Contacts of the helix formed by residues 266 - 276 (chain A) in PDB entry 2CZK
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 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A SER 4.5 0.2 - - - +
161A GLY* 3.6 28.0 - - - +
162A GLU 3.4 9.0 + - - -
163A THR* 3.3 21.1 - - + +
244A GLY 5.8 0.2 - - - -
245A ILE* 3.5 9.0 - - - +
264A ALA* 3.3 0.4 - - - +
265A SER* 1.3 87.1 + - - +
267A ARG* 1.3 53.6 + - - +
268A GLU* 3.1 14.2 + - - +
269A MET* 3.2 5.7 + - - +
270A ALA* 2.8 33.6 + - - +
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Residues in contact with ARG 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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245A ILE* 3.1 34.9 - - + +
246A VAL 5.6 0.4 + - - -
247A ILE* 4.0 11.1 - - - +
251A GLY 5.8 0.4 + - - -
266A THR* 1.3 68.8 - - - +
268A GLU* 1.3 73.0 + - - +
270A ALA* 3.5 7.6 - - - +
271A MET* 3.1 47.3 + - + +
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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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163A THR* 3.5 32.2 - - + +
266A THR* 3.4 21.3 + - - +
267A ARG* 1.3 84.5 + - - +
269A MET* 1.3 59.0 + - - +
271A MET* 3.0 9.6 + - - +
272A LEU* 2.6 31.2 + - + +
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Residues in contact with MET 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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162A GLU* 3.1 49.4 - - + +
163A THR 4.0 3.3 + - - +
164A ASP 3.6 11.2 - - - +
165A LEU* 3.6 34.1 - - - -
168A ALA* 3.4 25.4 - - + -
220A ASP* 4.0 5.2 - - + +
221A ALA* 3.9 11.9 - - + -
264A ALA* 3.7 18.4 - - + -
265A SER* 4.2 0.9 - - - +
266A THR* 3.2 7.9 + - - +
268A GLU* 1.3 79.4 - - - +
270A ALA* 1.3 57.9 + - - +
271A MET 2.9 1.2 + - - -
272A LEU* 3.3 7.4 + - - +
273A ILE* 2.8 39.7 + - + +
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Residues in contact with ALA 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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245A ILE* 3.5 36.3 - - + +
247A ILE* 3.3 25.8 - - + +
262A VAL* 3.5 10.1 - - + +
264A ALA* 3.6 11.8 - - + +
266A THR 2.8 21.2 + - - +
267A ARG 3.5 6.5 - - - +
268A GLU 3.2 0.4 - - - -
269A MET* 1.3 71.5 - - - +
271A MET* 1.3 56.0 + - + +
273A ILE* 4.6 0.2 - - - -
274A ALA* 3.4 16.8 + - - +
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Residues in contact with MET 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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247A ILE* 3.3 31.0 - - + -
251A GLY* 4.0 23.8 - - - +
267A ARG* 3.1 46.2 - - + +
268A GLU* 3.0 8.9 + - - +
269A MET 2.9 0.6 + - - -
270A ALA* 1.3 76.5 - - + +
272A LEU* 1.3 61.1 + - + +
273A ILE 2.9 2.0 - - - -
274A ALA* 2.8 4.3 + - - +
275A GLN* 2.5 40.2 + - + +
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Residues in contact with LEU 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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163A THR 4.0 13.9 - - - +
164A ASP* 5.3 0.2 - - - -
165A LEU* 3.6 41.3 - - + +
268A GLU* 2.6 43.0 + - + +
269A MET* 3.3 5.1 + - - +
271A MET* 1.3 79.5 - - + +
273A ILE* 1.3 61.7 + - + +
275A GLN* 3.1 30.9 + - - +
276A ALA* 3.2 15.8 - - - +
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Residues in contact with ILE 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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165A LEU* 3.3 38.1 - - + -
170A VAL* 4.8 4.0 - - + -
193A LEU* 4.2 12.7 - - + +
221A ALA* 4.4 13.7 - - + -
222A TYR 5.1 1.8 - - - +
223A TYR* 4.1 26.9 - - + -
262A VAL* 4.0 13.2 - - + -
269A MET* 2.8 39.9 - - + +
270A ALA* 4.4 1.6 - - - +
271A MET 2.9 0.2 - - - -
272A LEU* 1.3 75.9 - - + +
274A ALA* 1.3 63.9 + - - +
276A ALA* 3.2 3.8 + - - +
277A LEU* 2.8 42.0 + - + +
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Residues in contact with ALA 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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247A ILE* 4.3 2.5 - - + -
248A ASP 4.0 10.1 - - - +
249A THR* 3.6 31.1 - - - +
250A SER* 4.4 3.1 - - - -
251A GLY* 4.1 9.2 - - - +
262A VAL* 4.3 6.5 - - + +
270A ALA 3.4 16.9 + - - +
271A MET* 2.8 10.9 + - - +
273A ILE* 1.3 75.6 - - - +
275A GLN* 1.3 63.3 + - - +
277A LEU* 2.8 26.1 + - - +
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Residues in contact with GLN 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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192A ARG* 5.1 2.4 + - - -
250A SER 5.6 1.3 + - - -
271A MET* 2.5 31.3 + - + +
272A LEU* 3.1 29.5 + - - +
274A ALA* 1.3 74.1 - - - +
276A ALA* 1.3 66.3 + - - +
277A LEU 3.5 5.5 + - - +
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Residues in contact with ALA 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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189A ASN* 4.7 2.6 - - - +
192A ARG* 3.1 49.1 - - + +
193A LEU* 5.0 9.8 - - + +
272A LEU 3.2 17.0 - - - +
273A ILE* 3.2 4.6 + - - +
274A ALA 3.1 1.2 - - - -
275A GLN* 1.3 86.0 - - - +
277A LEU* 1.3 63.4 + - - +
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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