Contacts of the helix formed by residues 389 - 404 (chain A) in PDB entry 3W6R
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 CYS 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A GLY* 1.3 68.1 - - - -
390A ASP* 1.3 67.5 + - - +
391A ARG* 3.6 23.1 - - - -
392A THR* 3.0 24.2 + - - +
393A VAL* 3.0 23.3 + - - +
414A ASP* 4.6 5.4 + - - +
417A ALA* 4.8 3.6 - - - +
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Residues in contact with ASP 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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387A SER* 5.8 2.9 - - - -
388A GLY 3.2 8.0 + - - +
389A CYS* 1.3 72.2 - - - +
391A ARG* 1.3 56.9 + - - +
393A VAL* 3.9 7.1 - - - +
394A LYS* 3.0 31.4 + - - +
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Residues in contact with ARG 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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389A CYS* 3.2 13.9 - - - -
390A ASP* 1.3 75.9 - - - +
392A THR* 1.3 60.2 + - - +
394A LYS* 3.4 4.8 + - - +
395A GLU* 3.0 61.8 + - + +
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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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389A CYS* 3.0 27.0 + - - +
391A ARG* 1.3 78.7 - - - +
393A VAL* 1.3 57.8 + - - +
395A GLU* 3.5 6.1 + - - +
396A LEU* 3.1 46.9 + - + +
412A VAL* 5.0 11.0 - - + -
417A ALA* 4.4 15.7 - - + -
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Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLY 4.3 3.6 - - - +
389A CYS 3.0 18.9 + - - +
390A ASP* 3.9 7.9 - - - +
392A THR* 1.3 76.0 - - - +
394A LYS* 1.3 57.2 + - - +
396A LEU* 3.5 8.8 + - - +
397A LYS* 3.0 28.3 + - + +
417A ALA* 3.8 20.2 - - + +
420A SER* 3.7 28.7 - - - +
421A LEU* 3.9 27.0 - - + +
424A ASP* 4.1 18.2 - - + +
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Residues in contact with LYS 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ASP 3.0 19.0 + - - +
391A ARG* 3.9 5.4 - - - +
393A VAL* 1.3 77.1 - - - +
395A GLU* 1.3 58.0 + - + +
397A LYS* 3.7 8.3 - - + +
398A GLU* 2.8 34.9 + - + +
424A ASP* 5.8 1.6 - - - -
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Residues in contact with GLU 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 ARG* 3.0 53.2 + - + +
392A THR* 3.9 6.0 - - - +
394A LYS* 1.3 75.0 - - + +
396A LEU* 1.3 64.2 + - + +
398A GLU* 3.8 5.9 - - - +
399A LYS* 3.1 39.1 + - + +
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Residues in contact with LEU 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 THR* 3.1 39.2 + - + +
393A VAL* 3.8 7.9 - - - +
395A GLU* 1.3 76.6 - - + +
397A LYS* 1.3 57.4 + - - +
399A LYS* 4.0 11.3 - - - +
400A PHE* 3.1 28.2 + - - +
407A PRO* 4.0 31.1 - - + +
408A LEU 5.5 1.1 - - - +
409A LEU* 4.6 9.2 - - + -
412A VAL* 4.1 26.0 - - + -
417A ALA* 5.0 7.0 - - + +
418A ILE* 4.5 9.4 - - + -
421A LEU* 4.2 24.3 - - + +
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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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348A GLU* 3.2 25.1 + - - +
365A ILE* 6.3 0.2 - - + -
393A VAL 3.0 17.7 + - - +
394A LYS* 3.7 9.0 - - + +
396A LEU* 1.3 76.1 - - - +
398A GLU* 1.3 59.3 + - - +
400A PHE* 3.3 8.5 + - + +
401A LEU* 3.0 56.9 + - + +
421A LEU* 4.0 17.4 - - + +
424A ASP* 3.1 22.4 + - + +
425A PHE* 5.6 4.0 - - + +
428A ASN* 3.0 32.7 - - - +
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Residues in contact with GLU 398 (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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394A LYS* 2.8 25.1 + - + +
395A GLU* 3.8 6.2 - - - +
396A LEU 3.4 0.2 - - - -
397A LYS* 1.3 71.7 - - - +
399A LYS* 1.3 66.2 + - - +
401A LEU* 3.5 6.1 + - - +
402A ARG* 2.9 64.7 + - - +
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Residues in contact with LYS 399 (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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395A GLU* 3.1 29.8 + - + +
396A LEU* 4.0 10.3 - - - +
398A GLU* 1.3 85.0 - - - +
400A PHE* 1.3 65.1 + - - +
402A ARG* 4.1 17.5 - - - +
403A VAL* 3.1 33.6 + - + +
405A THR 4.4 2.2 - - - +
407A PRO* 3.5 31.8 - - + +
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Residues in contact with PHE 400 (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* 3.7 37.2 - + + -
364A SER* 6.2 0.4 - - - -
365A ILE* 3.6 52.9 - - + -
396A LEU 3.1 18.4 + - - +
397A LYS* 3.3 9.6 + - + +
399A LYS* 1.3 78.1 - - - +
401A LEU* 1.3 70.8 + - + +
404A LYS* 2.9 34.5 + - + +
405A THR* 3.7 29.2 - - - +
406A VAL* 4.1 12.1 - - + -
407A PRO* 4.3 7.7 - - + +
425A PHE* 3.8 13.2 - + - -
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Residues in contact with LEU 401 (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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347A MET 5.3 4.5 - - - +
348A GLU* 3.7 37.7 - - + +
354A PHE* 4.0 11.9 - - + -
397A LYS* 3.0 48.1 + - + +
398A GLU* 4.1 4.7 - - - +
400A PHE* 1.3 96.8 - - + +
402A ARG* 1.3 65.3 + - - +
404A LYS* 4.2 15.9 + - - +
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Residues in contact with ARG 402 (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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398A GLU* 2.9 52.7 + - - +
399A LYS* 4.1 17.8 - - - +
401A LEU* 1.3 80.5 - - - +
403A VAL* 1.3 78.9 + - - +
404A LYS* 4.9 5.2 + - - -
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Residues in contact with VAL 403 (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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399A LYS* 3.1 20.3 + - + +
402A ARG* 1.3 103.5 - - - +
404A LYS* 1.3 69.4 + - - +
405A THR* 3.6 25.9 - - + +
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Residues in contact with LYS 404 (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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353A ASP 5.4 8.1 - - - +
354A PHE* 5.2 15.7 - - + -
400A PHE* 2.9 23.6 + - + +
401A LEU* 4.2 14.5 + - - +
402A ARG 3.4 6.1 + - - -
403A VAL* 1.3 80.9 - - - +
405A THR* 1.3 60.7 + - - +
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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