Contacts of the helix formed by residues 325 - 342 (chain B) in PDB entry 1TAD
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 325 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B GLN* 2.8 33.2 + - - +
51B ILE* 4.1 16.6 - - + +
52B ILE* 3.7 20.9 - - + +
167B GLU* 4.9 4.0 + - - +
168B GLN* 5.7 0.2 + - - -
171B LEU* 3.8 10.6 - - - +
323B THR 3.5 1.8 + - - -
324B ASP* 1.3 70.6 + - - +
326B GLN* 1.3 70.3 + - - +
328B VAL 3.3 0.3 + - - -
329B LYS* 2.9 30.1 + - + +
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Residues in contact with GLN 326 (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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324B ASP* 3.3 9.1 + - - +
325B THR* 1.3 89.5 - - - +
327B ASN* 1.3 62.5 + - - +
329B LYS* 3.4 22.6 + - - +
330B PHE* 3.1 23.7 + - - +
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Residues in contact with ASN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LYS* 3.5 18.7 - - - +
319B MET 4.2 5.3 + - - -
320B THR* 3.3 13.7 - - - +
321B CYS 3.0 27.3 + - - +
324B ASP* 3.1 31.0 + - + +
326B GLN* 1.3 75.7 - - - +
328B VAL* 1.3 57.6 + - - +
330B PHE* 3.1 12.3 + - - +
331B VAL* 2.9 45.4 + - - +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 4.1 16.2 - - + -
48B GLN* 3.7 27.1 - - + -
49B MET* 3.8 19.5 - - + -
52B ILE* 4.2 1.6 - - + -
263B PHE* 5.7 4.7 - - + -
320B THR* 5.7 2.7 - - + -
321B CYS 3.6 10.8 - - - +
322B ALA* 3.5 29.8 - - - +
324B ASP 3.0 16.1 + - - +
325B THR 3.8 3.6 - - - +
327B ASN* 1.3 76.5 - - - +
329B LYS* 1.3 58.1 + - - +
331B VAL* 4.1 5.1 - - - +
332B PHE* 2.8 30.4 + - + +
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Residues in contact with LYS 329 (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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52B ILE* 3.7 37.4 - - + +
53B HIS* 5.7 2.7 - - - +
187B PHE* 5.8 0.7 - - - -
325B THR* 2.9 18.2 + - + +
326B GLN* 3.6 28.6 - - - +
328B VAL* 1.3 77.0 - - - +
330B PHE* 1.3 62.3 + - - +
332B PHE* 3.9 3.2 - - - +
333B ASP* 3.0 25.3 + - + +
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Residues in contact with PHE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B HIS* 5.2 9.4 - + - -
326B GLN 3.1 11.3 + - - +
327B ASN* 3.4 14.1 - - - +
329B LYS* 1.3 80.1 - - - +
331B VAL* 1.3 80.5 + - + +
333B ASP* 3.1 10.7 + - + +
334B ALA* 3.1 25.5 + - + +
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B PHE* 3.5 35.4 - - + -
318B HIS* 3.7 28.7 - - + +
319B MET 4.6 2.5 - - - +
320B THR* 4.0 17.0 - - + -
327B ASN* 2.9 36.1 + - - +
328B VAL* 4.1 4.7 - - - +
330B PHE* 1.3 89.4 - - + +
332B PHE* 1.3 55.8 + - - +
334B ALA* 3.1 9.4 + - - +
335B VAL* 2.9 25.3 + - - +
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Residues in contact with PHE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.9 10.8 - - + -
45B ILE* 5.7 1.8 - - + -
49B MET* 3.9 20.2 - - + -
53B HIS* 3.5 20.4 - + + -
185B PHE* 3.7 31.0 - + - -
187B PHE* 4.0 5.4 - + - -
192B PHE* 3.6 26.7 - + - -
194B MET* 3.7 21.1 - - + -
218B ILE* 4.1 14.6 - - + -
263B PHE* 5.1 4.9 - + + -
328B VAL* 2.8 23.8 + - + +
329B LYS* 4.1 2.9 - - - +
331B VAL* 1.3 70.8 - - - +
333B ASP* 1.3 60.8 + - - +
335B VAL* 3.6 11.2 - - + +
336B THR* 2.8 50.4 + - - -
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Residues in contact with ASP 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PHE* 3.5 22.5 - - + -
188B LYS* 3.0 20.3 + - - +
329B LYS* 3.0 16.7 + - + +
330B PHE* 3.1 13.3 + - + +
332B PHE* 1.3 74.3 - - - +
334B ALA* 1.3 64.6 + - - +
336B THR* 3.2 5.0 + - - -
337B ASP* 3.0 34.0 + - - +
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Residues in contact with ALA 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B HIS* 3.9 23.1 - - + +
330B PHE* 3.1 17.0 + - + +
331B VAL* 3.1 11.3 + - - +
333B ASP* 1.3 81.7 + - - +
335B VAL* 1.3 61.5 + - - +
337B ASP* 3.0 19.4 + - - +
338B ILE* 3.1 18.8 + - + +
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Residues in contact with VAL 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.9 0.4 - - + -
216B CYS* 4.2 24.9 - - - -
218B ILE* 4.3 13.0 - - + -
261B VAL* 4.0 19.3 - - + -
263B PHE* 3.8 31.6 - - + -
318B HIS* 4.7 4.5 - - - +
331B VAL* 2.9 20.2 + - + +
332B PHE* 3.2 17.7 + - + +
334B ALA* 1.3 73.7 - - - +
336B THR* 1.3 62.3 + - - +
338B ILE* 3.1 22.0 + - + +
339B ILE* 3.1 19.4 + - + +
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Residues in contact with THR 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PHE* 3.2 22.5 - - + -
188B LYS* 3.4 37.7 - - + +
190B LEU* 4.4 3.1 - - + -
192B PHE* 3.5 13.5 - - + -
332B PHE* 2.8 28.9 + - - -
333B ASP 3.4 9.0 - - - -
335B VAL* 1.3 76.5 - - - +
337B ASP* 1.3 63.0 + - - +
339B ILE* 3.4 10.7 + - - +
340B ILE* 3.1 27.3 + - + +
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Residues in contact with ASP 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LYS* 2.9 28.8 + - - -
333B ASP* 3.0 26.2 + - - +
334B ALA* 3.0 11.9 + - - +
336B THR* 1.3 76.1 - - - +
338B ILE* 1.3 63.2 + - + +
340B ILE* 3.4 10.2 + - - +
341B LYS* 3.2 24.5 + - - +
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Residues in contact with ILE 338 (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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259B SER* 4.4 18.2 - - - +
261B VAL* 4.2 9.6 - - + -
316B TYR* 3.5 66.2 - - + +
318B HIS* 4.9 7.0 - - - +
334B ALA* 3.1 16.1 + - + +
335B VAL* 3.1 16.1 + - - +
337B ASP* 1.3 74.1 - - + +
339B ILE* 1.3 56.9 + - + +
341B LYS* 3.0 15.7 + - + +
342B GLU* 2.8 35.5 + - - -
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Residues in contact with ILE 339 (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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28B ARG* 3.2 10.5 + - - +
30B VAL* 3.9 21.8 - - + -
32B LEU* 4.4 2.7 - - + -
190B LEU* 3.9 18.8 - - + -
192B PHE* 3.8 29.2 - - + -
215B THR* 4.4 6.5 - - + +
216B CYS* 3.9 36.3 - - + -
259B SER* 5.3 4.9 - - - -
335B VAL* 3.1 19.2 + - + +
336B THR* 3.6 8.5 - - - +
338B ILE* 1.3 82.4 - - + +
340B ILE* 1.3 59.0 + - - +
342B GLU* 2.8 29.8 + - - +
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Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 3.7 9.6 + - - +
188B LYS* 4.0 29.8 - - + +
190B LEU* 3.7 19.1 - - + -
336B THR* 3.1 33.6 + - + +
337B ASP* 3.7 9.9 - - - +
338B ILE 3.2 0.2 - - - -
339B ILE* 1.3 76.8 - - - +
341B LYS* 1.3 58.9 + - + +
342B GLU* 3.2 17.0 - - - +
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Residues in contact with LYS 341 (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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316B TYR* 5.9 3.1 - - - +
337B ASP 3.2 13.0 + - - +
338B ILE* 3.0 20.0 + - + +
340B ILE* 1.3 76.4 - - + +
342B GLU* 1.3 71.4 + - - +
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Residues in contact with GLU 342 (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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28B ARG* 3.0 25.0 + - - +
257B THR 5.7 0.3 - - - +
259B SER* 2.8 25.9 + - - -
316B TYR* 5.6 4.6 + - - -
338B ILE* 2.8 20.5 + - - +
339B ILE* 2.8 31.1 + - - +
340B ILE 3.1 10.2 - - - +
341B LYS* 1.3 86.9 - - - +
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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