Contacts of the helix formed by residues 329 - 344 (chain A) in PDB entry 5T8Y
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 ARG 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A LEU 5.8 0.2 + - - -
297A LYS* 3.7 20.9 - - - +
298A LYS* 3.7 44.5 - - + +
301A GLN* 2.8 34.1 + - - +
323A LEU* 5.4 1.6 - - - +
327A ASP* 2.9 34.6 + - - +
328A PRO* 1.3 89.0 - - + +
330A PRO* 1.3 69.9 - - + +
331A VAL 3.2 1.6 - - - +
332A ILE* 3.0 38.9 + - + +
333A ARG* 3.0 17.4 + - - +
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Residues in contact with PRO 330 (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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224A PHE* 3.2 14.0 - - + -
298A LYS* 6.0 2.0 - - - +
328A PRO 3.5 9.0 - - - +
329A ARG* 1.3 85.3 - - + +
331A VAL* 1.3 61.5 + - + +
333A ARG* 3.4 25.1 - - - +
334A GLY 3.0 23.6 + - - -
361A ASP* 3.6 35.7 - - + +
364A ALA* 3.5 5.3 - - + +
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Residues in contact with VAL 331 (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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222A LYS 3.5 26.9 - - - +
223A GLY* 3.7 24.2 - - - +
224A PHE* 3.6 20.0 - - + +
298A LYS* 3.7 26.2 - - + +
302A ARG* 3.8 21.8 - - + -
329A ARG 3.2 0.6 - - - -
330A PRO* 1.3 79.6 - - + +
332A ILE* 1.3 57.5 + - + +
335A THR* 2.4 39.3 + - - +
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Residues in contact with ILE 332 (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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298A LYS* 4.1 25.6 - - + +
301A GLN* 4.3 7.4 - - + -
302A ARG* 4.1 22.2 - - + +
305A ILE* 4.0 14.0 - - + +
323A LEU* 4.1 15.5 - - + -
327A ASP* 3.4 31.6 - - + +
329A ARG* 3.0 41.6 + - + +
331A VAL* 1.3 77.0 - - + +
333A ARG* 1.3 64.2 + - - +
335A THR* 3.5 2.5 + - - -
336A ALA* 3.0 24.4 + - - +
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Residues in contact with ARG 333 (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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323A LEU 3.5 13.5 - - - +
324A MET* 3.3 33.8 - - + +
325A HIS 4.8 6.3 - - - -
327A ASP 2.7 42.7 + - - +
328A PRO* 3.3 20.0 + - - +
329A ARG 3.0 8.5 + - - +
330A PRO* 3.4 35.8 - - + +
332A ILE* 1.3 77.8 - - - +
334A GLY* 1.3 62.4 + - - +
336A ALA* 3.9 1.9 - - - +
337A ALA* 3.2 23.4 + - - +
359A GLU* 2.9 40.7 + - - +
361A ASP* 4.3 2.4 - - - +
364A ALA* 4.7 2.2 - - + -
368A ILE* 5.2 3.5 - - + +
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Residues in contact with GLY 334 (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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224A PHE* 3.9 6.5 - - - -
330A PRO 3.0 15.7 + - - -
333A ARG* 1.3 75.5 - - - +
335A THR* 1.3 64.9 + - - +
337A ALA* 3.4 3.0 + - - +
338A TRP* 3.1 19.9 + - - +
364A ALA* 4.2 12.0 - - - +
367A GLU* 3.3 31.4 - - - +
368A ILE* 5.3 0.2 - - - -
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Residues in contact with THR 335 (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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224A PHE* 4.1 9.5 - - - -
230A ARG* 5.6 4.4 - - - +
302A ARG* 3.7 29.8 - - + +
305A ILE* 3.7 20.6 - - + -
306A LEU* 3.8 26.5 - - + -
331A VAL* 2.4 28.8 + - - +
332A ILE* 4.0 3.1 - - - -
334A GLY* 1.3 73.0 - - - +
336A ALA* 1.3 61.8 + - - +
338A TRP* 3.4 8.1 + - + +
339A ALA* 2.9 27.0 + - - +
367A GLU* 5.5 0.7 - - - -
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Residues in contact with ALA 336 (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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305A ILE* 3.8 16.3 - - + +
320A LEU* 3.4 35.6 - - + +
323A LEU* 4.4 7.9 - - + -
324A MET* 4.4 3.4 - - + +
332A ILE 3.0 18.9 + - - +
333A ARG 3.9 3.6 - - - +
335A THR* 1.3 78.8 - - - +
337A ALA* 1.3 57.0 + - - +
339A ALA* 3.1 3.5 + - - +
340A ILE* 2.9 34.8 + - - +
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Residues in contact with ALA 337 (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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324A MET* 3.6 23.1 - - - -
333A ARG 3.2 16.2 + - - +
334A GLY 3.7 4.3 - - - +
335A THR 3.3 0.2 - - - -
336A ALA* 1.3 79.5 - - - +
338A TRP* 1.3 63.3 + - - +
340A ILE* 3.3 7.0 + - - +
341A GLY 3.2 17.0 + - - -
352A LEU* 3.8 19.5 - - + +
367A GLU 4.7 0.2 - - - -
368A ILE* 3.9 24.5 - - + -
371A GLY* 3.8 5.3 - - - -
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Residues in contact with TRP 338 (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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227A ASP* 4.0 12.6 + - + -
230A ARG* 3.2 54.4 - - + +
231A THR* 5.1 5.4 - - + -
306A LEU* 3.9 23.1 - - + -
309A ALA* 4.0 20.2 - - + -
334A GLY 3.1 17.4 + - - +
335A THR* 3.7 7.6 - - + +
337A ALA* 1.3 76.4 - - - +
339A ALA* 1.3 62.9 + - + +
341A GLY 3.5 1.2 + - - -
342A LYS* 2.9 51.0 + - + +
367A GLU* 3.7 16.7 + - - +
370A LYS* 3.8 27.0 - - + +
371A GLY* 4.3 4.0 - - - -
374A LEU* 3.8 16.5 - - + +
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Residues in contact with ALA 339 (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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305A ILE* 3.6 21.8 - - + +
309A ALA* 3.7 19.7 - - + -
320A LEU* 4.0 11.0 - - + -
335A THR 2.9 14.6 + - - +
336A ALA 3.1 8.7 + - - +
338A TRP* 1.3 83.7 - - + +
340A ILE* 1.3 56.5 + - - +
342A LYS* 3.0 1.4 + - - +
343A ILE* 2.8 41.4 + - - +
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Residues in contact with ILE 340 (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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317A LEU* 4.0 21.2 - - + +
320A LEU* 4.0 15.7 - - + +
321A THR* 3.5 38.4 - - - +
324A MET* 4.3 21.5 - - + -
336A ALA 2.9 19.0 + - - +
337A ALA* 3.3 7.4 + - - +
339A ALA* 1.3 77.8 - - - +
341A GLY* 1.3 61.2 + - - +
343A ILE* 3.5 4.0 + - - +
344A GLY 3.4 13.9 + - - -
345A ASP 4.2 7.5 + - - +
348A TYR* 3.7 28.9 - - + +
351A GLU* 6.3 0.4 - - + -
352A LEU* 4.4 15.0 - - + -
375A LEU* 4.4 1.7 - - + +
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Residues in contact with GLY 341 (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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337A ALA 3.2 7.7 + - - -
339A ALA 3.2 0.4 - - - -
340A ILE* 1.3 78.8 - - - +
342A LYS* 1.3 63.2 + - - +
344A GLY* 3.3 14.0 + - - -
352A LEU* 4.7 0.6 - - - +
371A GLY* 3.3 32.3 - - - -
374A LEU* 3.3 19.4 - - - +
375A LEU* 3.9 11.7 - - - +
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Residues in contact with LYS 342 (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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231A THR* 4.4 24.0 - - - +
309A ALA* 4.0 22.2 - - + +
312A LYS* 3.0 32.6 + - - +
338A TRP* 2.9 44.3 + - + +
339A ALA* 3.0 9.4 + - - +
341A GLY* 1.3 75.4 - - - +
343A ILE* 1.3 62.5 + - - +
344A GLY* 3.4 1.0 + - - -
374A LEU* 3.5 19.7 - - + +
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Residues in contact with ILE 343 (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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308A LEU 4.7 3.6 - - - +
309A ALA* 4.2 10.3 - - - -
312A LYS* 4.0 46.8 + - - +
313A ASP 3.3 25.8 - - - +
314A ALA* 4.2 7.9 - - + -
316A ALA* 5.3 0.2 - - + -
317A LEU* 3.6 36.8 - - + -
320A LEU* 3.8 21.1 - - + -
339A ALA 2.8 20.1 + - - +
340A ILE 3.7 5.2 - - - +
342A LYS* 1.3 73.4 - - - +
344A GLY* 1.3 59.1 + - - +
345A ASP* 4.6 3.4 - - + +
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Residues in contact with GLY 344 (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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340A ILE 3.4 2.6 + - - -
341A GLY 3.3 15.1 + - - -
342A LYS 3.2 3.1 - - - -
343A ILE* 1.3 80.9 - - - +
345A ASP* 1.3 59.6 + - - +
346A PRO* 3.2 11.1 - - - +
374A LEU 5.5 2.2 - - - -
375A LEU* 3.7 9.6 - - - -
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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