Contacts of the helix formed by residues 347 - 361 (chain A) in PDB entry 5WWT
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 TYR 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A PRO* 3.8 26.5 - - + +
326A CYS* 3.5 23.1 + - - -
327A SER* 3.7 16.6 - - - -
339A TRP* 3.9 8.3 - + - -
343A GLU 3.5 17.3 - - - -
344A VAL 3.4 15.5 - - - -
345A ALA 3.1 1.6 - - - -
346A SER* 1.3 80.2 - - - +
348A GLN* 1.3 67.7 + - - +
349A PRO* 3.3 2.7 - - - -
350A LEU* 3.0 9.4 + - + +
351A GLN* 2.8 44.1 + - - +
379A GLU* 4.1 6.3 - - - +
3C G 3.6 22.7 - + - -
70C C 2.6 44.8 + + + -
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Residues in contact with GLN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ALA* 3.9 9.0 + - + +
347A TYR* 1.3 76.7 - - - +
349A PRO* 1.4 67.8 - - + +
351A GLN* 3.8 3.4 + - - -
352A ARG* 2.9 58.6 + - - +
378A ALA* 3.2 30.9 + - + +
379A GLU* 4.9 4.6 - - + +
382A GLU* 3.5 18.6 + - - +
383A GLN* 3.2 32.8 + - - +
2C A 4.3 8.2 - - - +
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Residues in contact with PRO 349 (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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345A ALA 4.3 3.8 - - - +
346A SER* 4.1 10.5 - - - +
347A TYR 3.4 4.9 - - - +
348A GLN* 1.4 95.0 - - + +
350A LEU* 1.3 56.5 + - - +
352A ARG* 3.2 7.3 + - + +
353A LYS* 2.9 34.7 + - - +
2C A 3.6 56.3 - - + +
3C G 3.6 24.0 - - - +
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Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LYS* 5.7 3.8 - - - +
293A ASP* 5.7 0.2 - - - +
295A THR* 3.8 24.5 - - + -
325A PRO* 3.8 24.9 - - + -
347A TYR* 3.0 12.4 + - + +
349A PRO* 1.3 76.0 - - - +
351A GLN* 1.3 61.2 + - - +
353A LYS* 3.3 7.9 + - + +
354A LEU* 2.9 46.2 + - + +
3C G 3.8 60.7 + - + +
70C C 5.8 0.2 - - - +
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Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LEU* 4.0 3.6 - - - +
324A ALA* 4.0 13.7 - - + -
325A PRO* 2.9 30.4 + - + +
326A CYS* 4.0 3.8 - - - +
347A TYR* 2.8 26.1 + - - +
348A GLN* 3.8 0.3 - - - -
350A LEU* 1.3 78.0 - - - +
352A ARG* 1.3 57.1 + - - +
354A LEU* 3.5 6.8 + - - +
355A PHE* 2.9 29.7 + - - +
370A TYR* 3.1 24.3 + - + +
372A THR* 4.6 2.4 - - - +
379A GLU* 3.1 39.1 + - - +
383A GLN* 2.8 26.9 + - - +
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Residues in contact with ARG 352 (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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348A GLN* 2.9 49.7 + - - +
349A PRO* 3.2 5.8 + - + +
351A GLN* 1.3 74.3 - - - +
353A LYS* 1.3 61.1 + - + +
355A PHE 3.3 0.2 + - - -
356A THR* 2.9 32.9 + - - -
382A GLU* 4.9 5.9 + - - +
383A GLN* 2.9 23.8 + - - +
386A TRP* 3.4 60.9 - - + +
2C A 3.0 51.5 + - + +
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Residues in contact with LYS 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR* 3.8 26.4 - - + +
349A PRO 2.9 18.8 + - - +
350A LEU* 3.6 14.6 - - + +
352A ARG* 1.3 76.8 - - + +
354A LEU* 1.3 62.5 + - - +
356A THR* 3.2 7.2 + - - -
357A ALA* 2.9 24.3 + - - +
3C G 3.0 53.0 + - + -
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Residues in contact with LEU 354 (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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241A LEU* 3.3 23.9 - - + +
242A CYS* 3.6 15.9 - - - -
294A GLY* 3.6 14.6 - - - +
295A THR* 3.6 33.4 - - + +
322A LEU* 3.7 15.9 - - + -
324A ALA* 4.9 0.2 - - + -
325A PRO* 3.6 34.3 - - + -
350A LEU* 2.9 28.5 + - + +
351A GLN* 3.8 5.2 - - - +
353A LYS* 1.3 75.8 - - - +
355A PHE* 1.3 57.9 + - - +
357A ALA* 3.5 3.0 + - - +
358A ALA* 2.9 24.4 + - - +
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Residues in contact with PHE 355 (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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322A LEU* 3.6 9.1 - - + +
351A GLN 2.9 17.5 + - - +
352A ARG 3.5 5.6 - - - +
353A LYS 3.2 0.4 - - - -
354A LEU* 1.3 74.6 - - - +
356A THR* 1.3 58.9 + - - +
358A ALA* 3.1 4.2 + - - +
359A VAL* 2.9 42.1 + - + +
368A LEU* 3.5 18.2 - - + -
370A TYR* 3.7 46.2 - + + -
383A GLN* 5.3 4.7 - - + -
384A VAL* 6.2 0.2 - - - -
386A TRP* 3.9 14.8 - + + -
387A ALA* 3.5 28.0 - - + -
391A PHE* 3.8 11.4 - + - -
394A LEU* 3.5 20.4 - - + -
463A PHE* 3.7 16.8 - + - -
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Residues in contact with THR 356 (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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352A ARG 2.9 15.3 + - - -
353A LYS* 3.6 10.1 - - - -
355A PHE* 1.3 74.3 - - - +
357A ALA* 1.3 63.7 + - - +
359A VAL* 3.2 3.1 + - - +
360A GLN* 2.9 46.3 + - + +
386A TRP* 3.8 7.8 - - - -
390A LYS* 4.3 10.0 - - - -
391A PHE* 3.5 31.9 - - + -
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Residues in contact with ALA 357 (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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241A LEU* 4.7 2.2 - - + -
294A GLY 3.6 24.5 - - - +
295A THR 4.3 9.2 - - - +
297A ALA* 5.3 1.6 - - + -
298A VAL* 3.9 22.4 - - + +
353A LYS 2.9 16.1 + - - +
354A LEU* 3.7 5.6 - - - +
356A THR* 1.3 78.1 - - - +
358A ALA* 1.3 62.1 + - - +
360A GLN* 3.5 3.4 + - - +
361A LEU* 3.2 30.7 + - + +
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Residues in contact with ALA 358 (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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241A LEU* 3.9 11.0 - - + +
320A ILE* 3.2 36.8 - - + +
322A LEU* 5.0 3.8 - - + -
354A LEU 2.9 15.4 + - - +
355A PHE* 3.1 11.4 + - - +
357A ALA* 1.3 74.1 - - - +
359A VAL* 1.3 64.9 + - - +
361A LEU* 3.1 11.6 + - - -
362A LEU* 3.2 11.2 + - - +
368A LEU* 3.8 16.2 - - + -
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Residues in contact with VAL 359 (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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355A PHE* 2.9 45.9 + - + +
356A THR 3.6 5.4 - - - +
358A ALA* 1.3 75.8 - - - +
360A GLN* 1.3 64.2 + - + +
362A LEU* 3.2 12.3 + - - +
368A LEU* 4.0 7.2 - - + -
391A PHE* 3.7 31.0 - - + -
393A CYS* 4.3 13.2 - - - -
394A LEU* 3.6 23.6 - - + -
465A LYS* 3.0 26.8 + - + -
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Residues in contact with GLN 360 (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 VAL* 3.3 36.1 - - + +
300A LEU* 6.0 0.3 - - - +
314A PRO* 3.3 13.4 - - + +
315A GLU* 2.9 23.9 + - - +
356A THR* 2.9 41.3 + - + +
357A ALA* 3.7 5.8 - - - +
358A ALA 3.2 0.2 - - - -
359A VAL* 1.3 77.7 - - + +
361A LEU* 1.3 57.9 + - - +
362A LEU 3.2 0.8 + - - -
391A PHE* 5.9 2.0 - - + -
465A LYS* 4.4 1.7 + - - +
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Residues in contact with LEU 361 (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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239A LEU* 4.0 21.5 - - + -
241A LEU* 4.9 3.1 - - + -
297A ALA* 3.9 30.5 - - + +
298A VAL* 4.3 8.3 - - + -
312A PHE* 3.3 40.4 - - + +
313A LEU 3.3 16.6 - - - +
314A PRO* 4.1 2.7 - - + -
315A GLU 3.5 5.4 - - - +
316A SER* 3.3 5.3 + - - +
317A PHE* 3.3 31.5 + - + +
320A ILE* 3.6 10.3 - - + -
357A ALA 3.2 19.6 + - - +
358A ALA* 3.1 7.8 + - - +
360A GLN* 1.3 76.0 - - - +
362A LEU* 1.3 58.1 + - - +
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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