Contacts of the helix formed by residues 292 - 304 (chain A) 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 TYR 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A LYS* 3.4 39.0 + - + +
270A PHE* 3.5 28.5 - + - -
271A SER* 3.4 32.8 - - - +
274A ILE* 3.7 19.1 - - + +
291A THR* 1.3 71.5 - - - +
293A GLU* 1.3 82.3 + - + +
296A GLY* 2.8 30.7 + - - -
319A MET* 3.7 25.0 - - + +
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Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A THR* 3.4 21.0 + - - +
292A TYR* 1.3 103.4 + - + +
294A ASP* 1.3 61.1 + - - +
296A GLY* 4.1 0.4 - - - -
297A ASN* 3.2 23.7 + - - +
319A MET* 5.8 2.5 - - - +
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Residues in contact with ASP 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A TYR* 2.6 28.2 + - - -
288A GLY* 4.2 1.4 - - - -
289A PRO* 3.6 29.0 - - + +
291A THR* 3.1 21.6 + - - +
293A GLU* 1.3 77.7 - - - +
295A ALA* 1.3 65.0 + - - +
297A ASN* 3.3 5.7 + - - +
298A TYR* 3.1 20.1 + - - +
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A PHE* 3.7 8.3 - - + -
274A ILE* 3.5 28.5 - - + -
279A LEU* 3.7 18.8 - - + +
286A TYR* 3.6 13.4 + - + +
289A PRO 4.8 0.2 - - - +
291A THR 2.7 23.2 + - - +
294A ASP* 1.3 73.4 - - - +
296A GLY* 1.3 55.6 + - - +
298A TYR* 3.3 2.4 + - - +
299A ILE* 3.0 34.7 + - - +
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Residues in contact with GLY 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A LEU* 4.6 1.3 - - - -
264A LEU* 4.3 6.8 - - - +
270A PHE* 3.8 8.6 - - - -
292A TYR 2.8 19.4 + - - -
293A GLU 4.1 0.7 - - - -
295A ALA* 1.3 78.2 - - - +
297A ASN* 1.3 60.9 + - - +
299A ILE* 3.5 5.7 + - - +
300A LYS* 3.1 22.0 + - - +
319A MET* 3.8 25.5 - - - +
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Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A GLU 3.2 19.8 + - - +
294A ASP* 3.7 6.0 + - - +
296A GLY* 1.3 73.6 - - - +
298A TYR* 1.3 67.5 + - - +
300A LYS* 3.2 32.0 + - - +
301A VAL* 3.0 37.3 + - - +
319A MET* 5.3 0.2 - - - -
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Residues in contact with TYR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A LEU* 3.9 10.3 - - + -
283A PHE* 3.7 35.6 - + + +
285A ASP* 4.3 9.0 - - - +
286A TYR* 3.5 53.1 + + + -
294A ASP 3.1 14.3 + - - +
295A ALA* 3.3 7.6 + - - +
297A ASN* 1.3 79.9 - - - +
299A ILE* 1.3 65.2 + - - +
301A VAL* 3.1 8.7 + - + +
302A GLN* 3.1 54.2 + - - -
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Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A LEU* 4.1 18.8 - - + +
226A TYR* 4.8 0.2 - - + -
239A MET* 3.7 33.7 - - + -
264A LEU* 4.2 4.3 - - + -
270A PHE* 3.7 30.7 - - + -
279A LEU* 3.9 25.8 - - + -
283A PHE* 4.1 9.9 - - + -
295A ALA 3.0 19.1 + - - +
296A GLY 3.7 4.7 - - - +
298A TYR* 1.3 78.0 - - - +
300A LYS* 1.3 63.4 + - - +
302A GLN* 3.0 18.6 + - - +
303A PHE* 3.3 26.9 + - + -
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Residues in contact with LYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LEU* 5.2 1.1 - - + -
264A LEU* 3.7 22.0 - - + -
296A GLY 3.1 14.1 + - - +
297A ASN* 3.2 36.3 + - - +
299A ILE* 1.3 76.5 - - - +
301A VAL* 1.3 68.2 + - - +
303A PHE* 3.2 6.6 + - - +
304A LEU* 2.9 51.9 + - + +
317A SER* 3.3 28.7 - - - +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ASN* 3.0 32.3 + - - +
298A TYR* 3.3 11.9 - - + +
300A LYS* 1.3 86.6 - - - +
302A GLN* 1.3 76.1 + - - +
304A LEU* 4.6 4.5 - - - +
305A GLU* 3.0 43.3 + - + +
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Residues in contact with GLN 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LEU* 3.8 13.2 - - + +
283A PHE* 3.8 37.4 - - + -
298A TYR* 3.1 53.1 + - + +
299A ILE 3.0 7.5 + - - +
301A VAL* 1.3 91.7 - - - +
303A PHE* 1.3 62.5 + - - +
305A GLU* 3.5 24.9 + - - +
306A LEU* 3.4 16.8 - - - +
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Residues in contact with PHE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A PHE* 4.5 1.3 - + - -
221A ALA* 3.6 15.5 - - + -
239A MET* 4.2 14.8 - - + -
242A SER* 3.5 44.9 - - - -
243A LEU* 3.7 25.6 - - + -
246A PHE* 3.1 41.9 - + + -
262A LEU* 3.6 24.0 - - + -
264A LEU* 4.2 11.9 - - + -
283A PHE* 5.8 0.2 - + - -
299A ILE* 3.3 39.8 + - + -
300A LYS 3.2 7.0 + - - +
302A GLN* 1.3 77.8 - - + +
304A LEU* 1.3 65.4 + - - +
306A LEU* 3.0 16.0 + - - +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PHE* 4.5 4.7 - - + -
262A LEU* 4.3 15.0 - - + -
300A LYS* 2.9 52.7 + - + +
301A VAL* 4.2 3.8 - - - +
303A PHE* 1.3 70.5 - - - +
305A GLU* 1.3 60.5 + - - +
306A LEU 3.0 6.6 + - - -
307A ASN* 3.1 22.2 + - + +
310A ARG* 5.3 6.4 - - - +
315A ILE* 3.8 44.6 - - + +
317A SER* 4.2 8.1 - - - +
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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