Contacts of the helix formed by residues 259 - 273 (chain A) in PDB entry 4IYM
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 ASP 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ALA* 1.3 69.8 - - - +
260A LEU* 1.3 60.4 + - - +
261A ASP* 3.2 18.5 + - - +
262A GLN* 3.3 37.9 + - + +
263A ALA* 2.9 28.6 + - - +
414A TYR* 4.7 4.0 - - + -
416A ARG* 3.5 21.3 + - - +
436A ASN* 5.8 1.0 + - - -
481B PRO* 3.9 26.7 - - + +
482B SER 5.3 0.3 + - - +
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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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254A ILE* 3.8 28.9 - - + -
255A MSE 4.8 1.3 - - - +
256A PRO 5.6 5.2 - - - +
258A ALA* 3.2 19.2 + - + +
259A ASP* 1.3 70.5 + - - +
261A ASP* 1.3 61.3 + - - +
263A ALA* 3.7 2.4 - - - +
264A ALA* 2.9 29.8 + - - +
292A THR* 4.2 17.0 - - + +
295A ARG* 3.5 51.8 - - + +
296A LEU* 3.9 16.9 - - + +
299A LYS* 3.9 18.0 - - + -
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Residues in contact with ASP 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 ASP* 3.2 8.6 + - - +
260A LEU* 1.3 77.2 - - - +
262A GLN* 1.3 58.9 + - + +
264A ALA* 3.4 5.4 + - - +
265A ASN* 3.0 38.6 + - - +
299A LYS* 2.8 30.4 + - - +
303A MSE 4.8 2.3 - - - +
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Residues in contact with GLN 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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259A ASP* 3.3 30.7 + - + +
261A ASP* 1.3 74.5 - - + +
263A ALA* 1.3 60.2 + - - +
265A ASN* 3.5 9.0 + - - +
266A ALA* 2.9 31.5 + - - +
414A TYR* 4.3 11.8 - - + -
436A ASN* 6.0 1.4 - - - +
481B PRO* 3.5 27.7 - - - +
482B SER* 5.2 3.2 - - - +
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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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252A MSE 4.3 1.7 - - - +
254A ILE* 4.3 22.2 - - + -
259A ASP 2.9 18.2 + - - +
260A LEU* 3.7 8.1 - - - +
261A ASP 3.3 0.2 - - - -
262A GLN* 1.3 76.1 - - - +
264A ALA* 1.3 61.6 + - - +
266A ALA* 3.3 2.8 + - - +
267A LEU* 3.0 27.7 + - - +
296A LEU* 4.0 15.7 - - + -
414A TYR* 4.0 23.7 - - + -
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Residues in contact with ALA 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 LEU 2.9 17.8 + - - +
261A ASP* 3.7 4.5 - - - +
263A ALA* 1.3 73.9 - - - +
265A ASN* 1.3 64.9 + - - +
267A LEU* 3.1 15.7 + - - +
268A ILE* 3.1 15.2 + - - +
296A LEU* 3.8 12.0 - - + +
299A LYS* 3.9 22.7 - - + -
300A LEU* 4.0 9.5 - - - +
303A MSE 3.9 22.7 - - + -
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Residues in contact with ASN 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 ASP* 3.0 25.2 + - - +
262A GLN* 3.7 9.7 - - - +
264A ALA* 1.3 75.1 - - - +
266A ALA* 1.3 61.3 + - - +
268A ILE* 3.1 24.4 - - - +
269A GLY* 3.4 5.0 + - - -
303A MSE 3.3 25.3 - - - +
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Residues in contact with ALA 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 MSE 3.8 4.0 - - + -
262A GLN 2.9 19.5 + - - +
263A ALA 3.5 5.2 - - - +
265A ASN* 1.3 72.9 - - - +
267A LEU* 1.3 58.7 - - - +
269A GLY* 3.6 1.0 + - - -
270A ALA* 2.8 33.1 + - - +
414A TYR* 3.2 31.2 - - + +
438A PRO* 3.8 18.0 - - + +
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Residues in contact with LEU 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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252A MSE 3.7 22.4 - - + -
254A ILE* 4.4 0.9 - - + -
263A ALA 3.0 20.4 + - - +
264A ALA* 3.1 5.3 + - - +
266A ALA* 1.3 76.4 - - - +
268A ILE* 1.3 58.0 + - - +
270A ALA* 4.4 0.4 - - - +
271A GLY* 2.7 32.7 + - - +
272A TYR* 4.1 3.5 - - - -
282A ILE* 3.7 30.3 - - + -
285A ALA* 4.0 22.2 - - + -
296A LEU* 4.0 30.5 - - + -
300A LEU* 4.1 25.6 - - + -
387A LEU* 4.3 10.3 - - + +
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Residues in contact with ILE 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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264A ALA 3.1 10.3 + - - +
265A ASN* 3.1 23.8 - - - +
267A LEU* 1.3 77.1 - - - +
269A GLY* 1.3 74.6 + - - +
272A TYR* 3.2 43.3 + - + +
273A GLY 3.9 0.7 + - - -
300A LEU* 4.2 3.5 - - + +
303A MSE 3.5 48.0 - - + +
304A VAL* 3.7 16.6 - - + +
307A LEU* 3.9 20.0 - - + +
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Residues in contact with GLY 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 ASN 3.4 6.3 + - - -
266A ALA* 4.0 2.2 - - - -
268A ILE* 1.3 88.4 - - - +
270A ALA* 1.3 56.5 + - - +
273A GLY* 3.0 30.0 + - - -
439A ILE* 4.8 4.7 - - - +
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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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266A ALA 2.8 23.1 + - - +
267A LEU* 4.5 0.9 - - - +
269A GLY* 1.3 74.1 - - - +
271A GLY* 1.3 62.0 + - - +
273A GLY* 4.8 2.3 + - - +
278A ARG* 6.0 0.5 - - - -
281A ALA* 3.4 12.0 - - - +
282A ILE* 3.1 45.7 + - + -
438A PRO* 3.9 7.6 - - + -
439A ILE* 3.8 29.5 - - + +
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Residues in contact with GLY 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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267A LEU* 2.7 19.1 + - - +
270A ALA* 1.3 80.4 - - - +
272A TYR* 1.3 71.3 + - - +
273A GLY 3.8 0.2 - - - -
276A GLY* 3.6 19.3 - - - -
281A ALA* 4.8 1.0 - - - +
282A ILE* 3.4 19.8 - - - +
384A GLY 4.5 5.2 - - - +
385A PRO* 4.6 0.9 - - - +
386A VAL 4.9 3.1 + - - -
387A LEU* 4.9 6.0 - - - +
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Residues in contact with TYR 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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267A LEU 4.4 2.0 - - - -
268A ILE* 3.2 32.0 + - + +
271A GLY* 1.3 79.7 - - - +
273A GLY* 1.3 69.4 + - - +
274A SER 3.4 0.3 + - - -
275A ALA* 3.0 17.2 + - - -
276A GLY 4.3 2.7 - - - +
300A LEU* 5.2 0.4 - - + -
304A VAL* 3.6 30.0 - - + +
307A LEU* 3.8 29.2 - - + -
318A ASP 4.9 0.8 - - - +
319A MSE 3.6 14.0 - - - +
365A GLY* 3.8 4.0 - - - -
366A CYS 2.6 31.0 + - - -
367A LEU* 3.8 5.2 - - - +
385A PRO* 3.4 42.2 - - + -
386A VAL 4.4 0.7 - - - -
387A LEU* 3.4 31.3 - - + +
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Residues in contact with GLY 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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95A ASP* 5.7 2.0 - - - -
268A ILE 3.9 1.0 + - - -
269A GLY* 3.0 22.9 + - - -
270A ALA 4.6 2.5 - - - +
271A GLY 4.9 0.3 - - - -
272A TYR* 1.3 75.7 + - - +
274A SER* 1.3 63.8 + - - -
276A GLY* 2.9 20.8 + - - -
277A GLU 4.2 0.2 + - - -
278A ARG* 4.4 9.4 - - - -
318A ASP 5.1 5.4 - - - -
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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