Contacts of the helix formed by residues 378 - 393 (chain A) in PDB entry 3HF8
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 378 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A GLU* 6.0 2.0 - - - -
321A CYS* 5.3 5.2 - - - -
323A GLN* 6.1 2.7 - - - +
376A SER* 3.5 5.9 - - - -
377A GLU* 1.3 80.0 - - - +
379A PHE* 1.3 62.2 + - - +
380A GLU* 3.5 17.4 + - - +
381A ASP* 3.0 23.3 + - - +
382A ALA* 2.9 28.9 + - - +
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Residues in contact with PHE 379 (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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190A CYS* 4.0 8.1 - - + -
192A GLU* 3.5 42.4 + - + -
280A LEU* 3.7 23.8 - - + -
283A GLU* 4.7 0.7 - - + -
285A SER* 3.5 37.8 - - - +
286A PHE* 3.9 25.1 - + + -
289A PHE* 4.5 8.8 - + + +
321A CYS* 5.2 5.4 - - + -
323A GLN* 5.8 0.7 - - - -
330A PHE* 3.6 47.1 - + + -
376A SER* 6.2 0.2 - - - -
378A SER* 1.3 73.2 - - - +
380A GLU* 1.3 69.1 + - - +
382A ALA* 3.9 6.5 - - + +
383A LYS* 3.1 24.4 + - - +
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Residues in contact with GLU 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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192A GLU* 5.4 3.1 - - - +
285A SER* 4.0 22.7 + - - -
378A SER* 3.2 18.1 - - - +
379A PHE* 1.3 82.2 + - - +
381A ASP* 1.3 61.4 + - - +
383A LYS* 3.4 18.9 + - - +
384A GLU* 3.1 28.2 + - + +
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Residues in contact with ASP 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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377A GLU* 3.7 30.3 + - + +
378A SER* 3.0 21.6 + - - +
380A GLU* 1.3 74.5 - - - +
382A ALA* 1.3 59.8 + - - +
384A GLU* 3.1 10.6 + - - +
385A LYS* 2.9 58.1 + - - +
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Residues in contact with ALA 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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289A PHE* 3.7 21.5 - - + -
315A THR* 5.2 0.9 - - + -
330A PHE* 5.8 2.7 - - + -
354A PHE* 4.0 16.0 - - + -
376A SER* 4.0 20.8 - - - +
378A SER 2.9 18.3 + - - +
379A PHE* 3.9 7.4 - - + +
381A ASP* 1.3 76.4 + - - +
383A LYS* 1.3 57.0 + - - +
385A LYS* 3.4 3.1 + - - +
386A MET* 2.9 33.3 + - - +
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Residues in contact with LYS 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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285A SER* 5.2 4.3 - - - +
288A GLN* 4.0 19.9 - - + +
289A PHE* 3.6 25.2 - - + +
292A GLU* 3.7 21.8 - - + +
379A PHE 3.1 17.6 + - - +
380A GLU* 3.5 17.9 - - - +
382A ALA* 1.3 76.9 - - - +
384A GLU* 1.3 67.0 + - - +
386A MET* 3.3 3.7 + - - +
387A ARG* 2.9 71.2 + - - +
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Residues in contact with GLU 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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380A GLU* 3.1 17.1 + - + +
381A ASP* 3.1 14.6 + - - +
383A LYS* 1.3 80.0 + - - +
385A LYS* 1.3 65.5 + - + +
387A ARG* 3.3 35.4 + - - +
388A GLU* 3.1 24.0 + - - +
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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
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354A PHE* 3.6 35.8 + - + +
355A ASP* 5.0 7.9 + - - +
356A PRO* 3.7 20.7 - - + +
377A GLU* 5.6 2.2 - - - -
381A ASP* 2.9 43.2 + - - +
382A ALA 3.7 4.7 - - - +
384A GLU* 1.3 76.2 - - + +
386A MET* 1.3 58.2 + - - +
388A GLU* 3.1 25.0 + - - +
389A PHE* 3.0 28.2 + - - +
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Residues in contact with MET 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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289A PHE* 3.7 22.4 - - + -
292A GLU* 6.5 1.6 - - + -
293A ILE* 4.4 15.9 - - + -
308A LEU* 3.7 30.3 - - + -
311A CYS* 3.7 40.6 - - + -
354A PHE* 3.9 14.8 - - + -
356A PRO* 3.9 8.3 - - - -
382A ALA 2.9 20.7 + - - +
383A LYS* 3.7 6.1 - - - +
384A GLU 3.3 0.2 - - - -
385A LYS* 1.3 73.2 - - - +
387A ARG* 1.3 60.7 + - + +
389A PHE* 3.7 7.9 - - + +
390A THR* 2.9 41.6 + - + +
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Residues in contact with ARG 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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288A GLN* 4.5 4.4 - - - +
292A GLU* 2.7 43.3 + - - +
383A LYS* 2.9 47.6 + - - +
384A GLU* 3.6 35.4 + - - +
385A LYS 3.3 0.2 - - - -
386A MET* 1.3 76.0 - - + +
388A GLU* 1.3 62.1 + - - +
390A THR* 3.1 17.9 + - - -
391A LYS* 3.6 22.9 + - - +
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Residues in contact with GLU 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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355A ASP* 5.6 1.7 - - - +
356A PRO* 5.8 1.6 - - + +
357A LYS* 5.5 6.6 + - - -
384A GLU 3.1 14.9 + - - +
385A LYS* 3.1 36.8 + - - +
387A ARG* 1.3 78.4 - - - +
389A PHE* 1.3 62.2 + - + +
391A LYS* 3.6 23.0 + - - +
392A THR* 3.7 12.5 + - - +
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Residues in contact with PHE 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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307A LYS* 4.2 13.0 - - + -
308A LEU* 5.1 0.7 - - + -
311A CYS* 4.2 13.5 - - - -
356A PRO* 3.4 26.9 - - + -
357A LYS* 3.9 28.0 - - + -
360A CYS* 4.0 22.0 - - - -
385A LYS 3.0 17.8 + - - +
386A MET* 3.7 19.1 - - + +
387A ARG 3.3 0.2 - - - -
388A GLU* 1.3 78.5 - - + +
390A THR* 1.3 63.0 + - + +
392A THR* 2.7 42.6 + - - -
393A ILE* 3.4 36.9 + - + +
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Residues in contact with THR 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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292A GLU 5.6 0.7 - - - +
293A ILE* 6.2 0.2 - - - -
296A ALA* 3.8 19.6 - - + +
308A LEU* 3.7 31.0 - - + -
386A MET* 2.9 25.1 + - + +
387A ARG* 3.1 18.0 + - - -
389A PHE* 1.3 77.2 - - + +
391A LYS* 1.3 60.7 + - - +
393A ILE* 3.2 28.3 + - + +
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Residues in contact with LYS 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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387A ARG* 3.6 20.1 + - - +
388A GLU* 3.6 14.4 - - - +
389A PHE 3.2 0.4 - - - -
390A THR* 1.3 80.7 + - - +
392A THR* 1.3 62.6 + - + +
393A ILE 3.3 5.2 + - - +
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Residues in contact with THR 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 GLU 3.9 11.9 - - - +
389A PHE* 2.7 33.0 + - - -
391A LYS* 1.3 80.9 - - + +
393A ILE* 1.3 63.2 + - - +
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Residues in contact with ILE 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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304A ALA* 3.9 45.1 - - + +
307A LYS* 4.2 22.4 - - + +
308A LEU* 4.3 12.3 - - + -
389A PHE* 3.9 40.8 - - + +
390A THR* 3.2 26.1 - - + +
391A LYS 3.3 5.2 - - - +
392A THR* 1.3 91.6 + - - +
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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