Contacts of the helix formed by residues 389 - 400 (chain A) in PDB entry 3WOO
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 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A GLN 4.3 6.3 + - - +
386A SER* 3.4 7.2 + - - -
387A LYS 3.1 0.6 - - - -
388A ALA* 1.3 90.6 - - + +
390A ARG* 1.3 55.4 + - - +
391A ASP 3.3 2.6 + - - -
392A ARG* 3.4 36.4 + - - +
393A ASP* 2.7 48.7 + - - -
470A ASP 5.9 0.9 - - - +
471A GLN* 3.5 11.2 - - - +
541A GLU* 5.0 3.3 + - - +
545A ARG* 5.0 5.1 + - - +
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Residues in contact with ARG 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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287A ASN* 3.8 24.2 + - - +
291A TRP* 3.3 73.6 - - + +
386A SER 3.4 11.8 + - - +
387A LYS* 3.1 54.1 + - - +
388A ALA 3.6 0.6 - - - -
389A THR* 1.3 76.7 - - - +
391A ASP* 1.3 66.8 + - - +
393A ASP* 3.9 4.8 - - - +
394A LEU* 2.9 32.7 + - - +
471A GLN* 3.9 0.6 - - - +
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Residues in contact with ASP 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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291A TRP* 3.2 32.7 + - - -
295A THR* 5.6 0.9 - - - +
389A THR 3.3 0.6 - - - -
390A ARG* 1.3 80.4 + - - +
392A ARG* 1.3 61.7 + - - +
394A LEU* 3.9 1.2 - - - +
395A THR* 2.7 36.1 + - - +
467A LEU* 3.5 22.0 - - + -
468A PRO* 5.8 0.2 - - + -
471A GLN* 3.5 13.1 + - + +
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A THR* 3.5 33.3 + - - +
391A ASP* 1.3 81.1 - - - +
393A ASP* 1.3 82.8 + - - +
395A THR* 4.0 0.3 - - - -
396A LEU* 2.9 37.2 + - + +
464A TYR* 6.1 0.2 - - + -
467A LEU* 3.8 8.5 - - + +
470A ASP 5.5 3.6 + - - -
471A GLN* 3.1 45.0 - - - +
472A ARG 4.5 4.3 + - - -
473A VAL* 4.1 25.1 - - + -
537A LYS* 5.4 5.5 - - - +
538A LEU* 3.5 24.3 - - - +
541A GLU* 3.4 26.9 + - - -
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Residues in contact with ASP 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A SER 4.6 2.8 - - - +
389A THR* 2.7 39.0 + - - +
390A ARG* 3.9 4.6 + - - +
392A ARG* 1.3 109.5 + - - +
394A LEU* 1.3 64.2 + - - +
396A LEU* 4.3 2.9 - - - +
397A ALA* 3.2 24.4 + - - +
538A LEU* 3.8 13.4 - - + +
541A GLU* 5.3 0.7 - - - +
542A ARG* 5.9 4.1 - - - +
545A ARG* 4.5 12.0 + - - -
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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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291A TRP* 3.7 25.8 - - + -
292A THR* 5.9 0.9 - - + -
295A THR* 3.8 22.4 - - + -
296A ILE* 4.2 24.7 - - + -
299A HIS* 4.7 7.6 - - + +
390A ARG 2.9 17.2 + - - +
391A ASP* 4.0 2.2 - - - +
393A ASP* 1.3 76.1 - - - +
395A THR* 1.3 65.8 + - - +
397A ALA* 3.4 5.6 + - + +
398A LEU* 3.0 47.4 + - + +
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Residues in contact with THR 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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299A HIS* 5.0 5.9 + - - -
391A ASP* 2.7 28.2 + - - +
392A ARG 4.0 1.6 - - - -
394A LEU* 1.3 74.9 - - - +
396A LEU* 1.3 57.6 + - - +
398A LEU 3.9 0.2 - - - -
399A PHE* 2.9 28.4 + - + +
460A TRP* 4.1 27.5 - - + +
463A GLU* 4.3 5.9 + - + +
464A TYR* 3.9 38.4 - - + +
467A LEU* 4.2 15.9 - - + +
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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 ARG* 2.9 18.6 + - + +
393A ASP* 4.3 2.0 - - - +
395A THR* 1.3 73.6 - - - +
397A ALA* 1.3 65.7 + - - +
399A PHE* 3.4 8.3 + - + +
400A ASN* 3.1 49.8 + - - +
464A TYR* 5.4 9.7 - - + -
473A VAL* 4.0 25.8 - - + -
476A VAL* 4.0 18.6 - - + -
527A TYR* 4.0 14.1 - - - +
531A VAL* 5.5 2.0 - - + -
534A THR* 4.8 4.7 - - + -
535A LEU* 4.0 20.0 - - + -
538A LEU* 4.0 20.4 - - + -
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Residues in contact with ALA 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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393A ASP 3.2 18.3 + - - +
394A LEU* 3.7 7.6 - - + +
396A LEU* 1.3 77.8 - - - +
398A LEU* 1.3 61.9 + - + +
400A ASN* 3.5 7.8 + - - +
401A ASN* 3.1 26.6 + - - +
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Residues in contact with LEU 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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296A ILE* 5.6 3.6 - - + -
299A HIS* 4.6 6.1 - - + -
300A TYR* 4.8 25.6 - - + +
394A LEU* 3.0 41.9 + - + +
397A ALA* 1.3 77.9 - - + +
399A PHE* 1.3 65.9 + - - +
401A ASN* 3.1 33.6 + - + +
402A THR* 3.6 4.3 + - - +
460A TRP* 3.4 50.0 + - + -
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Residues in contact with PHE 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 THR* 2.9 20.4 + - + +
396A LEU* 3.4 10.5 + - + +
398A LEU* 1.3 77.3 - - - +
400A ASN* 1.3 58.1 + - - +
401A ASN 3.3 0.5 + - - -
402A THR* 3.0 26.0 + - - +
405A LEU* 3.3 25.3 - - + +
457A GLN* 3.9 23.1 - - + -
460A TRP* 3.5 33.0 - - + +
461A LEU* 3.4 38.4 - - + -
464A TYR* 5.9 6.7 - + + -
476A VAL* 4.9 8.3 - - + -
479A TRP* 4.3 11.7 - + - -
495A LEU* 4.8 1.3 - - + -
527A TYR* 3.5 33.4 - + - -
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Residues in contact with ASN 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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396A LEU* 3.1 28.2 + - - +
397A ALA* 3.7 7.9 - - - +
399A PHE* 1.3 76.2 - - - +
401A ASN* 1.3 56.1 + - - +
402A THR 3.5 0.7 - - - -
405A LEU* 3.6 6.6 - - - +
406A GLY* 3.0 29.1 + - - -
409A THR* 4.2 12.3 + - + +
527A TYR* 2.7 38.5 + - - -
531A VAL* 4.9 0.6 - - - +
535A LEU* 3.7 34.7 - - + +
806A GOL 5.4 1.3 + - - +
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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