Contacts of the helix formed by residues 273 - 280 (chain A) in PDB entry 1T0R
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 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A GLN* 3.3 31.4 + - + +
269A PHE* 3.0 40.6 + - + -
272A LEU* 1.3 81.2 - - - +
274A GLY* 1.3 68.2 + - - +
275A PRO 3.4 1.1 - - - -
276A ILE* 3.0 15.9 + - + +
277A MET* 3.1 35.3 + - + +
290A PHE* 4.3 3.1 - - + -
293A PHE* 5.4 3.1 - - + -
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Residues in contact with GLY 274 (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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269A PHE 3.2 7.0 + - - -
273A THR* 1.3 81.8 - - - +
275A PRO* 1.3 68.7 - - - +
276A ILE 3.2 0.2 + - - -
277A MET* 3.5 1.7 + - - +
278A ASP* 3.4 17.0 + - - +
290A PHE* 3.5 35.3 - - - +
328A HIS* 3.6 18.9 - - - -
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Residues in contact with PRO 275 (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 SER 3.2 21.5 - - - +
271A VAL* 3.4 27.1 - - - +
273A THR 3.7 1.3 - - - -
274A GLY* 1.3 87.4 - - - +
276A ILE* 1.3 63.0 + - + +
279A TYR* 3.1 44.0 + - + +
280A TYR* 3.3 10.2 - - + +
328A HIS* 3.9 14.8 - - + +
331A MET 4.4 1.6 - - - +
332A HIS* 3.9 28.0 - - + +
335A VAL* 5.7 3.1 - - + -
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Residues in contact with ILE 276 (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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89A TRP* 5.9 0.4 - - + -
92A THR* 3.7 35.7 - - + +
95A LEU* 3.3 26.9 - - + -
208A LEU* 6.1 1.8 - - + -
211A ASP* 6.0 1.8 - - - +
271A VAL 4.6 1.6 - - - +
272A LEU 3.0 26.2 - - - +
273A THR* 3.0 11.4 + - + +
275A PRO* 1.3 87.6 - - + +
277A MET* 1.3 62.4 + - + +
280A TYR* 3.1 44.6 + - + +
281A THR* 3.2 17.5 + - + +
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Residues in contact with MET 277 (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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211A ASP* 4.9 14.6 - - - +
273A THR* 3.1 32.6 + - + +
276A ILE* 1.3 79.5 - - + +
278A ASP* 1.3 61.0 + - - +
281A THR* 2.9 21.3 + - + -
286A ARG* 4.1 11.8 - - - +
288A GLN* 4.2 15.5 - - + +
289A SER 3.7 6.3 - - - +
290A PHE* 3.6 39.5 - - + +
293A PHE* 3.3 43.5 - - + -
357A TRP* 4.7 1.2 - - - -
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Residues in contact with ASP 278 (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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274A GLY 3.4 13.1 + - - +
276A ILE 3.3 0.4 - - - -
277A MET* 1.3 81.8 - - - +
279A TYR* 1.3 82.5 + - + +
286A ARG* 3.3 22.5 + - - +
289A SER* 3.5 4.7 - - - -
290A PHE* 2.7 28.3 + - - +
328A HIS* 3.0 13.3 + - - +
329A HIS* 4.2 0.9 - - - -
349A GLY 5.0 0.2 - - - +
357A TRP* 3.8 14.1 - - + -
358A LEU* 4.0 6.9 - - + +
362A TYR* 2.6 40.9 + - - -
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Residues in contact with TYR 279 (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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275A PRO* 3.1 16.1 + - + +
277A MET 3.6 0.6 - - - -
278A ASP* 1.3 95.2 - - + +
280A TYR* 1.3 65.7 + - - +
281A THR 3.5 1.7 - - - +
286A ARG* 3.8 11.3 + - - +
328A HIS* 4.6 3.8 - + - -
329A HIS* 2.5 40.6 + + - +
332A HIS* 3.3 61.7 - + + -
347A ALA* 3.9 8.8 - - - +
348A ALA 3.6 3.1 - - - +
349A GLY* 3.5 33.0 - - - -
350A VAL* 4.6 2.2 - - + -
354A GLU* 4.3 1.9 - - - +
358A LEU* 3.9 24.9 - - + -
365A TRP* 3.1 20.7 + + - -
369A TRP* 5.4 0.2 - - - +
373A TRP* 5.1 1.3 + - - -
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Residues in contact with TYR 280 (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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86A ASP* 4.4 1.7 - - - +
88A GLY* 3.4 41.9 - - - +
91A SER* 4.1 9.6 - - - -
92A THR* 3.9 13.7 - - - +
95A LEU* 5.0 1.6 - - + -
275A PRO* 3.3 20.9 - - + +
276A ILE* 3.1 29.5 + - + +
279A TYR* 1.3 79.1 - - + +
281A THR* 1.3 64.6 + - - +
282A PRO* 3.7 5.0 - - - +
332A HIS* 3.7 28.0 + + - -
335A VAL* 3.9 9.4 - - - +
344A TRP* 3.2 37.4 + + - -
346A PRO* 3.5 23.2 - - + +
347A ALA* 3.9 18.0 - - + +
483A HIS* 5.4 1.4 - - - -
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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