Contacts of the helix formed by residues 383 - 397 (chain A) in PDB entry 2W8D
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 LYS 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A GLU* 3.2 30.5 + - - +
376A ASN* 2.8 16.4 + - - +
377A THR 4.1 14.8 + - - -
378A LYS* 4.2 18.6 - - + -
381A GLY 3.5 0.2 + - - -
382A MSE 1.3 73.3 - - - +
384A ASP* 1.3 64.9 + - - +
386A PRO* 3.3 11.8 - - + +
387A PHE* 3.0 22.5 + - - +
410A SER* 3.4 7.0 - - - +
417A MSE 4.1 15.9 - - + -
418A ASP* 4.3 21.7 + - - +
421A ASP* 2.8 30.3 + - - +
443A TYR* 3.6 13.7 - - - +
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Residues in contact with ASP 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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382A MSE 4.4 0.3 - - - +
383A LYS* 1.3 71.6 - - - +
385A LYS* 1.3 57.6 + - - +
387A PHE* 4.0 8.5 - - - -
388A PHE* 2.8 40.3 + - + -
408A THR* 3.4 17.9 - - - -
409A LEU* 2.9 24.8 + - - +
410A SER* 3.0 27.5 + - - +
411A ASN 4.5 1.2 + - - -
443A TYR* 4.0 2.9 + - + -
444A LEU* 3.4 25.1 - - - +
447A SER* 3.3 22.0 - - - +
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Residues in contact with LYS 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP* 1.3 77.1 - - - +
386A PRO* 1.4 64.5 - - + +
389A LYS* 3.2 17.7 + - - +
421A ASP 3.4 19.6 + - - -
443A TYR* 3.1 36.1 + - + +
446A GLN* 3.1 44.3 + - - -
447A SER* 3.6 15.5 - - - +
450A GLN* 3.3 27.8 + - - +
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Residues in contact with PRO 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU 5.4 0.7 - - - +
376A ASN* 4.0 21.3 - - + +
382A MSE 3.8 20.0 - - + -
383A LYS* 3.3 24.9 - - + +
385A LYS* 1.4 92.5 - - + +
387A PHE* 1.3 62.4 + - - +
389A LYS* 3.7 8.0 - - + +
390A GLU* 3.1 37.4 + - - +
443A TYR* 3.8 6.3 - - - +
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Residues in contact with PHE 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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342A PHE* 3.7 17.5 - - + -
343A HIS* 3.6 20.0 - - - -
344A GLY* 3.9 11.9 - - - -
370A TYR* 3.3 34.7 - + - -
382A MSE 3.9 19.4 - - + +
383A LYS 3.0 21.2 + - - +
384A ASP* 3.6 15.5 - - - +
386A PRO* 1.3 76.7 - - - +
388A PHE* 1.3 92.5 + + - +
391A SER* 2.8 30.3 + - - -
406A PHE* 3.8 19.1 - + + -
407A ILE 4.2 16.4 - - - -
408A THR* 4.8 0.7 - - - -
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Residues in contact with PHE 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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250A VAL* 4.3 6.1 - - + -
384A ASP* 2.8 30.7 + - + +
387A PHE* 1.3 80.9 - + - +
389A LYS* 1.3 66.1 + - - +
391A SER* 3.5 8.6 + - - -
392A MSE 3.5 21.0 + - - +
406A PHE* 3.7 30.7 - + + -
408A THR* 3.7 28.0 - - + -
447A SER* 3.7 24.7 - - - -
448A ILE* 3.9 27.4 - - + -
450A GLN* 3.4 18.4 - - - +
451A PHE* 3.5 39.0 - + + -
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Residues in contact with LYS 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 LYS 3.2 12.8 + - - +
386A PRO* 3.4 11.4 + - + +
388A PHE* 1.3 74.3 - - - +
390A GLU* 1.3 65.8 + - + +
392A MSE 3.2 23.8 + - + +
393A PRO* 3.7 4.3 - - - +
450A GLN* 3.3 24.5 - - - +
454A ASP* 2.8 31.7 + - - +
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Residues in contact with GLU 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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369A TYR 4.7 2.9 - - - +
370A TYR* 3.5 23.7 - - + +
371A ASP* 2.9 36.8 + - - +
376A ASN* 3.7 19.8 + - - -
382A MSE 3.7 7.2 - - - +
386A PRO* 3.1 21.2 + - - +
389A LYS* 1.3 79.2 - - + +
391A SER* 1.3 62.7 + - - +
392A MSE 3.4 0.5 + - - -
393A PRO* 3.5 16.6 - - - +
394A LEU* 3.7 13.5 - - - +
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Residues in contact with SER 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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342A PHE* 4.0 3.8 - - - -
370A TYR* 2.7 26.6 + - - -
387A PHE* 2.8 29.4 + - - -
388A PHE* 3.8 7.6 - - - -
389A LYS 3.3 0.6 - - - -
390A GLU* 1.3 77.4 - - - +
392A MSE 1.3 53.0 + - - +
394A LEU* 3.2 8.8 + - - +
395A LEU* 2.8 36.5 + - - +
406A PHE* 3.5 27.5 - - - -
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Residues in contact with MSE 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 PHE 3.5 15.9 - - - +
389A LYS* 3.2 16.4 + - + +
391A SER* 1.3 76.9 - - - +
393A PRO* 1.4 66.2 - - + +
395A LEU* 2.9 12.8 + - + +
396A GLU* 2.8 43.9 + - - +
451A PHE* 3.7 24.9 - - - -
454A ASP* 3.8 35.9 - - + +
455A LEU* 3.7 25.1 - - + +
458A ASP* 3.0 28.3 - - - +
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Residues in contact with PRO 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 LYS 3.7 6.1 - - - +
390A GLU* 3.5 15.3 - - - +
392A MSE 1.4 93.7 - - + +
394A LEU* 1.3 67.2 + - + +
396A GLU* 3.9 13.2 - - + +
397A SER* 3.2 23.2 + - - -
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Residues in contact with LEU 394 (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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342A PHE* 3.8 13.9 - - + -
365A PHE* 4.1 33.9 - - + -
369A TYR* 4.2 31.9 - - + +
370A TYR* 4.4 12.1 - - + +
390A GLU 3.7 20.2 - - - +
391A SER* 3.5 11.4 - - - +
392A MSE 3.1 0.6 - - - -
393A PRO* 1.3 80.3 - - + +
395A LEU* 1.3 62.4 + - - +
397A SER* 3.1 23.1 + - - +
398A LEU* 3.4 11.5 - - - +
1637A PG4 6.0 1.6 - - - -
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Residues in contact with LEU 395 (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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248A ILE* 4.5 4.7 - - + -
342A PHE* 4.1 15.6 - - + -
391A SER 2.8 17.7 + - - +
392A MSE 2.9 12.8 + - + +
394A LEU* 1.3 78.1 - - - +
396A GLU* 1.3 56.5 + - + +
397A SER 3.2 0.2 - - - -
398A LEU* 3.2 28.2 + - + +
402A PHE* 3.8 34.7 - - + -
404A THR* 3.8 23.3 - - + +
406A PHE* 4.2 16.2 - - + -
451A PHE* 4.8 0.9 - - + -
455A LEU* 4.0 20.6 - - + -
460A LEU* 3.8 21.0 - - + +
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Residues in contact with GLU 396 (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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392A MSE 2.8 37.5 + - + +
393A PRO* 3.9 10.1 - - + +
395A LEU* 1.3 75.7 - - + +
397A SER* 1.3 59.8 + - - +
398A LEU 3.3 3.6 + - - +
458A ASP* 2.5 45.4 - - + +
460A LEU* 4.2 13.0 - - + -
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Residues in contact with SER 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A PRO 3.2 14.6 + - - -
394A LEU* 3.1 15.2 + - - +
395A LEU 3.2 1.6 - - - -
396A GLU* 1.3 77.3 - - - +
398A LEU* 1.3 62.6 + - - +
399A PRO* 3.5 2.6 - - - +
1637A PG4 3.4 39.3 - - - -
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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