Contacts of the helix formed by residues 271 - 281 (chain A) in PDB entry 1TFZ
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 SER 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A GLY* 2.7 31.0 + - - -
263A PRO* 3.3 26.2 - - - +
264A VAL 3.9 13.8 + - - -
265A HIS* 5.3 3.8 - - - +
270A LYS* 1.3 78.0 - - - +
272A GLN* 1.3 70.6 + - - +
273A ILE* 3.2 12.5 + - - +
274A GLN* 3.3 8.9 + - - +
275A THR* 3.3 21.7 + - - -
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Residues in contact with GLN 272 (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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242A SER 3.2 25.6 + - - +
243A GLY* 4.1 5.1 - - - -
244A LEU* 5.4 3.8 - - + +
270A LYS 3.6 12.7 - - - +
271A SER* 1.3 79.0 + - - +
273A ILE* 1.3 71.0 + - + +
275A THR* 3.3 9.5 + - - -
276A TYR* 3.1 21.1 + - - +
286A GLN* 6.3 0.4 - - - +
551A 869 5.2 22.2 - - + -
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASN* 3.4 45.5 - - + +
210A VAL 4.5 1.3 - - - +
244A LEU* 3.8 37.9 - - + -
261A ASN* 4.2 4.7 - - + +
262A GLU* 4.0 8.7 - - - +
263A PRO* 3.8 24.9 - - + -
271A SER* 3.1 12.3 - - - +
272A GLN* 1.3 83.6 - - + +
274A GLN* 1.3 63.9 + - - +
276A TYR* 3.4 2.4 + - - +
277A LEU* 3.1 23.5 + - + +
286A GLN* 3.8 19.3 - - - +
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Residues in contact with GLN 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A PRO* 3.8 11.9 - - + +
265A HIS* 3.3 29.5 + - + -
270A LYS* 4.0 11.0 - - + -
271A SER* 3.3 26.0 + - - +
272A GLN 3.2 0.6 - - - -
273A ILE* 1.3 76.5 - - - +
275A THR* 1.3 65.6 + - - +
277A LEU* 3.2 14.4 + - - +
278A GLU* 3.0 62.1 + - - +
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Residues in contact with THR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LYS* 3.6 22.0 + - - +
271A SER 3.3 11.1 + - - -
272A GLN* 3.3 11.3 + - - -
274A GLN* 1.3 79.1 - - - +
276A TYR* 1.3 62.7 + - - +
278A GLU* 3.3 10.0 + - - +
279A HIS* 3.1 50.8 + - + +
368A PRO* 5.1 10.3 - - + +
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Residues in contact with TYR 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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209A ASN* 3.1 42.0 - - + +
272A GLN 3.1 12.9 + - - +
273A ILE 3.4 4.9 - - - +
274A GLN 3.2 0.4 - - - -
275A THR* 1.3 76.1 - - - +
277A LEU* 1.3 59.2 + - + +
279A HIS* 3.3 1.6 + - - +
280A ASN* 2.8 66.7 + - + +
282A GLY 3.7 7.2 - - - -
284A GLY* 3.1 22.3 - - - -
285A LEU 2.7 26.6 + - - -
286A GLN* 3.9 9.0 - - + -
368A PRO 4.3 11.6 + - - +
369A THR* 3.5 45.2 - - - +
370A ILE* 5.4 0.2 - - - +
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Residues in contact with LEU 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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209A ASN 4.0 14.1 - - - +
210A VAL 4.1 3.6 - - - +
211A PRO* 4.0 30.3 - - + -
263A PRO* 4.0 15.5 - - + -
273A ILE* 3.1 16.5 + - + +
274A GLN* 3.2 22.9 + - - +
276A TYR* 1.3 86.7 - - + +
278A GLU* 1.3 58.4 + - - +
281A GLU* 3.0 8.5 + - - -
282A GLY* 2.8 53.4 + - - +
283A ALA* 3.7 10.3 - - - +
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Residues in contact with GLU 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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270A LYS* 2.8 36.2 + - - -
274A GLN* 3.0 39.4 + - - +
275A THR* 3.6 7.8 - - - +
276A TYR 3.2 0.2 - - - -
277A LEU* 1.3 76.4 - - - +
279A HIS* 1.3 68.5 + - + +
281A GLU* 3.3 17.0 + - - +
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Residues in contact with HIS 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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270A LYS* 6.1 0.2 + - - -
275A THR* 3.1 47.0 + - + +
276A TYR 4.1 2.0 - - - +
278A GLU* 1.3 82.9 + - + +
280A ASN* 1.3 57.9 + - - +
281A GLU* 3.6 1.6 + - - +
367A ARG* 2.9 32.7 + - + +
368A PRO* 3.4 38.4 - - + +
369A THR* 4.1 8.3 - - + -
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Residues in contact with ASN 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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114A HIS* 2.7 64.4 + - - +
116A LEU 5.8 1.6 + - - -
276A TYR* 2.8 46.8 + - + +
279A HIS* 1.3 72.0 - - - +
281A GLU* 1.3 60.6 + - - +
282A GLY 3.2 21.3 - - - +
283A ALA 3.6 10.9 - - - +
284A GLY* 4.0 2.4 - - - -
367A ARG* 4.2 2.7 - - - +
369A THR* 3.7 20.3 + - + +
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Residues in contact with GLU 281 (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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112A SER 4.6 3.3 - - - +
113A SER* 3.0 42.7 + - - +
114A HIS* 3.4 14.0 - - - -
277A LEU 3.0 7.7 + - - -
278A GLU 3.3 10.7 + - - +
279A HIS 3.3 2.1 - - - +
280A ASN* 1.3 83.0 - - - +
282A GLY* 1.3 57.1 + - - +
367A ARG* 4.3 7.6 + - - +
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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