Contacts of the helix formed by residues 384 - 393 (chain D) in PDB entry 6T8G
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 LEU 384 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377C LYS* 4.4 15.0 - - - -
347D LEU* 4.5 11.7 - - + -
350D PHE* 4.3 28.7 - - + -
351D GLY 5.3 1.1 - - - +
352D VAL* 4.2 22.4 - - + -
380D ARG* 3.3 25.1 - - + +
381D ILE* 2.8 15.4 + - + +
383D ASN* 1.3 87.3 - - + +
385D ALA* 1.3 59.2 + - - +
386D LYS 3.5 1.3 - - - -
387D ASP* 3.8 24.5 - - + +
388D LEU* 2.9 35.3 + - + +
399D VAL* 6.0 0.4 - - - -
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Residues in contact with ALA 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D ILE 4.3 1.0 + - - -
382D SER 4.0 10.0 + - - +
383D ASN 3.6 2.2 - - - -
384D LEU* 1.3 76.5 - - - +
386D LYS* 1.3 62.5 + - + +
388D LEU* 3.8 3.4 - - - +
389D ALA* 2.9 29.7 + - - +
397D VAL* 4.0 24.0 - - - +
399D VAL* 5.0 8.3 - - + -
671D GLN* 3.7 27.1 - - - +
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Residues in contact with LYS 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378C VAL* 5.3 12.7 - - + +
401C GLU* 2.5 43.9 + - - -
385D ALA* 1.3 79.1 - - + +
387D ASP* 1.3 63.7 + - - +
389D ALA* 3.2 7.2 + - - +
390D ARG* 3.0 31.0 + - - +
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Residues in contact with ASP 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C LYS* 3.3 35.8 - - - +
378C VAL* 3.3 30.8 + - - +
350D PHE* 3.7 24.7 - - + -
383D ASN 4.4 4.3 - - - +
384D LEU* 3.5 21.9 + - + +
385D ALA 3.3 0.4 - - - -
386D LYS* 1.3 80.8 - - - +
388D LEU* 1.3 56.3 + - - +
390D ARG* 3.3 13.0 + - - +
391D SER* 2.9 29.7 + - - -
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Residues in contact with LEU 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D LEU* 3.9 14.6 - - + -
346D LYS* 4.7 6.7 - - + -
347D LEU* 3.8 29.6 - - + -
350D PHE* 4.8 3.7 - - + -
381D ILE* 6.3 0.9 - - + -
384D LEU* 2.9 21.3 + - + +
385D ALA* 3.9 3.1 - - - +
387D ASP* 1.3 74.2 - - - +
389D ALA* 1.3 59.5 + - - +
391D SER* 2.9 23.9 + - - +
392D LEU* 2.9 38.2 + - + +
397D VAL* 3.8 25.8 - - + -
399D VAL* 5.5 3.1 - - + -
411D ILE* 4.0 23.3 - - + -
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Residues in contact with ALA 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D ALA 2.9 18.8 + - - +
386D LYS* 3.4 9.9 - - - +
387D ASP 3.2 0.2 - - - -
388D LEU* 1.3 76.3 - - - +
390D ARG* 1.3 57.6 + - - +
392D LEU 3.1 1.2 + - - -
393D ALA* 2.7 26.7 + - - -
394D VAL* 3.4 22.0 + - + +
395D ILE 4.4 14.4 - - - +
396D SER* 4.5 3.6 - - - -
397D VAL* 3.7 17.9 - - + +
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Residues in contact with ARG 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C GLN* 4.7 6.1 - - - +
372C PRO* 3.4 33.8 + - - +
373C ALA 5.0 3.0 + - - -
376C VAL* 2.5 33.7 + - - +
377C LYS* 4.1 4.4 + - - +
378C VAL* 3.4 28.8 - - - +
401C GLU 5.3 7.4 - - - +
402C VAL* 6.3 1.8 - - + -
406C LYS 5.0 2.5 - - - +
407C THR* 3.3 44.9 + - - +
408C THR 4.9 2.9 - - - +
409C VAL* 3.8 17.0 - - - +
350D PHE* 3.9 12.6 - - - -
386D LYS 3.0 14.4 + - - +
387D ASP* 3.3 16.1 + - - +
389D ALA* 1.3 76.9 - - - +
391D SER* 1.3 66.3 + - - +
392D LEU 3.3 0.2 - - - -
393D ALA* 4.0 2.9 + - - +
394D VAL 5.7 0.2 - - - -
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Residues in contact with SER 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C THR* 4.8 8.1 - - - +
342D LEU* 5.4 1.7 - - - +
346D LYS* 3.7 41.6 - - - +
350D PHE* 4.6 9.5 - - - -
387D ASP 2.9 16.0 + - - -
388D LEU* 2.9 29.1 + - - +
390D ARG* 1.3 85.4 - - - +
392D LEU* 1.3 66.0 + - - +
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Residues in contact with LEU 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C THR* 5.5 0.2 - - - -
339D MET* 5.5 6.1 - - - +
342D LEU* 3.9 37.2 - - + +
343D LEU* 3.8 20.6 - - + +
346D LYS* 4.6 7.0 - - + -
388D LEU* 2.9 29.2 + - + +
389D ALA* 4.1 2.5 - - - +
391D SER* 1.3 89.7 - - - +
393D ALA* 1.3 69.4 + - - +
394D VAL* 4.1 13.8 - - + +
397D VAL* 5.1 2.0 - - + -
413D ILE* 3.8 32.5 - - + -
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Residues in contact with ALA 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C GLY* 3.9 28.4 - - - +
406C LYS 4.2 18.8 - - - +
407C THR* 4.4 9.2 - - + -
389D ALA 2.7 10.3 + - - -
390D ARG* 4.0 3.1 + - - +
391D SER 3.7 1.4 - - - -
392D LEU* 1.3 81.8 - - - +
394D VAL* 1.3 61.5 + - - +
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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