Contacts of the helix formed by residues 386 - 398 (chain B) in PDB entry 3K6G
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 386 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B TYR* 3.3 23.9 - - - -
382B VAL* 2.8 26.1 + - - -
385B PHE* 1.3 77.9 - - - +
387B ALA* 1.3 66.1 + - - -
388B GLN 3.3 3.1 + - - -
389B ASN 3.4 0.6 + - - -
390B VAL* 3.2 19.6 + - - +
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Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B VAL* 3.9 23.1 - - + +
386B GLY* 1.3 71.0 - - - -
388B GLN* 1.3 64.2 + - + +
390B VAL* 3.3 6.0 + - - +
391B ALA* 3.1 24.6 + - - +
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Residues in contact with GLN 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B GLY 3.3 0.8 - - - -
387B ALA* 1.3 80.3 - - + +
389B ASN* 1.3 59.5 + - - +
391B ALA* 3.3 6.0 + - - +
392B ARG* 3.0 57.8 + - - +
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Residues in contact with ASN 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B SER* 5.2 0.7 + - - -
342B GLU* 4.4 1.7 - - - +
355B ARG* 2.9 38.8 + - - +
357B ASP* 3.1 10.1 + - - +
359B TYR* 3.4 9.7 - - - +
362B TRP* 3.7 13.5 + - - +
385B PHE* 2.8 35.8 + - + +
386B GLY 3.4 2.6 + - - -
388B GLN* 1.3 79.9 - - - +
390B VAL* 1.3 57.6 + - - +
392B ARG* 3.0 26.9 + - - +
393B ARG* 2.8 30.3 + - - +
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B TRP* 4.1 13.0 - - + -
370B LEU* 3.9 20.0 - - + -
378B ARG* 4.1 18.6 - - - +
381B LEU* 3.7 31.4 - - + +
382B VAL* 3.9 10.8 - - + +
385B PHE* 4.1 7.2 - - + -
386B GLY 3.2 15.3 + - - +
387B ALA 3.7 7.4 - - - +
388B GLN 3.2 0.2 - - - -
389B ASN* 1.3 76.4 - - - +
391B ALA* 1.3 63.4 + - - +
393B ARG* 3.3 2.8 + - - +
394B ILE* 3.0 29.3 + - + +
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Residues in contact with ALA 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B ALA 3.1 16.1 + - - +
388B GLN* 3.8 6.1 - - - +
390B VAL* 1.3 77.8 - - - +
392B ARG* 1.3 63.7 + - - +
394B ILE* 3.3 11.3 + - - +
395B GLU* 3.1 27.1 + - + +
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Residues in contact with ARG 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B SER* 4.5 13.7 - - - +
342B GLU* 3.4 38.4 + - - -
355B ARG* 4.9 0.4 - - - +
357B ASP* 5.5 0.2 + - - -
388B GLN* 3.0 51.8 + - - +
389B ASN* 3.0 31.9 + - - +
391B ALA* 1.3 78.0 - - - +
393B ARG* 1.3 51.2 + - - +
395B GLU* 3.3 6.6 + - + +
396B PHE* 2.8 36.1 + - + +
282E THR* 5.7 5.2 - - + -
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Residues in contact with ARG 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B LEU 2.7 30.7 + - - -
338B LYS* 4.1 8.5 - - - +
340B SER* 3.0 33.5 + - - +
362B TRP* 3.4 46.6 - - + +
367B ASP* 2.7 35.5 + - - +
370B LEU* 3.4 20.0 - - + -
389B ASN 2.8 17.9 + - - +
390B VAL 3.6 4.3 - - - +
392B ARG* 1.3 74.3 - - - +
394B ILE* 1.3 65.2 + - - +
396B PHE* 3.7 8.2 - - - -
397B ARG* 2.9 45.1 + - - +
309E ASP* 4.7 1.6 + - - -
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Residues in contact with ILE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B LEU* 3.8 23.1 - - + +
378B ARG* 3.9 31.2 - - - +
390B VAL* 3.0 25.3 + - + +
391B ALA* 3.3 11.6 + - - +
393B ARG* 1.3 74.8 - - - +
395B GLU* 1.3 66.7 + - + +
397B ARG* 3.6 1.5 + - - +
398B LYS* 3.0 38.6 + - + +
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Residues in contact with GLU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B ALA 3.1 16.4 + - - +
392B ARG* 3.7 9.6 - - + +
394B ILE* 1.3 82.4 - - + +
396B PHE* 1.3 65.3 + - - +
398B LYS* 3.5 31.2 + - - +
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Residues in contact with PHE 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B PHE 4.3 4.0 - - - -
337B LEU* 3.9 23.1 - - + -
340B SER* 3.3 42.4 - - - +
341B GLY* 3.7 10.3 - - - -
392B ARG* 2.8 20.8 + - + +
393B ARG* 3.2 15.0 + - - +
395B GLU* 1.3 75.7 - - - +
397B ARG* 1.3 67.8 + - + +
398B LYS 3.5 2.4 + - - -
282E THR* 5.2 2.7 - - + -
283E ILE 3.4 25.1 - - - -
284E GLY* 4.6 2.7 - - - -
285E MSE 3.4 58.8 + - + +
288E LEU* 4.6 4.0 - - + -
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Residues in contact with ARG 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B ARG* 3.8 15.1 - - - +
367B ASP* 3.4 38.3 + - - +
370B LEU* 4.9 6.1 - - + -
371B GLN* 6.5 0.4 - - - -
393B ARG* 2.9 44.3 + - - +
394B ILE* 3.8 2.2 - - - +
396B PHE* 1.3 82.3 - - + +
398B LYS* 1.3 63.0 + - - +
285E MSE 4.0 24.7 - - - +
309E ASP* 2.8 43.2 + - - -
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Residues in contact with LYS 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B ILE* 3.0 25.2 + - + +
395B GLU* 3.5 28.4 + - - +
396B PHE 3.3 4.6 - - - -
397B ARG* 1.3 82.0 - - - +
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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