Contacts of the helix formed by residues 266 - 276 (chain A) in PDB entry 5DTI
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 ASP 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A LEU* 3.8 13.2 - - - +
163A GLY 5.2 0.5 - - - -
164A SER* 3.8 27.7 + - - -
166A GLU* 4.8 0.4 - - - +
245A ARG* 2.8 46.5 + - - -
265A ASN* 1.3 75.2 + - - +
267A THR* 1.3 60.2 + - - +
269A LEU* 3.3 8.1 + - - +
270A ILE* 2.9 39.7 + - + +
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Residues in contact with THR 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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165A ARG* 4.5 5.2 + - - +
166A GLU* 2.6 36.4 + - + +
265A ASN* 2.8 23.9 + - - +
266A ASP* 1.3 73.7 - - - +
268A GLU* 1.3 56.6 + - - +
270A ILE* 3.5 2.1 + - - +
271A ALA* 2.9 31.3 + - + +
274A ARG* 5.2 2.9 + - - +
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Residues in contact with GLU 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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258A PRO* 4.2 23.1 - - + +
265A ASN* 2.9 25.7 + - - +
267A THR* 1.3 73.3 - - - +
269A LEU* 1.3 61.3 + - - +
271A ALA* 3.7 6.4 - - + +
272A CYS* 2.9 30.2 + - + +
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Residues in contact with LEU 269 (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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161A LEU* 3.7 28.5 - - + -
248A ALA 4.8 2.7 - - - +
249A THR* 4.7 21.5 - - + +
252A ALA* 3.7 30.7 - - + -
257A CYS* 4.4 1.3 - - + +
258A PRO* 4.1 34.9 - - + +
265A ASN 3.6 12.7 + - - +
266A ASP* 3.3 11.8 + - - +
268A GLU* 1.3 78.2 - - - +
270A ILE* 1.3 58.9 + - - +
272A CYS* 3.2 4.6 + - - +
273A LEU* 2.9 36.1 + - + +
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Residues in contact with ILE 270 (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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47A PHE* 3.9 21.1 - - + -
161A LEU* 3.4 24.5 - - + -
164A SER* 3.7 11.9 - - - +
166A GLU* 3.6 35.2 - - + +
167A ALA* 3.6 21.5 - - + -
266A ASP 2.9 24.2 + - - +
267A THR 3.9 2.9 - - - +
269A LEU* 1.3 75.9 - - - +
271A ALA* 1.3 56.6 + - - +
273A LEU* 3.2 10.9 + - + +
274A ARG* 2.9 45.1 + - - +
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Residues in contact with ALA 271 (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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267A THR* 2.9 20.7 + - + +
268A GLU* 3.7 9.0 - - + +
269A LEU 3.3 0.2 - - - -
270A ILE* 1.3 73.3 - - - +
272A CYS* 1.3 67.0 + - - +
274A ARG* 2.9 39.2 + - - +
275A THR* 3.0 18.1 + - - +
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Residues in contact with CYS 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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256A GLY 4.2 3.8 - - - -
257A CYS* 2.1 52.9 - - + -
258A PRO* 4.0 11.2 - - + -
268A GLU* 2.9 17.5 + - + +
269A LEU 3.5 3.6 - - - +
271A ALA* 1.3 75.1 - - - +
273A LEU* 1.3 63.5 + - - +
275A THR* 2.5 33.7 + - - -
276A ARG* 3.5 6.6 - - - +
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Residues in contact with LEU 273 (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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46A ARG* 3.0 19.9 + - - -
47A PHE* 3.6 15.7 - - + -
159A LEU* 4.0 33.9 - - + -
161A LEU* 5.1 0.4 - - + -
248A ALA 4.8 1.3 - - - +
251A LEU* 4.7 3.6 - - + -
252A ALA* 3.9 17.7 - - + +
255A VAL* 3.8 27.6 - - + -
257A CYS* 3.7 3.3 - - - -
269A LEU* 2.9 38.0 + - + +
270A ILE* 3.2 12.5 + - - +
272A CYS* 1.3 77.0 - - - +
274A ARG* 1.3 58.2 + - - +
276A ARG* 3.1 13.4 + - - +
281A LEU* 4.2 15.6 - - + +
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Residues in contact with ARG 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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43A GLY* 3.5 28.9 - - - +
44A SER* 3.8 23.0 + - - +
46A ARG* 3.7 34.3 + - + +
47A PHE* 3.9 16.4 - - + -
48A MET* 5.5 2.8 - - - +
166A GLU* 3.9 20.2 + - - +
267A THR* 5.2 3.2 + - - +
270A ILE* 2.9 36.5 + - - +
271A ALA* 2.9 33.1 + - - +
273A LEU* 1.3 75.9 - - - +
275A THR* 1.3 60.8 + - - +
276A ARG 3.5 1.2 + - - +
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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
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271A ALA* 3.0 14.3 + - + +
272A CYS* 2.5 27.3 + - - -
274A ARG* 1.3 79.2 - - + +
276A ARG* 1.3 74.5 + - - +
277A PRO* 3.8 4.9 - - - +
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Residues in contact with ARG 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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46A ARG* 2.6 30.5 + - - -
255A VAL* 3.5 31.6 + - + +
257A CYS* 3.9 17.5 - - - -
272A CYS* 3.5 18.2 - - - +
273A LEU* 3.1 17.0 + - - +
274A ARG 4.1 0.5 - - - +
275A THR* 1.3 91.5 + - - +
277A PRO* 1.3 85.4 - - + +
280A ASP* 3.2 24.7 + - + -
281A LEU* 4.2 11.7 - - + -
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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