Contacts of the helix formed by residues 384 - 399 (chain B) in PDB entry 2Y48
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 THR 384 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382B ARG* 3.5 7.8 + - + +
383B TRP* 1.3 76.6 - - - +
385B THR* 1.3 64.4 + - - +
386B GLU* 3.7 12.4 + - - +
387B GLU* 2.9 52.3 + - - +
388B GLN* 3.0 9.4 + - - +
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Residues in contact with THR 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B TRP 3.6 1.2 + - - -
384B THR* 1.3 72.6 - - - +
386B GLU* 1.3 63.9 + - - +
388B GLN* 3.4 20.6 + - + +
389B LEU* 3.2 37.4 + - + +
428B PHE* 6.4 0.2 - - + -
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ILE* 4.1 25.0 - - + +
477A GLU* 4.3 12.8 - - - +
481A LYS* 4.9 4.2 + - - -
384B THR* 3.7 12.3 + - - +
385B THR* 1.3 76.9 - - - +
387B GLU* 1.3 66.0 + - + +
389B LEU* 3.2 9.3 + - - +
390B LEU* 3.0 40.8 + - + +
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B ARG 3.1 3.3 - - - +
383B TRP* 4.2 12.8 - - + -
384B THR* 2.9 44.0 + - - +
386B GLU* 1.3 83.9 - - + +
388B GLN* 1.3 66.1 + - - +
389B LEU 3.1 1.6 - - - -
390B LEU* 3.6 10.8 - - + +
391B ALA* 3.0 23.9 + - - +
409B ILE* 4.0 17.1 - - + +
411B ASN* 3.3 34.9 + - - +
412B LYS* 2.8 20.5 + - - -
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Residues in contact with GLN 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B TRP* 3.3 34.1 + - + +
384B THR 3.0 13.0 + - - +
385B THR* 3.4 20.3 + - + +
387B GLU* 1.3 76.8 - - - +
389B LEU* 1.3 58.0 + - + +
391B ALA* 3.2 8.2 - - - +
392B VAL* 3.0 31.2 + - - +
420B PHE* 4.2 9.0 - - + -
424B TYR* 3.9 22.0 + - - -
428B PHE* 3.2 36.8 - - + -
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A ILE* 4.0 32.3 - - + -
385B THR* 3.2 26.6 + - + +
386B GLU* 3.5 8.3 - - - +
387B GLU 3.1 0.4 - - - -
388B GLN* 1.3 78.6 - - + +
390B LEU* 1.3 67.8 + - - +
391B ALA 3.2 0.2 + - - -
392B VAL* 3.3 11.2 + - + +
393B GLN* 3.2 28.6 + - + +
428B PHE* 5.9 6.7 - - + -
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ILE* 4.5 13.9 - - + +
477A GLU* 4.6 3.1 - - + -
478A PHE* 3.8 45.1 - - + +
481A LYS* 3.8 29.6 - - + +
386B GLU* 3.0 31.3 + - + +
387B GLU* 3.6 16.4 - - + +
389B LEU* 1.3 73.7 - - - +
391B ALA* 1.3 50.3 + - - +
393B GLN* 3.1 9.2 + - - +
394B ALA* 2.8 35.4 + - - +
408B VAL* 4.7 3.4 - - + +
409B ILE* 4.3 24.9 - - + +
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Residues in contact with ALA 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B TRP* 4.3 1.8 - - + -
387B GLU 3.0 13.2 + - - +
388B GLN* 3.2 10.8 - - - +
389B LEU 3.1 0.2 - - - -
390B LEU* 1.3 72.9 - - - +
392B VAL* 1.3 68.5 + - - +
394B ALA* 2.7 17.8 + - - +
395B ILE* 2.8 18.0 + - + +
405B ILE* 4.9 3.4 - - + -
409B ILE* 3.6 24.4 - - + +
420B PHE* 3.9 25.8 - - + -
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Residues in contact with VAL 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B GLN 3.0 12.6 + - - +
389B LEU* 3.3 14.8 + - + +
391B ALA* 1.3 75.0 - - - +
393B GLN* 1.3 65.3 + - + +
395B ILE* 3.5 13.3 + - + +
396B ARG* 3.2 21.0 + - + +
420B PHE* 4.9 3.1 - - + -
428B PHE* 3.4 49.1 - - + +
430B ILE* 5.9 0.4 - - + -
433B VAL* 4.1 17.5 - - + +
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Residues in contact with GLN 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ILE* 3.4 36.1 + - - +
475A THR* 3.5 22.2 - - - +
478A PHE* 3.2 53.7 - - + +
389B LEU* 3.2 15.9 + - - +
390B LEU* 3.1 7.6 + - - +
391B ALA 3.0 0.6 - - - -
392B VAL* 1.3 78.3 - - + +
394B ALA* 1.3 66.3 + - - +
396B ARG* 3.2 16.3 + - - +
397B LYS* 3.3 10.2 + - - +
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A PHE* 3.6 15.7 - - + -
390B LEU 2.8 12.8 + - - +
391B ALA* 2.7 11.2 + - - +
393B GLN* 1.3 75.7 - - - +
395B ILE* 1.3 55.9 + - - +
397B LYS 3.3 0.3 + - - -
398B TYR* 2.9 41.7 + - + +
405B ILE* 3.9 30.3 - - + +
408B VAL* 4.2 13.5 - - + -
409B ILE* 5.1 0.4 - - + -
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Residues in contact with ILE 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B ALA* 2.8 16.8 + - + +
392B VAL* 3.6 13.9 - - + +
394B ALA* 1.3 72.0 - - - +
396B ARG* 1.3 58.7 + - - +
397B LYS 2.8 11.2 + - - -
399B GLY* 3.0 23.7 + - - +
405B ILE* 3.8 22.7 - - + -
420B PHE* 4.3 24.9 - - + -
421B PHE* 3.9 14.4 - - + -
430B ILE* 4.1 23.3 - - + -
433B VAL* 3.3 27.1 - - + -
434B LEU* 4.2 24.5 - - + +
437B TRP* 4.2 2.8 - - - +
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Residues in contact with ARG 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B VAL* 3.2 11.1 + - + +
393B GLN* 3.2 12.8 + - - +
395B ILE* 1.3 77.8 - - - +
397B LYS* 1.3 57.3 + - + +
433B VAL* 3.9 18.4 - - + +
436B GLU* 4.0 44.8 + - - +
437B TRP* 3.5 16.9 - - - +
440B GLU* 3.1 36.4 + - - +
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Residues in contact with LYS 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A PHE* 3.9 21.1 - - + -
482A SER* 3.5 15.0 + - - +
483A LYS* 4.6 11.9 - - - +
486A ASP* 3.7 12.1 + - - -
393B GLN 3.3 13.8 + - - +
394B ALA 4.1 2.0 - - - +
395B ILE 2.9 0.8 - - - -
396B ARG* 1.3 80.1 - - + +
398B TYR* 1.3 111.5 + - + +
437B TRP* 3.8 11.2 + - - -
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Residues in contact with TYR 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A PHE* 4.7 2.0 - + - -
482A SER* 3.7 7.8 + - - -
485A ARG* 3.5 24.3 + - - -
486A ASP* 2.5 34.7 + - - -
394B ALA* 2.9 34.2 + - + +
395B ILE 3.9 0.2 - - - -
397B LYS* 1.3 113.7 - - + +
399B GLY* 1.3 67.2 + - - +
400B ARG 3.0 4.0 + - - -
401B ASP* 3.1 21.1 + - + +
404B ALA* 4.0 19.3 - - + -
405B ILE* 4.3 12.3 - - + +
408B VAL* 3.9 20.0 - - + -
437B TRP* 3.7 12.1 - - - +
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Residues in contact with GLY 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ILE* 3.0 12.9 + - - +
398B TYR* 1.3 73.5 - - - +
400B ARG* 1.3 58.7 + - - -
405B ILE* 4.0 7.1 - - - +
421B PHE* 3.9 14.7 - - - -
434B LEU* 3.7 22.5 - - - +
437B TRP* 3.3 36.8 - - - +
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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