Contacts of the helix formed by residues 255 - 266 (chain B) in PDB entry 1Z19
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 MSE 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B LEU* 4.9 2.7 - - + -
208B VAL* 3.7 30.4 - - + +
209B THR* 4.1 15.9 - - + -
229B LEU* 4.2 23.1 - - + -
242B ILE* 4.0 16.6 - - + +
243B PRO 3.7 14.8 - - - +
244B THR* 3.2 41.7 - - + +
246B LEU* 3.1 28.1 + - - +
254B SER* 1.3 70.0 - - - +
256B LYS* 1.3 52.7 + - - +
258B THR* 2.9 6.5 + - - -
259B LEU* 2.7 55.4 + - + +
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Residues in contact with LYS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B THR* 3.4 31.0 + - - +
245B ALA* 5.4 1.8 - - - -
246B LEU 4.6 0.4 + - - -
254B SER* 3.3 5.5 + - - +
255B MSE 1.3 79.4 - - - +
257B GLU* 1.3 64.4 + - - +
259B LEU* 3.3 10.4 + - + +
260B ASP* 3.0 53.2 + - - +
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Residues in contact with GLU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B SER* 2.9 31.8 + - - +
256B LYS* 1.3 77.5 - - - +
258B THR* 1.3 63.3 + - - +
260B ASP* 3.1 10.6 + - + +
261B LYS* 3.1 43.5 + - + +
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Residues in contact with THR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B LEU* 4.5 6.0 - - + +
204B GLU* 3.3 40.8 + - + +
205B LEU* 4.1 19.5 - - + +
208B VAL* 5.6 0.2 - - - -
253B ILE* 4.0 6.3 - - - +
254B SER 2.8 21.4 + - - -
255B MSE 3.2 11.4 - - - -
257B GLU* 1.3 75.0 - - - +
259B LEU* 1.3 67.0 + - - +
261B LYS* 3.2 13.1 + - - +
262B CYS* 3.1 32.6 + - - -
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LEU* 3.5 29.4 - - + -
221B TRP* 3.2 20.3 - - + -
224B ILE* 4.0 20.6 - - + -
229B LEU* 5.6 2.5 - - + -
244B THR* 4.1 13.7 - - + -
255B MSE 2.7 49.0 + - + +
256B LYS* 3.8 8.5 - - + +
258B THR* 1.3 73.8 - - - +
260B ASP* 1.3 59.0 + - - +
262B CYS* 3.2 4.4 + - - -
263B LYS* 3.0 23.2 + - - +
271B ILE* 4.0 27.8 - - + -
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Residues in contact with ASP 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B LYS* 3.0 46.2 + - - +
257B GLU* 3.3 12.1 - - + +
258B THR 3.1 0.2 - - - -
259B LEU* 1.3 81.2 - - - +
261B LYS* 1.3 62.3 + - + +
263B LYS* 3.3 12.6 + - - +
264B GLU* 3.3 30.0 + - - +
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Residues in contact with LYS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B TYR* 4.3 6.9 + - - -
201B LEU* 4.0 18.5 - - + +
204B GLU* 3.5 33.3 + - - -
257B GLU* 3.1 31.3 + - + +
258B THR* 3.2 15.0 + - - +
260B ASP* 1.3 78.0 - - + +
262B CYS* 1.3 58.2 + - - +
264B GLU* 4.2 9.6 - - - +
265B ILE* 3.0 52.6 + - + +
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Residues in contact with CYS 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B LEU* 3.7 36.1 - - - -
205B LEU* 5.0 2.7 - - - -
221B TRP* 3.7 11.3 - - + -
258B THR* 3.1 23.4 + - - -
259B LEU* 3.4 11.2 - - - +
260B ASP 3.2 0.2 - - - -
261B LYS* 1.3 77.6 - - - +
263B LYS* 1.3 55.7 + - - +
266B LEU* 3.0 28.4 + - - +
267B GLY 3.1 7.4 + - - -
271B ILE* 3.6 26.9 - - + +
272B ILE* 4.2 10.8 - - - -
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Residues in contact with LYS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B TRP* 3.5 53.0 - - + +
259B LEU 3.0 13.2 + - - +
260B ASP* 3.5 14.1 - - - +
261B LYS 3.3 0.2 - - - -
262B CYS* 1.3 77.9 - - - +
264B GLU* 1.3 61.0 + - + +
267B GLY* 3.3 22.6 + - - +
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Residues in contact with GLU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ASP* 3.3 21.8 + - - +
261B LYS* 4.2 10.0 - - - +
263B LYS* 1.3 82.6 - - + +
265B ILE* 1.3 73.1 + - + +
266B LEU 3.2 2.1 + - - -
267B GLY* 3.9 4.0 + - - -
277B ARG* 5.5 4.2 + - - -
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Residues in contact with ILE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B CYS* 4.2 22.3 - - + -
201B LEU* 4.6 7.2 - - + -
261B LYS* 3.0 39.6 + - + +
264B GLU* 1.3 87.4 - - + +
266B LEU* 1.3 74.5 + - + +
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B CYS* 4.2 10.3 - - - -
198B TRP* 4.1 22.7 - - + -
201B LEU* 3.4 33.0 - - + -
262B CYS* 3.0 20.7 + - - +
264B GLU 3.2 1.1 - - - -
265B ILE* 1.3 96.0 - - + +
267B GLY* 1.3 70.2 + - - +
268B GLY 5.3 0.2 - - - +
271B ILE 4.0 12.3 - - - +
272B ILE* 4.4 3.6 - - + -
273B ALA* 3.9 41.2 - - + +
274B SER 4.4 6.2 - - - +
275B THR* 6.2 0.9 - - - -
277B ARG* 3.6 17.1 - - - +
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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