Contacts of the helix formed by residues 249 - 260 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97F MET* 4.2 21.5 - - + -
247F VAL* 3.9 0.7 - - - +
248F PHE* 1.3 89.3 - - + +
250F PRO* 1.3 76.0 - - + +
251F ARG* 3.4 10.3 + - - +
252F GLN* 3.2 28.5 + - + +
253F ALA* 3.0 18.7 + - - +
272F ALA* 5.0 1.3 - - - +
281F ILE* 3.5 9.9 - - - +
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Residues in contact with PRO 250 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287E ALA* 4.2 10.5 - - + -
249F THR* 1.3 89.8 - - - +
251F ARG* 1.3 56.0 + - - +
253F ALA* 3.3 1.9 + - - +
254F PHE* 2.9 24.4 + - - +
272F ALA* 5.5 3.1 - - + +
277F GLY* 3.9 27.1 - - - +
280F LYS* 4.1 19.5 - - + -
281F ILE* 3.6 16.6 - - + -
284F MET* 3.4 30.8 - - + +
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Residues in contact with ARG 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A HIS* 6.2 0.9 - - - -
225A ASP* 3.5 51.8 + - + +
226A ASP* 5.2 2.6 - - - +
227A LEU* 5.3 3.2 - - - +
228A ALA 6.1 0.4 - - - +
287E ALA* 3.8 26.9 - - + +
288E CYS* 5.6 3.1 - - - +
249F THR* 3.1 9.1 + - - +
250F PRO* 1.3 80.4 - - - +
252F GLN* 1.3 67.1 + - + +
254F PHE* 3.2 25.1 + - - +
255F GLU* 3.2 47.1 + - - +
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Residues in contact with GLN 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225F ASP* 5.5 4.8 + - - -
245F GLU 5.5 1.2 + - - -
246F SER 3.9 20.2 + - - +
247F VAL* 4.1 5.4 - - - -
248F PHE* 3.1 38.1 + - - +
249F THR* 3.2 18.7 + - - +
251F ARG* 1.3 78.3 - - + +
253F ALA* 1.3 65.4 + - - +
255F GLU* 3.3 8.7 + - - +
256F VAL* 3.2 26.2 + - - +
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Residues in contact with ALA 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247F VAL* 3.4 23.6 - - + +
249F THR 3.0 10.3 + - - +
250F PRO* 3.4 9.0 - - + +
252F GLN* 1.3 75.3 - - - +
254F PHE* 1.3 59.1 + - - +
256F VAL* 3.3 4.3 + - - +
257F LEU* 2.8 46.1 + - + +
265F ILE* 4.5 3.8 - - + -
281F ILE* 3.9 24.0 - - + -
284F MET* 4.5 3.1 - - - -
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Residues in contact with PHE 254 (chain F).
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* 3.4 32.9 - + - -
257E LEU* 3.9 13.0 - - + -
258E GLN* 3.9 29.8 - - + -
284E MET* 5.1 2.9 - - + -
287E ALA* 5.8 0.7 - - + -
288E CYS* 3.7 32.1 - - - -
250F PRO 2.9 13.6 + - - +
251F ARG* 3.2 28.4 + - - +
253F ALA* 1.3 76.7 - - - +
255F GLU* 1.3 57.7 + - - +
257F LEU* 3.7 4.1 - - - +
258F GLN* 2.8 59.0 + - + +
284F MET* 3.9 21.7 - - + -
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Residues in contact with GLU 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F LEU* 3.8 22.4 - - + -
251F ARG* 3.2 36.1 + - - +
252F GLN* 3.6 11.0 - - - +
253F ALA 3.2 0.2 - - - -
254F PHE* 1.3 79.2 - - - +
256F VAL* 1.3 52.1 + - - +
258F GLN* 2.9 26.5 + - - +
259F THR* 2.7 47.8 + - + +
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Residues in contact with VAL 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F LEU* 4.4 20.9 - - + -
230F LEU* 5.2 1.3 - - + -
243F ALA* 4.4 3.1 - - + -
246F SER* 4.4 8.3 - - - +
247F VAL* 3.4 32.1 - - + -
252F GLN 3.2 10.9 + - - +
253F ALA* 3.3 3.8 + - - +
255F GLU* 1.3 75.3 - - - +
257F LEU* 1.3 59.7 + - + +
259F THR* 3.4 5.1 + - - -
260F ARG* 2.9 22.5 + - - -
261F SER* 3.1 16.8 + - - -
262F ALA* 4.0 32.5 + - + +
265F ILE* 4.7 11.0 - - + -
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Residues in contact with LEU 257 (chain F).
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* 3.7 19.9 - - + -
253F ALA* 2.8 30.6 + - + +
256F VAL* 1.3 76.5 - - + +
258F GLN* 1.3 63.4 + - - +
260F ARG* 3.3 23.2 + - - +
262F ALA 5.8 1.1 - - - +
265F ILE* 4.3 11.4 - - + -
281F ILE 4.9 0.2 - - - +
284F MET* 3.7 33.7 - - + +
285F ALA* 3.7 14.6 - - + +
288F CYS* 3.9 18.3 - - + +
290F VAL* 3.5 41.1 - - + -
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Residues in contact with GLN 258 (chain F).
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* 3.9 14.1 - - + -
258E GLN* 3.3 62.7 + - + +
254F PHE* 2.8 27.2 + - + +
255F GLU* 2.9 33.9 + - - +
257F LEU* 1.3 78.4 - - - +
259F THR* 1.3 69.6 + - + +
260F ARG* 3.6 8.8 + - - -
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Residues in contact with THR 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F LEU* 4.5 4.9 - - + +
231F LYS* 2.8 39.2 + - - -
255F GLU* 2.7 33.5 + - + +
256F VAL* 3.4 3.8 + - - -
258F GLN* 1.3 90.3 - - + +
260F ARG* 1.3 53.7 + - - +
261F SER* 2.7 24.4 + - - -
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Residues in contact with ARG 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D PRO* 4.9 2.2 - - - +
226D ASP* 2.6 34.9 + - - -
228D ALA* 3.6 18.7 - - - +
229D GLY* 3.0 23.6 - - - +
232D LYS* 4.6 16.0 - - - +
251E ARG* 4.6 10.5 - - - +
231F LYS* 3.1 18.7 + - - +
234F THR* 4.1 9.7 - - - +
235F ASP* 4.6 1.2 - - - +
256F VAL 2.9 10.8 + - - -
257F LEU* 3.3 16.1 + - - +
258F GLN 3.3 9.4 - - - -
259F THR* 1.3 78.1 - - - +
261F SER* 1.3 62.5 + - - +
262F ALA 3.3 9.9 + - - +
288F CYS* 6.6 0.2 - - + -
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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