + - - +
251E ARG* 1.3 75.3 - - + +
253E ALA* 1.3 67.7 + - - +
255E GLU* 3.2 7.3 + - - +
256E VAL* 3.0 27.0 + - + +
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Residues in contact with ALA 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E VAL* 3.7 23.3 - - + +
249E THR 2.9 14.8 + - - +
250E PRO* 3.3 10.5 - - + +
251E ARG 3.2 0.2 - - - -
252E GLN* 1.3 76.7 - - - +
254E PHE* 1.3 63.9 + - - +
256E VAL* 3.2 3.3 + - - +
257E LEU* 3.0 31.1 + - + +
265E ILE* 4.6 6.5 - - + -
281E ILE* 3.9 25.1 - - + -
284E MET* 4.6 3.6 - - - -
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Residues in contact with PHE 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E PRO 2.9 14.1 + - - +
251E ARG* 3.5 17.9 - - - +
252E GLN 3.2 0.2 - - - -
253E ALA* 1.3 76.4 - - - +
255E GLU* 1.3 59.4 + - + +
257E LEU* 3.3 6.0 + - - +
258E GLN* 2.9 41.7 + - + +
284E MET* 3.7 27.8 - - + -
254F PHE* 3.4 34.2 - + - -
257F LEU* 3.7 32.8 - - + -
258F GLN* 3.8 27.4 - - + -
284F MET* 4.7 2.2 - - + -
287F ALA* 5.6 0.4 - - + -
288F CYS* 3.7 24.7 - - - -
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Residues in contact with GLU 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D ASP 5.1 3.1 - - - +
255D GLU* 5.2 5.0 - - - +
227E LEU* 3.6 26.0 - - + +
251E ARG* 3.3 31.5 + - - +
252E GLN* 3.2 10.1 + - - +
254E PHE* 1.3 81.4 - - - +
256E VAL* 1.3 54.7 + - + +
258E GLN* 3.7 17.3 - - - +
259E THR* 2.7 38.5 + - + +
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Residues in contact with VAL 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E LEU* 3.5 25.8 - - + -
230E LEU* 5.1 1.3 - - + -
243E ALA* 4.6 4.3 - - + -
246E SER* 4.7 9.2 - - - +
247E VAL* 3.5 31.2 - - + -
252E GLN* 3.0 11.7 + - + +
253E ALA* 3.6 7.4 - - - +
255E GLU* 1.3 75.9 - - - +
257E LEU* 1.3 61.1 + - + +
259E THR* 3.4 3.9 + - - -
260E ARG* 3.0 8.1 + - - -
261E SER* 3.0 28.7 + - - -
262E ALA* 4.0 30.8 + - + +
265E ILE* 4.8 10.3 - - + -
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Residues in contact with LEU 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E ALA* 3.0 25.5 + - + +
254E PHE* 3.7 3.8 - - - +
256E VAL* 1.3 77.7 - - + +
258E GLN* 1.3 62.0 + - - +
260E ARG* 3.4 20.9 + - - +
262E ALA 5.8 2.5 - - - +
265E ILE* 4.1 13.7 - - + -
284E MET* 3.7 19.3 - - + +
285E ALA* 3.6 33.0 - - + +
288E CYS* 4.1 14.2 - - + +
290E VAL* 3.6 41.1 - - + -
254F PHE* 3.9 16.8 - - + -
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Residues in contact with GLN 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E PHE* 2.9 25.4 + - + +
255E GLU* 3.7 24.4 - - - +
256E VAL 3.3 0.2 - - - -
257E LEU* 1.3 79.6 - - - +
259E THR* 1.3 69.3 + - - +
260E ARG* 3.2 8.9 + - - +
254F PHE* 3.9 11.7 - - + -
258F GLN* 3.3 61.6 + - + +
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Residues in contact with THR 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E LEU* 4.1 13.4 - - + +
231E LYS* 2.8 38.3 + - - +
255E GLU* 2.7 25.1 + - + +
256E VAL* 3.4 3.6 + - - -
258E GLN* 1.3 88.0 - - - +
260E ARG* 1.3 55.9 + - - +
261E SER* 2.9 23.6 + - - -
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Residues in contact with ARG 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A PRO* 4.3 3.4 - - - +
226A ASP* 3.5 20.4 + - - -
228A ALA* 3.4 29.7 + - - +
229A GLY* 3.4 24.4 - - - +
232A LYS* 3.2 32.5 + - - +
231E LYS* 3.5 20.2 + - - +
234E THR* 4.3 8.8 - - - +
235E ASP* 4.5 3.2 - - - +
256E VAL 3.0 8.2 + - - -
257E LEU* 3.4 16.4 + - - +
258E GLN 3.2 7.7 - - - +
259E THR* 1.3 79.6 - - - +
261E SER* 1.3 60.3 + - - +
262E ALA 3.2 11.6 + - - +
288E CYS* 5.2 7.7 + - - +
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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