Contacts of the helix formed by residues 384 - 397 (chain A) in PDB entry 5I94
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 GLY 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A GLU* 3.8 11.4 - - - -
381A ARG 3.4 6.9 + - - -
382A GLU 3.8 1.2 + - - -
383A SER* 1.3 78.6 - - - +
385A ASP* 1.3 68.5 + - - +
386A ARG* 3.2 3.1 - - - -
387A ASN* 3.3 23.4 + - - +
388A PHE* 3.2 22.9 + - - -
414A PHE* 4.2 0.8 - - - -
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Residues in contact with ASP 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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382A GLU 5.2 3.5 - - - +
383A SER* 3.9 4.4 - - - -
384A GLY* 1.3 81.6 + - - +
386A ARG* 1.3 58.4 + - - +
388A PHE* 2.9 11.3 + - - +
389A ALA* 2.7 28.5 + - - +
392D TYR* 3.6 32.2 - - + +
395D LYS* 2.8 44.4 + - + +
396D GLU* 4.4 13.5 - - + +
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Residues in contact with ARG 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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318A ASN 2.9 27.8 + - - -
319A LYS* 5.0 4.4 + - - +
321A PHE* 3.5 31.9 - - + -
334A ASN* 5.2 11.1 - - - +
384A GLY* 3.2 1.0 - - - -
385A ASP* 1.3 78.1 - - - +
387A ASN* 1.3 64.9 + - - +
389A ALA* 3.2 9.9 + - + +
390A ILE* 3.0 36.9 + - + +
393D TYR* 4.3 16.5 + - + -
396D GLU* 3.7 40.0 - - + +
397D LYS* 5.5 5.1 - - - +
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Residues in contact with ASN 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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334A ASN* 3.1 28.3 + - - +
338A ILE* 4.1 11.7 - - + +
380A GLU* 4.4 10.1 + - - -
384A GLY* 3.3 14.5 + - - +
385A ASP 3.2 0.4 - - - -
386A ARG* 1.3 80.2 - - - +
388A PHE* 1.3 57.3 + - - +
390A ILE* 3.4 9.9 + - - +
391A GLY 3.0 22.5 + - - -
410A LEU* 3.7 13.9 - - + +
413A TYR* 4.0 14.9 - - + -
414A PHE* 3.2 36.4 - - + -
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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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381A ARG* 4.1 14.1 - - + -
384A GLY 3.2 23.6 + - - -
385A ASP* 2.9 10.1 + - - +
387A ASN* 1.3 75.2 - - - +
389A ALA* 1.3 66.3 + - - +
391A GLY* 3.2 0.7 + - - -
392A TYR* 3.1 40.8 + + - -
407A VAL* 4.3 20.0 - - + -
410A LEU* 3.5 26.9 - - + +
411A ASP* 4.7 9.9 - - - -
414A PHE* 3.8 26.0 - + - -
392D TYR* 3.9 36.8 - + + -
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Residues in contact with ALA 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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321A PHE* 4.8 3.8 - - + -
385A ASP 2.7 16.0 + - - +
386A ARG* 3.2 14.6 - - + +
388A PHE* 1.3 74.5 - - - +
390A ILE* 1.3 63.4 + - + +
392A TYR 3.5 0.2 + - - -
393A TYR* 3.1 21.7 + - - +
389D ALA* 3.9 15.9 - - - +
392D TYR* 3.7 8.6 - - - +
393D TYR* 3.6 39.3 - - + +
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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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321A PHE* 3.7 41.3 - - + -
334A ASN* 4.0 26.7 - - + -
335A ALA* 3.8 28.7 - - + +
338A ILE* 4.1 7.4 - - + -
386A ARG* 3.0 32.1 + - + +
387A ASN* 3.7 12.1 - - - +
389A ALA* 1.3 76.0 - - - +
391A GLY* 1.3 53.4 + - - +
393A TYR* 3.2 3.0 + - - +
394A LEU* 2.8 48.1 + - + +
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Residues in contact with GLY 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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338A ILE* 5.0 0.4 - - - +
387A ASN 3.0 15.2 + - - -
388A PHE 3.2 4.2 + - - -
390A ILE* 1.3 77.5 - - - +
392A TYR* 1.3 57.0 + - - +
394A LEU* 3.4 8.1 + - - +
395A LYS* 2.9 28.6 + - - +
400A PHE* 4.9 1.6 - - - -
406A MET* 3.6 29.0 - - - +
410A LEU* 4.4 7.4 - - - -
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Residues in contact with TYR 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* 3.1 35.0 + + - +
391A GLY* 1.3 72.2 - - - +
393A TYR* 1.3 65.7 + - - +
395A LYS* 3.3 7.6 + - + +
396A GLU* 3.0 24.8 + - - +
406A MET* 3.5 24.2 - - + -
407A VAL* 4.2 13.1 - - + +
385D ASP* 3.6 30.9 - - + +
388D PHE* 3.8 30.6 - + + -
389D ALA* 3.5 24.0 - - - +
392D TYR* 3.6 33.0 + + - -
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Residues in contact with TYR 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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321A PHE* 4.0 26.0 - + + -
322A LEU* 3.6 30.7 - - + -
389A ALA 3.1 15.5 + - - +
390A ILE 3.2 7.8 + - - +
392A TYR* 1.3 78.0 - - - +
394A LEU* 1.3 63.7 + - + +
396A GLU* 3.3 5.6 + - + +
397A LYS* 3.1 44.7 + - + +
601A 69V 2.6 46.7 + - - -
319D LYS* 5.1 2.4 + - - +
321D PHE* 4.1 25.8 - + - -
386D ARG* 4.9 18.3 + - + -
389D ALA* 3.7 16.5 - - + +
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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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321A PHE* 4.9 1.8 - - + +
322A LEU* 4.1 9.9 - - + -
328A PRO* 4.1 18.8 - - + -
335A ALA* 3.7 21.1 - - + +
338A ILE* 3.6 31.2 - - + -
339A VAL* 3.8 6.1 - - + -
390A ILE* 2.8 31.8 + - + +
391A GLY 3.6 0.7 - - - +
393A TYR* 1.3 76.9 - - + +
395A LYS* 1.3 62.4 + - - +
397A LYS 3.3 1.7 + - - -
398A LYS 3.0 17.2 + - - -
399A CYS* 3.2 38.3 + - + -
400A PHE* 3.5 22.7 - - + -
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Residues in contact with LYS 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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391A GLY 2.9 18.2 + - - +
392A TYR* 3.6 10.9 - - + +
393A TYR 3.2 0.2 - - - -
394A LEU* 1.3 76.2 - - - +
396A GLU* 1.3 62.4 + - - +
398A LYS* 3.2 18.7 + - - +
400A PHE* 3.8 11.6 - - + -
404A THR 5.7 4.0 - - - +
406A MET* 4.2 31.8 - - + +
385D ASP* 2.9 36.3 + - - +
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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 TYR 3.0 16.2 + - - +
393A TYR* 3.8 6.1 - - + +
394A LEU 3.3 0.2 - - - -
395A LYS* 1.3 77.9 - - - +
397A LYS* 1.3 70.6 + - + +
398A LYS* 3.1 16.3 + - - +
383D SER 4.8 4.7 - - - +
385D ASP* 4.0 20.9 + - + +
386D ARG* 3.9 43.2 + - + +
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Residues in contact with LYS 397 (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* 3.9 13.9 - - + -
326A ASP* 3.7 26.3 + - - +
393A TYR* 3.1 39.2 + - + +
396A GLU* 1.3 82.8 - - + +
398A LYS* 1.3 72.1 + - - +
399A CYS* 3.6 18.2 - - - -
601A 69V 3.6 28.7 + - - -
319D LYS* 4.9 5.7 - - - +
386D ARG* 6.3 2.7 - - - +
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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