Contacts of the helix formed by residues 255 - 266 (chain A) in PDB entry 1Z1B
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 MET 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A LEU* 4.9 2.7 - - + -
208A VAL* 3.6 31.4 - - + +
209A THR* 4.1 13.7 - - + -
229A LEU* 4.1 31.4 - - + -
242A ILE* 4.0 16.2 - - + -
243A PRO 3.6 15.5 - - - +
244A THR* 3.4 29.8 - - + +
246A LEU* 3.0 23.4 + - - +
254A SER* 1.3 72.1 - - - +
256A LYS* 1.3 53.3 + - - +
258A THR* 3.1 4.4 + - - -
259A LEU* 2.7 58.9 + - + +
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Residues in contact with LYS 256 (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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244A THR* 3.2 31.7 + - - +
245A ALA* 5.3 2.0 - - - -
254A SER* 3.3 7.9 + - - +
255A MET* 1.3 79.6 - - - +
257A GLU* 1.3 63.0 + - - +
259A LEU* 3.0 12.9 + - + +
260A ASP* 3.0 52.2 + - - +
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Residues in contact with GLU 257 (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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252A GLY 5.4 2.3 - - - +
254A SER* 3.4 28.0 + - - +
255A MET 3.3 0.4 - - - -
256A LYS* 1.3 77.4 - - - +
258A THR* 1.3 64.9 + - - +
260A ASP* 3.1 12.8 + - + +
261A LYS* 3.1 36.0 + - + +
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Residues in contact with THR 258 (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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201A LEU* 4.0 15.0 - - + +
204A GLU* 3.1 39.7 + - + +
205A LEU* 4.2 16.6 - - + +
208A VAL* 5.8 0.4 - - - -
253A ILE* 3.8 10.0 - - - +
254A SER 2.7 23.8 + - - -
255A MET* 3.4 6.1 - - - -
257A GLU* 1.3 78.5 - - - +
259A LEU* 1.3 61.9 + - - +
261A LYS* 3.4 10.7 + - - +
262A CYS* 3.1 32.8 + - - -
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Residues in contact with LEU 259 (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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205A LEU* 3.8 25.6 - - + -
221A TRP* 3.3 23.0 - - + -
224A ILE* 4.1 18.6 - - + -
229A LEU* 5.6 1.6 - - + -
244A THR* 4.1 18.2 - - + -
255A MET* 2.7 45.0 + - + +
256A LYS* 3.0 13.7 + - + +
258A THR* 1.3 74.6 - - - +
260A ASP* 1.3 65.1 + - - +
262A CYS* 3.4 2.8 + - - +
263A LYS* 3.1 18.4 + - - +
271A ILE* 4.0 26.2 - - + -
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Residues in contact with ASP 260 (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 LYS* 3.0 44.6 + - - +
257A GLU* 3.1 11.6 + - + +
259A LEU* 1.3 76.4 - - - +
261A LYS* 1.3 65.6 + - + +
263A LYS* 2.9 19.0 + - - +
264A GLU* 3.1 23.7 + - + +
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Residues in contact with LYS 261 (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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189A TYR* 4.2 7.5 + - - -
201A LEU* 3.8 19.6 - - + +
204A GLU* 3.5 30.6 + - - -
257A GLU* 3.1 23.0 + - + +
258A THR* 3.4 15.9 + - - +
260A ASP* 1.3 75.5 - - + +
262A CYS* 1.3 58.9 + - - +
263A LYS 3.3 0.2 + - - -
264A GLU* 4.5 8.5 - - - +
265A ILE* 2.9 55.0 + - + +
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Residues in contact with CYS 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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201A LEU* 3.6 36.8 - - - -
205A LEU* 5.4 2.2 - - - -
221A TRP* 3.9 10.7 - - + -
258A THR* 3.1 26.0 + - - -
259A LEU* 3.5 11.7 - - - +
261A LYS* 1.3 75.9 - - - +
263A LYS* 1.3 62.4 + - - +
266A LEU* 3.1 27.5 + - + +
267A GLY 3.1 4.5 + - - -
271A ILE* 3.7 21.3 - - + +
272A ILE* 4.3 15.0 - - - -
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Residues in contact with LYS 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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221A TRP* 3.7 50.1 - - + +
259A LEU 3.1 12.5 + - - +
260A ASP* 2.9 14.4 + - - +
262A CYS* 1.3 79.3 - - - +
264A GLU* 1.3 63.3 + - + +
267A GLY* 3.5 18.3 + - - +
268A GLY 5.3 0.6 + - - -
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Residues in contact with GLU 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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260A ASP* 3.1 20.3 + - + +
261A LYS* 4.2 9.1 - - - +
263A LYS* 1.3 80.6 - - + +
265A ILE* 1.3 74.2 + - + +
266A LEU 3.5 0.9 + - - -
267A GLY* 4.3 3.1 + - - -
277A ARG* 5.2 6.9 + - - -
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Residues in contact with ILE 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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197A CYS* 4.1 31.7 - - + -
201A LEU* 4.8 6.7 - - + -
261A LYS* 2.9 45.3 + - + +
264A GLU* 1.3 82.7 - - + +
266A LEU* 1.3 66.5 + - + +
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Residues in contact with LEU 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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197A CYS* 4.6 7.0 - - - -
198A TRP* 3.8 30.5 - - + +
201A LEU* 3.6 29.2 - - + -
262A CYS* 3.1 14.7 + - - +
264A GLU 4.6 0.7 - - - -
265A ILE* 1.3 91.3 - - + +
267A GLY* 1.3 70.4 + - - +
271A ILE 4.1 12.1 - - - +
272A ILE* 4.2 10.1 - - + -
273A ALA* 3.7 47.5 - - + +
274A SER 4.4 6.9 - - - +
275A THR* 6.0 1.3 - - - -
277A ARG* 3.9 13.0 - - - +
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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