Contacts of the helix formed by residues 231 - 242 (chain A) in PDB entry 1TF5
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 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A SER* 1.3 73.0 + - - +
232A LYS* 1.3 69.1 + - - +
233A LEU 3.1 3.4 - - - -
234A TYR* 2.8 22.9 + - - +
235A VAL* 3.3 13.5 + - - +
345A ILE* 3.6 47.7 - - + +
347A ASN* 2.8 28.9 - - + +
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Residues in contact with LYS 232 (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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230A SER* 3.0 22.8 + - - +
231A THR* 1.3 79.4 + - - +
233A LEU* 1.3 69.2 + - + +
235A VAL* 3.2 13.2 + - - +
236A GLN* 3.1 56.7 + - - +
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Residues in contact with LEU 233 (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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230A SER 4.9 4.0 + - - +
231A THR 3.0 1.4 + - - -
232A LYS* 1.3 83.1 - - + +
234A TYR* 1.3 60.9 + - - +
236A GLN* 3.6 24.2 - - + +
237A ALA* 2.9 33.2 + - + +
285A ALA* 4.5 6.7 - - + -
286A LEU* 3.7 41.1 - - + +
289A HIS* 3.8 37.5 - - + +
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Residues in contact with TYR 234 (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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229A LYS* 4.0 13.0 + - + +
230A SER 3.9 14.1 - - - -
231A THR* 2.8 30.0 + - - +
233A LEU* 1.3 74.3 - - - +
235A VAL* 1.3 58.7 + - - +
237A ALA* 3.7 3.4 - - - +
238A ASN* 2.9 31.4 + - - +
289A HIS* 3.4 29.6 - + - -
292A GLN* 6.3 1.1 - - + -
293A ALA* 5.4 0.5 - - - +
332A GLY* 3.9 15.8 - - - -
335A GLN* 3.4 38.6 + - + +
336A ALA* 4.3 12.1 - - + +
339A ALA* 4.1 7.8 - - + +
345A ILE* 3.5 21.3 - - + -
347A ASN* 4.0 14.8 - - + +
348A GLU* 3.8 21.1 + - - -
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Residues in contact with VAL 235 (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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231A THR* 3.6 17.0 - - - +
232A LYS* 3.3 13.0 - - - +
233A LEU 3.2 0.2 - - - -
234A TYR* 1.3 76.8 - - - +
236A GLN* 1.3 62.4 + - + +
238A ASN* 3.1 7.1 + - - +
239A ALA* 2.8 30.7 + - + +
339A ALA* 5.0 2.2 - - + -
345A ILE* 4.1 15.7 - - + +
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Residues in contact with GLN 236 (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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232A LYS* 3.1 41.0 + - + +
233A LEU* 3.6 22.6 - - + +
235A VAL* 1.3 83.4 - - + +
237A ALA* 1.3 58.7 + - - +
239A ALA* 3.3 7.9 + - - +
240A PHE* 2.9 30.0 + - - +
273A PHE* 4.1 22.3 - - + -
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Residues in contact with ALA 237 (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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233A LEU* 2.9 22.1 + - + +
234A TYR* 3.7 4.7 - - - +
236A GLN* 1.3 75.6 - - - +
238A ASN* 1.3 63.9 + - - +
240A PHE* 3.3 6.2 + - - +
241A VAL* 3.0 28.6 + - - +
273A PHE* 4.5 7.3 - - + -
286A LEU* 5.6 0.2 - - + -
289A HIS* 3.7 38.4 - - + +
290A ILE* 4.2 7.4 - - + +
293A ALA* 4.0 4.0 - - + -
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Residues in contact with ASN 238 (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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234A TYR 2.9 18.7 + - - +
235A VAL* 3.5 4.0 - - - +
237A ALA* 1.3 73.4 - - - +
239A ALA* 1.3 68.2 + - - +
241A VAL* 3.2 13.0 + - - +
242A ARG* 3.4 31.3 + - - +
293A ALA* 4.1 11.3 - - + +
297A HIS* 2.6 34.1 - - - -
336A ALA 4.5 1.6 - - - +
339A ALA* 3.6 24.5 + - + -
340A LYS* 3.3 17.5 + - - +
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Residues in contact with ALA 239 (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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235A VAL* 2.8 20.1 + - + +
236A GLN* 3.5 9.0 - - - +
238A ASN* 1.3 80.1 - - - +
240A PHE* 1.3 63.3 + - - +
242A ARG* 3.4 20.5 + - - +
243A THR* 3.9 6.4 + - - -
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Residues in contact with PHE 240 (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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236A GLN 2.9 16.4 + - - +
237A ALA 3.5 3.4 - - - +
239A ALA* 1.3 76.5 - - - +
241A VAL* 1.3 62.4 + - + +
243A THR* 2.9 36.1 + - + -
244A LEU* 3.6 36.7 + - + +
261A LEU* 5.0 1.3 - - + -
265A GLY 3.8 3.6 - - - -
268A LYS* 3.7 17.9 - - + -
269A ALA* 3.4 45.8 - - + -
272A ALA* 3.9 11.4 - - + -
273A PHE* 3.5 28.3 - + + -
290A ILE* 4.0 24.9 - - + -
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Residues in contact with VAL 241 (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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237A ALA 3.0 18.0 + - - +
238A ASN 3.2 5.8 + - - +
240A PHE* 1.3 86.6 - - + +
242A ARG* 1.3 60.3 + - - +
243A THR 3.0 1.6 + - - -
244A LEU* 3.4 20.0 + - - +
250A TYR* 5.3 2.7 - - + -
290A ILE* 4.1 11.0 - - + +
293A ALA* 3.4 28.3 - - + +
294A LEU* 3.6 39.3 - - + +
297A HIS* 4.2 17.7 - - + +
298A VAL* 6.0 0.2 - - + -
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Residues in contact with ARG 242 (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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238A ASN* 3.4 26.0 + - - +
239A ALA* 3.4 13.2 + - - +
240A PHE 3.1 1.4 + - - -
241A VAL* 1.3 77.5 - - - +
243A THR* 1.3 59.6 + - - +
244A LEU 3.4 4.9 - - - +
297A HIS* 3.8 31.1 + - + +
340A LYS* 3.5 24.4 + - - +
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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