Contacts of the helix formed by residues 261 - 268 (chain A) in PDB entry 5TYZ
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 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A LEU* 4.2 5.6 - - - -
240A PHE* 3.7 7.3 - - - -
260A ARG* 1.3 84.5 - - + +
262A LEU* 1.3 64.2 + - - +
263A ASP* 3.5 9.2 + - - +
264A ASP* 2.8 52.2 + - - +
265A LEU* 3.4 10.7 + - - +
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Residues in contact with LEU 262 (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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239A LEU* 3.9 31.1 - - + +
240A PHE* 4.7 0.4 - - + -
243A ILE* 3.7 33.2 - - + -
261A THR* 1.3 75.6 - - - +
263A ASP* 1.3 59.1 - - - +
265A LEU* 3.0 12.5 + - + +
266A ARG* 2.9 49.5 + - - +
280A LEU* 4.0 12.3 - - + +
283A HIS* 3.4 35.4 - - + +
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Residues in contact with ASP 263 (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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261A THR* 3.3 7.4 + - - +
262A LEU* 1.3 74.6 - - - +
264A ASP* 1.3 67.0 + - - +
266A ARG* 3.4 32.1 + - + +
267A GLU* 3.0 39.1 + - + +
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Residues in contact with ASP 264 (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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258A GLY 4.9 1.1 - - - +
259A LEU* 3.8 31.7 - - + +
260A ARG* 3.0 15.0 + - - +
261A THR* 2.8 47.4 + - - +
262A LEU 3.2 0.2 - - - -
263A ASP* 1.3 79.7 - - - +
265A LEU* 1.3 60.7 + - - +
267A GLU* 3.6 30.1 + - - +
268A GLN* 4.0 7.4 + - - +
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Residues in contact with LEU 265 (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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240A PHE* 3.7 20.4 - - + -
243A ILE* 3.5 31.2 - - + -
254A TRP* 3.4 44.2 - - + -
259A LEU* 4.0 18.4 - - + -
261A THR 3.4 10.3 + - - +
262A LEU* 3.0 12.4 + - + +
264A ASP* 1.3 75.9 - - - +
266A ARG* 1.3 64.0 + - - +
267A GLU 3.4 0.3 + - - -
268A GLN* 3.4 21.0 + - - +
269A PRO 3.9 0.7 - - - -
272A LEU* 3.9 15.9 - - + +
280A LEU* 3.8 15.5 - - + -
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Residues in contact with ARG 266 (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* 2.9 29.7 + - - +
263A ASP* 3.2 33.1 + - + +
265A LEU* 1.3 76.5 - - - +
267A GLU* 1.3 63.5 + - + +
269A PRO* 3.3 19.6 - - - +
272A LEU* 5.4 0.4 - - - -
280A LEU* 2.8 57.4 + - + +
281A GLN* 4.7 5.1 + - - +
283A HIS* 4.6 6.9 - - - +
284A GLN* 5.6 2.0 - - - +
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Residues in contact with GLU 267 (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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263A ASP* 3.0 33.6 + - + +
264A ASP* 3.8 23.5 - - - +
265A LEU 3.2 0.8 - - - -
266A ARG* 1.3 77.9 - - + +
268A GLN* 1.3 58.0 + - + +
269A PRO* 3.4 7.3 - - - +
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Residues in contact with GLN 268 (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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264A ASP 4.0 6.2 + - - +
265A LEU* 3.4 11.4 + - - +
266A ARG 3.2 0.4 - - - -
267A GLU* 1.3 78.3 - - + +
269A PRO* 1.3 62.5 - - - +
270A GLN* 3.1 8.8 + - + -
271A LYS* 3.5 16.3 + - + +
272A LEU* 4.3 3.8 - - - +
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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