Contacts of the helix formed by residues 255 - 266 (chain D) in PDB entry 1Z1G
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205D LEU* 5.2 0.4 - - + -
208D VAL* 3.6 33.2 - - + +
209D THR* 3.6 18.2 - - + -
229D LEU* 3.5 40.4 - - + -
242D ILE* 3.9 16.8 - - + +
243D PRO 3.4 23.8 - - - +
244D THR* 4.0 13.0 - - - +
246D LEU* 2.9 26.3 + - - +
254D SER* 1.3 69.0 - - - +
256D LYS* 1.3 58.8 + - - +
258D THR* 3.1 5.8 + - - -
259D LEU* 2.8 54.1 + - + +
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Residues in contact with LYS 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D GLY* 5.1 4.4 - - - -
244D THR* 3.3 45.8 + - - +
245D ALA* 5.6 0.4 - - - -
254D SER* 3.3 5.8 + - - +
255D MSE 1.3 78.8 - - - +
257D GLU* 1.3 62.2 + - + +
259D LEU* 3.3 9.8 + - + +
260D ASP* 3.1 38.6 + - - +
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Residues in contact with GLU 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D SER* 3.1 26.3 + - - +
256D LYS* 1.3 75.1 - - + +
258D THR* 1.3 66.6 + - - +
260D ASP* 3.8 2.2 + - - +
261D LYS* 3.4 36.5 + - - +
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Residues in contact with THR 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D LEU* 3.7 16.4 - - + +
204D GLU* 3.3 32.1 + - + +
205D LEU* 3.9 23.6 - - + +
208D VAL* 5.3 1.1 - - + -
253D ILE* 3.1 21.5 - - - +
254D SER 2.7 27.9 + - - -
255D MSE 3.4 7.9 - - - -
257D GLU* 1.3 74.7 - - - +
259D LEU* 1.3 53.2 + - - +
261D LYS* 3.3 13.7 + - - +
262D CYS* 2.5 29.4 + - - -
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Residues in contact with LEU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D LEU* 3.9 22.9 - - + -
221D TRP* 3.2 18.3 - - + -
224D ILE* 4.1 16.6 - - + -
229D LEU* 5.1 3.6 - - + -
244D THR* 3.9 30.5 - - + -
255D MSE 2.8 44.9 + - + +
256D LYS* 3.6 7.9 - - + +
258D THR* 1.3 73.8 - - - +
260D ASP* 1.3 63.5 + - - +
262D CYS* 3.1 25.0 + - - +
271D ILE* 3.6 28.3 - - + -
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Residues in contact with ASP 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D TRP* 4.3 1.7 - - - -
256D LYS* 3.1 31.7 + - - +
257D GLU* 3.8 3.1 + - - +
258D THR 3.4 0.4 - - - -
259D LEU* 1.3 78.3 - - - +
261D LYS* 1.3 63.7 + - - +
262D CYS 3.1 1.8 - - - -
263D LYS* 3.0 39.1 + - + +
264D GLU* 3.2 23.0 + - - +
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Residues in contact with LYS 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D TYR* 5.4 2.2 + - - -
201D LEU* 3.8 15.2 - - + +
204D GLU* 3.7 30.9 + - - -
257D GLU* 3.4 31.1 + - - +
258D THR* 3.3 10.5 + - - +
260D ASP* 1.3 77.0 - - - +
262D CYS* 1.3 56.3 + - - +
264D GLU* 4.8 2.9 - - + +
265D ILE* 3.0 55.9 + - + +
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Residues in contact with CYS 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D LEU* 3.8 29.6 - - + -
205D LEU* 4.9 6.7 - - - -
221D TRP* 3.8 8.2 + - + -
258D THR* 2.5 40.2 - - - -
259D LEU* 3.1 15.3 - - - +
261D LYS* 1.3 75.6 - - - +
263D LYS* 1.3 61.9 + - - +
266D LEU* 3.1 27.5 + - + +
267D GLY 3.3 3.3 + - - -
271D ILE* 3.7 30.7 - - + +
272D ILE* 5.5 0.2 - - - -
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Residues in contact with LYS 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D TRP* 2.9 45.8 - - + -
259D LEU 3.2 7.3 + - - -
260D ASP* 3.0 41.2 + - + +
262D CYS* 1.3 75.1 - - - +
264D GLU* 1.3 65.5 + - + +
267D GLY* 3.5 20.7 + - - +
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Residues in contact with GLU 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D ASP 3.2 16.2 + - - +
261D LYS* 4.8 1.6 - - + +
263D LYS* 1.3 80.8 - - + +
265D ILE* 1.3 76.6 + - + +
267D GLY* 4.7 1.9 + - - -
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Residues in contact with ILE 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D CYS* 3.7 34.6 - - + -
201D LEU* 4.8 7.9 - - + -
261D LYS* 3.0 51.3 + - + +
264D GLU* 1.3 83.6 - - + +
266D LEU* 1.3 66.6 + - + +
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Residues in contact with LEU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D CYS* 4.0 22.7 - - - -
198D TRP* 3.7 33.0 - - + -
201D LEU* 3.8 23.1 - - + -
262D CYS* 3.1 15.4 + - - +
264D GLU 5.0 0.2 - - - -
265D ILE* 1.3 91.2 - - + +
267D GLY* 1.3 68.5 + - - +
268D GLY 5.4 0.2 - - - +
270D THR 5.8 0.4 - - - +
271D ILE 3.8 14.6 - - - +
272D ILE* 4.2 7.6 - - + -
273D ALA* 3.7 32.0 - - + +
274D SER 4.5 10.8 - - - +
275D THR* 6.5 0.2 - - - -
277D ARG* 4.2 11.1 + - - +
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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