Contacts of the helix formed by residues 379 - 393 (chain A) in PDB entry 6YB9
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 SER 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A CYS* 3.6 6.2 - - - -
377A VAL* 3.9 1.6 - - - +
378A LEU* 1.3 76.3 - - - +
380A PRO* 1.3 64.5 - - - +
381A GLU* 3.6 13.7 + - - +
382A GLY* 3.1 19.3 + - - -
383A SER* 3.0 22.2 + - - -
505A EDO 3.1 36.8 + - - -
370B SER* 5.8 4.5 - - - -
372B LEU 5.3 0.4 - - - -
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Residues in contact with PRO 380 (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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280A HIS* 4.0 32.8 - - + +
283A LYS* 4.2 17.9 - - + -
284A ILE* 3.7 29.6 - - + +
350A CYS* 3.7 9.9 - - - -
378A LEU 3.6 7.1 - - - +
379A SER* 1.3 82.6 - - - +
381A GLU* 1.3 78.8 + - - +
383A SER* 2.9 18.4 + - - +
384A ALA* 3.4 4.9 + - - +
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Residues in contact with GLU 381 (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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283A LYS* 4.0 25.8 - - - +
287A ALA* 4.1 23.1 - - + +
291A PHE* 5.5 0.9 - - - -
379A SER* 3.6 11.6 + - - +
380A PRO* 1.3 84.7 - - - +
382A GLY* 1.3 62.4 + - - +
384A ALA* 3.2 5.7 + - - +
385A GLN* 3.0 23.5 + - - +
371B GLY 6.3 1.1 - - - +
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Residues in contact with GLY 382 (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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377A VAL* 3.6 8.2 - - - +
379A SER* 3.1 22.0 + - - -
380A PRO 3.2 0.2 - - - -
381A GLU* 1.3 78.1 - - - +
383A SER* 1.3 55.2 + - - +
385A GLN* 3.3 8.3 + - - +
386A PHE* 2.9 29.3 + - - +
372B LEU 3.9 20.6 - - - -
373B GLY* 3.7 4.7 - - - -
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Residues in contact with SER 383 (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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284A ILE* 3.7 22.5 - - - +
326A VAL* 4.1 7.4 - - - +
348A ILE* 4.0 14.6 - - - +
350A CYS* 4.0 16.6 - - - -
377A VAL* 3.7 15.7 - - - +
379A SER 3.0 12.5 + - - -
380A PRO* 2.9 20.5 + - - +
382A GLY* 1.3 72.0 - - - +
384A ALA* 1.3 59.8 + - - +
386A PHE* 3.4 4.1 + - - +
387A ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 384 (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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268A VAL* 6.4 0.2 - - - -
284A ILE* 3.8 10.8 - - + +
287A ALA* 3.6 28.9 - - + +
288A CYS* 3.8 27.2 - - - +
291A PHE* 4.5 3.4 - - + -
293A ILE* 5.3 1.0 - - - +
326A VAL* 6.3 0.2 - - - -
380A PRO 3.4 3.8 + - - +
381A GLU 3.2 8.9 + - - +
383A SER* 1.3 78.8 + - - +
385A GLN* 1.3 54.8 + - - +
387A ALA* 3.1 7.4 + - - +
388A ALA* 2.8 34.8 + - - +
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Residues in contact with GLN 385 (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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291A PHE* 3.9 22.5 - - + -
381A GLU 3.0 12.0 + - - +
382A GLY* 3.3 11.0 + - - +
384A ALA* 1.3 77.1 - - - +
386A PHE* 1.3 55.5 + - - +
388A ALA* 3.2 2.8 + - - +
389A GLN* 2.8 55.4 + - - +
402A LEU* 4.2 13.9 - - + +
405A SER* 5.7 3.8 + - - -
406A ILE* 6.0 3.6 - - - +
340B SER 5.5 2.0 + - - -
371B GLY* 3.3 39.4 + - - -
372B LEU 3.5 5.4 + - - +
373B GLY* 3.8 9.5 - - - +
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Residues in contact with PHE 386 (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 ILE* 3.6 20.9 - - + -
377A VAL* 4.5 4.5 - - + -
382A GLY 2.9 12.9 + - - +
383A SER* 3.7 6.7 - - - +
384A ALA 3.2 0.2 - - - -
385A GLN* 1.3 72.2 - - - +
387A ALA* 1.3 65.1 + - - +
389A GLN* 3.1 16.5 + - - +
390A ILE* 3.0 32.9 + - + +
346B PRO* 3.9 25.4 - - + -
347B VAL 3.4 23.8 - - - -
348B ILE* 4.4 4.3 - - + -
373B GLY* 3.0 26.4 - - - +
375B SER* 3.3 24.9 - - - -
386B PHE* 3.3 34.8 - + - -
390B ILE* 4.5 1.8 - - + -
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Residues in contact with ALA 387 (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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268A VAL* 3.8 31.0 - - + -
288A CYS* 5.3 0.2 - - - -
293A ILE* 4.7 0.9 - - + -
324A VAL* 4.3 15.7 - - + -
326A VAL* 5.2 1.3 - - + -
348A ILE* 4.3 3.6 - - + +
383A SER 2.9 14.9 + - - +
384A ALA* 3.1 11.0 + - - +
386A PHE* 1.3 76.5 - - - +
388A ALA* 1.3 59.6 + - - +
390A ILE* 3.3 14.5 + - - +
391A PHE* 3.1 29.8 + - - -
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Residues in contact with ALA 388 (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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291A PHE* 3.7 34.1 - - + -
293A ILE* 3.7 15.4 - - + +
384A ALA 2.8 15.7 + - - +
385A GLN 3.4 8.7 - - - +
387A ALA* 1.3 71.1 - - - +
389A GLN* 1.3 54.0 + - - +
391A PHE 3.0 2.1 + - - +
392A GLY* 2.7 31.9 + - - -
398A VAL* 3.2 17.1 - - + +
402A LEU* 3.8 8.7 - - + -
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Residues in contact with GLN 389 (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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385A GLN* 2.8 47.4 + - - +
386A PHE* 3.1 29.7 + - - +
388A ALA* 1.3 71.3 - - - +
390A ILE* 1.3 63.6 + - - +
392A GLY* 3.3 9.7 + - - -
393A LEU* 3.6 6.9 + - - +
402A LEU* 3.6 17.5 - - + +
340B SER* 4.6 8.7 + - - +
343B THR 4.3 11.7 + - - -
344B ALA* 3.3 20.8 - - - +
345B TYR* 4.1 8.0 - - - +
346B PRO* 3.8 30.6 - - + +
347B VAL* 4.5 2.3 + - - -
373B GLY* 4.2 12.0 - - - +
374B CYS 4.7 0.2 + - - -
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Residues in contact with ILE 390 (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 VAL* 4.0 18.6 - - + -
346A PRO* 4.5 4.9 - - + -
348A ILE* 4.6 3.4 - - + -
386A PHE* 3.0 44.2 + - + +
387A ALA* 3.4 10.3 - - - +
388A ALA 3.2 0.2 - - - -
389A GLN* 1.3 75.5 - - - +
391A PHE* 1.3 61.8 + - - +
393A LEU* 3.4 21.1 + - - +
394A SER* 4.5 2.3 + - - -
346B PRO* 4.2 8.7 - - + -
386B PHE* 4.4 6.7 - - + -
390B ILE* 3.7 40.5 - - + +
393B LEU* 3.3 33.6 - - + +
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Residues in contact with PHE 391 (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 GLN 4.7 1.6 - - - -
266A CYS* 3.6 35.2 - - + -
267A ARG 3.3 38.4 - - - -
268A VAL* 4.3 7.9 - - + -
293A ILE* 4.1 9.6 - - + -
322A PRO* 3.6 22.9 - - + -
324A VAL* 3.6 27.8 - - + -
387A ALA 3.1 20.4 + - - -
388A ALA 3.0 7.3 + - - +
390A ILE* 1.3 72.6 - - - +
392A GLY* 1.3 59.3 + - - +
393A LEU 3.1 1.1 - - - -
394A SER* 3.0 12.0 + - - -
395A ASN* 2.8 28.6 + - - +
398A VAL* 4.5 8.3 - - + -
393B LEU* 4.0 22.0 - - + -
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Residues in contact with GLY 392 (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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388A ALA 2.7 19.7 + - - -
389A GLN 3.7 5.8 - - - -
390A ILE 3.2 0.8 - - - -
391A PHE* 1.3 74.0 - - - +
393A LEU* 1.3 56.8 + - - +
394A SER 3.1 0.6 + - - -
395A ASN 3.7 11.0 - - - -
398A VAL* 4.0 0.9 - - - +
399A TRP* 3.6 32.4 - - - +
402A LEU* 4.6 1.8 - - - -
503A EDO 2.9 25.3 + - - -
345B TYR* 5.2 0.4 - - - -
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Residues in contact with LEU 393 (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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389A GLN 3.6 6.4 + - - +
390A ILE 3.4 10.3 + - - +
391A PHE 3.1 0.6 - - - -
392A GLY* 1.3 75.0 - - - +
394A SER* 1.3 60.8 + - - +
503A EDO 3.9 13.7 + - - -
322B PRO* 4.1 25.7 - - + +
323B THR 3.6 23.1 - - - +
324B VAL* 4.1 3.4 - - + -
345B TYR* 3.5 33.7 - - + -
346B PRO* 4.0 12.6 - - + -
390B ILE* 3.5 33.7 - - + +
391B PHE* 3.9 20.2 - - + -
394B SER* 5.6 1.1 - - - +
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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