Contacts of the helix formed by residues 396 - 407 (chain B) in PDB entry 6WCZ
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 396 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395B CYS* 1.3 75.3 - - - +
397B LYS* 1.3 79.5 + - - +
398B GLU* 3.2 36.2 + - + +
399B GLU* 2.9 35.9 + - + +
400B PHE 3.5 3.8 + - - -
484B PHE* 4.6 5.2 - - - -
487B PHE* 3.7 8.8 - - - -
488B GLU* 5.1 1.6 - - - -
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Residues in contact with LYS 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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396B THR* 1.3 86.3 + - - +
398B GLU* 1.3 55.2 + - - +
400B PHE* 2.6 24.1 + - - +
401B ILE* 2.8 17.9 + - + +
433B TRP* 3.7 31.2 - - + -
440B ARG* 5.9 4.0 - - - +
484B PHE* 3.7 22.3 - - + -
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Residues in contact with GLU 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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396B THR* 3.2 25.3 + - + +
397B LYS* 1.3 78.1 - - - +
399B GLU* 1.3 74.6 + - - +
401B ILE* 3.6 14.4 - - + +
402B ASN* 3.0 34.0 + - - +
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Residues in contact with GLU 399 (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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395B CYS* 3.2 16.9 - - - +
396B THR* 2.9 42.4 + - + +
398B GLU* 1.3 90.8 - - - +
400B PHE* 1.3 48.9 + - - +
402B ASN* 3.9 2.4 - - - -
403B LYS* 2.6 38.2 + - - +
487B PHE* 4.6 8.9 - - + -
495B GLU* 5.5 16.4 - - - +
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Residues in contact with PHE 400 (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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396B THR 3.5 0.2 + - - -
397B LYS 2.6 18.1 + - - +
399B GLU* 1.3 73.2 - - - +
401B ILE* 1.3 60.0 + - - -
403B LYS* 3.9 8.3 - - + -
404B VAL* 2.9 46.4 + - + +
427B VAL* 6.1 3.1 - - + -
432B PHE* 6.2 4.3 - + - -
433B TRP* 5.4 7.9 - + - -
480B LEU* 5.0 15.9 - - + -
483B ARG* 5.0 6.3 - - + -
484B PHE* 3.5 41.1 - + + -
487B PHE* 3.6 48.0 - + + -
606B VAL* 6.6 0.2 - - + -
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Residues in contact with ILE 401 (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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397B LYS* 2.8 33.1 + - + +
398B GLU* 3.6 11.2 - - + +
400B PHE* 1.3 77.2 - - + +
402B ASN* 1.3 58.8 + - - +
404B VAL* 3.1 12.4 + - - +
405B ARG* 2.9 59.9 + - + +
427B VAL* 3.6 33.0 - - + -
428B ASN* 5.9 0.9 - - - +
433B TRP* 3.5 29.4 - - + -
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Residues in contact with ASN 402 (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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398B GLU* 3.0 19.7 + - - +
399B GLU* 4.5 3.4 - - - +
401B ILE* 1.3 76.9 - - - +
403B LYS* 1.3 61.9 + - - +
405B ARG* 3.4 45.4 + - - +
406B SER* 3.9 5.5 + - - -
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Residues in contact with LYS 403 (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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399B GLU 2.6 21.3 + - - +
400B PHE* 3.8 10.1 - - + +
401B ILE 3.1 0.4 - - - -
402B ASN* 1.3 77.4 - - - +
404B VAL* 1.3 60.7 + - - +
405B ARG 3.1 1.2 + - - -
406B SER* 3.5 12.4 + - - -
407B ASN* 4.2 2.4 + - - +
408B ALA* 3.9 23.6 + - + +
487B PHE* 3.3 39.3 - - + -
494B ASN* 4.2 20.8 + - - +
495B GLU* 4.2 17.9 + - - +
606B VAL* 5.4 7.8 - - - +
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Residues in contact with VAL 404 (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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400B PHE* 2.9 35.4 + - + +
401B ILE* 3.2 17.3 - - - +
403B LYS* 1.3 74.8 - - - +
405B ARG* 1.3 64.7 + - + +
406B SER 3.3 0.8 + - - -
407B ASN* 4.4 5.3 + - - -
408B ALA* 4.1 22.4 + - + +
409B ALA* 5.0 5.2 - - + +
410B LEU* 5.3 8.2 - - + +
423B ALA* 5.1 17.0 - - + +
424B VAL* 4.3 20.1 - - + +
427B VAL* 4.7 18.8 - - + -
480B LEU* 6.1 2.2 - - + -
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Residues in contact with ARG 405 (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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401B ILE* 2.9 38.5 + - + +
402B ASN* 3.4 41.2 + - - +
403B LYS 3.1 0.8 - - - -
404B VAL* 1.3 80.5 - - + +
406B SER* 1.3 64.1 + - - +
424B VAL* 5.8 3.4 - - - +
427B VAL* 6.2 2.2 - - + -
428B ASN* 5.9 1.4 + - - -
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Residues in contact with SER 406 (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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402B ASN 3.9 4.6 + - - -
403B LYS 3.5 8.0 + - - -
404B VAL 3.3 1.1 - - - -
405B ARG* 1.3 83.6 - - - +
407B ASN* 1.3 74.6 + - - +
410B LEU* 6.0 0.2 - - - +
806B MET* 6.0 3.8 - - - +
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Residues in contact with ASN 407 (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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403B LYS 4.2 2.3 + - - +
404B VAL 4.9 2.0 - - - -
405B ARG 3.9 0.2 - - - -
406B SER* 1.3 90.2 + - - +
408B ALA* 1.3 69.5 + - - +
409B ALA 3.2 2.0 + - - -
410B LEU* 3.6 14.1 - - - +
794B ARG* 2.4 42.0 + - - +
801B GLY 5.0 9.9 + - - -
802B LYS 5.0 7.9 + - - -
803B GLY* 5.5 3.6 - - - -
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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