Contacts of the helix formed by residues 259 - 269 (chain A) in PDB entry 4I2C
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 GLY 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A THR* 3.7 8.3 - - - -
258A VAL* 1.3 73.2 - - - +
260A LEU* 1.3 58.2 + - - -
261A LYS 3.4 3.7 + - - -
263A ALA* 3.0 29.5 + - - +
3C A 3.2 40.6 + - - -
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Residues in contact with LEU 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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180A GLU* 4.6 22.0 - - + +
181A LEU* 4.2 30.1 - - + +
183A GLU* 6.4 0.9 - - + -
249A PHE* 3.6 29.3 - - + -
253A THR* 4.1 3.4 - - - +
259A GLY* 1.3 70.5 - - - +
261A LYS* 1.3 57.9 + - + +
263A ALA* 3.6 5.9 + - - +
264A GLU* 3.0 30.8 + - - +
3C A 3.8 3.3 + - - +
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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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259A GLY 3.4 1.0 - - - -
260A LEU* 1.3 75.0 - - + +
262A THR* 1.4 61.0 + - - +
264A GLU* 3.4 10.9 + - - +
265A LYS* 3.0 27.3 + - - +
2C A 3.0 46.6 + - - +
3C A 3.7 11.0 + - - +
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Residues in contact with THR 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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258A VAL* 4.1 9.4 - - + -
261A LYS* 1.4 68.1 - - - +
263A ALA* 1.3 65.4 + - - +
265A LYS* 3.3 12.4 + - + +
266A TRP* 3.0 61.4 + - + +
289A GLN* 3.8 22.0 + - - +
2C A 3.8 5.2 - - - -
3C A 2.6 27.1 + - - -
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Residues in contact with ALA 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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248A SER 5.8 0.2 - - - -
249A PHE* 4.5 14.1 - - + -
252A PHE* 3.5 35.6 - - + -
253A THR* 3.8 19.7 - - + -
258A VAL* 4.0 2.6 - - + +
259A GLY 3.0 18.0 + - - +
260A LEU* 3.8 5.2 - - - +
262A THR* 1.3 77.4 - - - +
264A GLU* 1.4 54.9 + - - +
267A PHE* 3.1 27.1 + - - +
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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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181A LEU* 6.4 1.6 - - + -
183A GLU* 5.3 5.2 - - - +
245A ARG* 3.7 32.1 + - - +
260A LEU 3.0 18.3 + - - +
261A LYS* 3.6 10.1 - - - +
262A THR 3.3 0.2 - - - -
263A ALA* 1.4 72.3 - - - +
265A LYS* 1.3 66.8 + - - +
267A PHE* 3.4 7.0 + - - +
268A ARG* 2.7 67.6 + - - +
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Residues in contact with LYS 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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261A LYS 3.0 14.8 + - - +
262A THR* 3.3 15.1 + - + +
264A GLU* 1.3 75.3 + - - +
266A TRP* 1.3 76.5 + - + +
268A ARG* 3.3 8.8 + - - +
269A MET* 3.1 47.9 + - + +
283A LEU* 5.1 5.1 - - - +
284A ARG 5.6 4.2 + - - -
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Residues in contact with TRP 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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252A PHE* 3.7 31.6 - + + -
258A VAL* 3.7 34.8 - - + -
262A THR* 3.0 38.0 + - + +
265A LYS* 1.3 90.9 - - + +
267A PHE* 1.3 60.2 + - - +
269A MET* 3.2 10.2 + - - -
270A GLY 3.3 0.2 + - - -
271A PHE* 3.0 38.8 + + + -
274A LEU* 5.4 0.9 - - + -
277A ILE* 3.7 37.9 - - + -
283A LEU* 4.0 28.1 - - + +
284A ARG 5.6 2.4 + - - -
285A PHE* 3.8 28.0 - + - -
289A GLN* 4.5 5.2 - - - -
293A PHE* 4.2 10.1 - + - -
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Residues in contact with PHE 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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244A GLU* 3.9 7.9 - - + -
245A ARG* 3.7 57.9 - - + +
248A SER* 3.6 19.5 - - - -
252A PHE* 3.8 4.9 - - + -
263A ALA 3.1 16.6 + - - +
264A GLU* 3.6 6.3 - - - +
266A TRP* 1.3 77.0 - - - +
268A ARG* 1.3 69.1 + - + +
270A GLY* 2.9 16.8 + - - -
271A PHE 3.9 3.4 - - - -
272A ARG* 3.0 56.6 + - - +
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Residues in contact with ARG 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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245A ARG* 4.4 11.1 - - - +
264A GLU* 2.7 61.1 + - - +
265A LYS* 3.3 6.5 + - - +
267A PHE* 1.3 85.2 - - + +
269A MET* 1.3 60.0 + - - +
270A GLY 3.2 1.3 - - - -
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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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265A LYS* 3.1 43.4 + - + +
266A TRP* 3.5 12.6 - - - +
267A PHE 3.2 0.6 - - - -
268A ARG* 1.3 76.8 - - - +
270A GLY* 1.3 58.8 + - - +
271A PHE* 3.5 24.5 - - + -
280A ASP* 6.0 0.7 - - - +
282A SER* 6.3 2.5 - - - -
283A LEU* 3.9 23.1 - - + -
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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