Contacts of the helix formed by residues 249 - 259 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B MET* 3.9 26.0 - - + -
247B VAL* 4.1 1.2 - - - +
248B PHE* 1.3 84.3 - - + +
250B PRO* 1.3 70.1 - - + +
251B ARG* 3.5 9.3 + - - +
252B GLN* 3.2 29.1 + - - +
253B ALA* 3.0 27.2 + - - +
272B ALA* 5.0 0.7 - - - +
281B ILE* 3.8 6.2 - - - +
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Residues in contact with PRO 250 (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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287A ALA* 4.2 9.2 - - + -
248B PHE 4.7 0.2 - - - +
249B THR* 1.3 89.3 - - + +
251B ARG* 1.3 60.6 + - - +
253B ALA* 3.3 0.6 + - + -
254B PHE* 3.0 19.8 + - - +
272B ALA 5.3 3.8 - - - +
277B GLY* 3.8 33.4 - - - +
280B LYS* 4.0 18.4 - - + -
281B ILE* 3.7 9.8 - - + -
284B MET* 3.3 33.2 - - + +
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Residues in contact with ARG 251 (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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260A ARG* 3.9 19.4 - - - +
287A ALA* 3.2 31.9 + - + +
288A CYS* 5.0 9.1 - - - +
249B THR* 3.3 9.7 + - - +
250B PRO* 1.3 79.1 - - - +
252B GLN* 1.3 63.5 + - + +
254B PHE* 3.4 19.2 + - - +
255B GLU* 3.2 44.8 + - - +
223G HIS* 5.5 4.3 - - - +
225G ASP* 3.3 46.7 + - + +
226G ASP* 3.7 14.1 - - - +
227G LEU 4.7 1.0 - - - +
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Residues in contact with GLN 252 (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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245B GLU 5.3 1.0 + - - -
246B SER* 3.8 21.9 + - - +
247B VAL* 4.4 1.8 - - - -
248B PHE* 3.0 42.3 + - - +
249B THR* 3.2 20.2 + - - +
250B PRO 3.3 0.6 - - - -
251B ARG* 1.3 77.8 - - + +
253B ALA* 1.3 64.3 + - - +
255B GLU* 3.4 6.9 + - - +
256B VAL* 3.1 27.2 + - - +
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Residues in contact with ALA 253 (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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247B VAL* 3.7 21.4 - - + +
249B THR 3.0 16.2 + - - +
250B PRO* 3.6 5.6 - - + +
251B ARG 3.3 0.2 - - - -
252B GLN* 1.3 74.7 - - - +
254B PHE* 1.3 64.5 + - - +
256B VAL* 3.3 5.2 + - - +
257B LEU* 3.0 33.8 + - + +
265B ILE* 4.2 7.6 - - + -
281B ILE* 3.9 23.6 - - + -
284B MET* 4.5 7.0 - - - -
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Residues in contact with PHE 254 (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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254A PHE* 3.5 40.0 - + - -
257A LEU* 3.9 10.1 - - + -
258A GLN* 3.9 35.7 - - + -
260A ARG* 6.4 0.4 - - - -
284A MET* 4.8 5.8 - - + -
287A ALA* 5.5 2.0 - - + -
288A CYS* 3.8 33.0 - - - -
250B PRO 3.0 14.0 + - - +
251B ARG* 3.5 23.1 - - - +
253B ALA* 1.3 76.7 - - - +
255B GLU* 1.3 59.5 + - - +
257B LEU* 3.3 5.5 + - - +
258B GLN* 2.9 37.0 + - + +
284B MET* 3.8 20.1 - - + -
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Residues in contact with GLU 255 (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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227B LEU* 3.7 25.6 - - + +
251B ARG* 3.2 34.6 + - - +
252B GLN* 3.8 7.0 - - - +
253B ALA 3.3 0.2 - - - -
254B PHE* 1.3 82.4 - - - +
256B VAL* 1.3 53.4 + - + +
258B GLN* 4.3 15.3 - - - +
259B THR* 2.7 38.3 + - + +
225G ASP 5.2 2.4 - - - +
255G GLU* 5.5 2.8 - - - +
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Residues in contact with VAL 256 (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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227B LEU* 3.3 27.6 - - + -
230B LEU* 4.9 0.9 - - + -
243B ALA* 4.5 2.7 - - + -
246B SER* 4.6 7.4 - - - +
247B VAL* 3.7 27.1 - - + -
252B GLN 3.1 19.1 + - - +
253B ALA 3.7 4.9 - - - +
255B GLU* 1.3 77.3 - - - +
257B LEU* 1.3 59.7 + - + +
259B THR* 3.8 4.3 - - - -
260B ARG* 3.2 4.2 + - - -
261B SER* 3.0 31.3 + - - -
262B ALA* 4.1 29.9 + - + +
265B ILE* 4.7 10.8 - - + -
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Residues in contact with LEU 257 (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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254A PHE* 3.8 17.5 - - + -
253B ALA* 3.0 25.0 + - + +
254B PHE 3.7 2.9 - - - +
256B VAL* 1.3 80.9 - - + +
258B GLN* 1.3 64.9 + - - +
260B ARG* 3.4 20.4 + - - +
262B ALA 5.6 2.7 - - - +
265B ILE* 4.4 12.6 - - + -
281B ILE 5.1 0.2 - - - +
284B MET* 3.8 23.3 - - + +
285B ALA* 3.8 22.7 - - + +
288B CYS* 4.0 15.9 - - + +
290B VAL* 3.5 43.1 - - + -
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Residues in contact with GLN 258 (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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254A PHE* 3.6 11.6 - - + -
258A GLN* 3.2 65.1 + - + +
260A ARG* 5.1 7.7 - - - +
254B PHE* 2.9 27.5 + - + +
255B GLU* 4.1 15.1 - - - +
257B LEU* 1.3 79.2 - - - +
259B THR* 1.3 76.5 + - + +
260B ARG* 3.2 7.5 + - - +
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Residues in contact with THR 259 (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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227B LEU* 3.9 13.9 - - + +
231B LYS* 2.9 32.5 + - - +
255B GLU* 2.7 25.7 + - + +
256B VAL* 3.5 4.9 + - - -
258B GLN* 1.3 90.2 - - + +
260B ARG* 1.3 62.5 + - - +
261B SER* 2.7 24.6 + - - -
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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