Contacts of the helix formed by residues 406 - 416 (chain A) in PDB entry 4PJW
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 406 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A LYS* 4.2 10.7 + - - +
404A VAL 4.4 3.1 - - - +
405A LEU* 1.3 77.3 - - - +
407A ALA* 1.3 65.3 + - - +
408A GLU* 3.5 21.7 + - - +
409A ASP* 2.7 39.3 + - - +
410A CYS* 3.0 26.0 + - - -
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Residues in contact with ALA 407 (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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406A THR* 1.3 74.8 - - - +
408A GLU* 1.3 69.2 + - + +
410A CYS* 3.4 6.3 + - - +
411A GLU* 2.8 32.0 + - - +
414A TYR* 5.6 0.2 - - - -
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Residues in contact with GLU 408 (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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406A THR* 3.1 17.8 + - - +
407A ALA* 1.3 90.6 + - + +
409A ASP* 1.3 66.2 + - - +
411A GLU* 3.9 6.0 - - - +
412A ASN* 3.1 35.4 + - - +
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Residues in contact with ASP 409 (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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372A LYS* 2.9 40.0 + - - +
373A ASP* 4.5 1.9 - - - +
376A VAL* 4.1 27.1 - - + +
405A LEU* 4.4 10.8 - - + -
406A THR* 2.7 42.4 + - - +
408A GLU* 1.3 80.4 - - - +
410A CYS* 1.3 62.5 + - - +
412A ASN* 3.4 8.8 + - - +
413A VAL* 3.4 24.4 + - - +
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Residues in contact with CYS 410 (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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405A LEU* 4.0 25.8 - - - -
406A THR 3.0 18.0 + - - +
407A ALA* 3.8 6.1 - - - +
409A ASP* 1.3 78.6 - - - +
411A GLU* 1.3 64.9 + - - +
413A VAL* 3.0 4.5 + - - +
414A TYR* 3.0 47.9 + - + +
431A PHE* 4.1 14.4 - - + -
435A LYS* 3.3 31.2 - - - -
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Residues in contact with GLU 411 (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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407A ALA 2.8 22.8 + - - +
408A GLU* 3.9 8.1 - - - +
410A CYS* 1.3 72.6 - - - +
412A ASN* 1.3 63.8 + - - +
414A TYR* 3.2 33.8 + - - +
415A HIS* 3.2 45.5 + - + +
467A PHE* 5.8 0.9 - - - -
470A GLU* 5.1 9.0 - - - +
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Residues in contact with ASN 412 (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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376A VAL* 4.8 15.8 - - + +
379A THR* 5.3 5.1 + - - +
408A GLU* 3.1 25.7 + - - +
409A ASP* 3.5 9.8 + - - +
410A CYS 3.2 0.4 - - - -
411A GLU* 1.3 78.5 - - - +
413A VAL* 1.3 62.7 + - + +
415A HIS* 3.4 33.6 + - - +
416A LEU* 3.8 10.6 - - - +
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Residues in contact with VAL 413 (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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376A VAL* 5.4 3.1 - - + -
379A THR* 4.3 11.2 - - + +
391A ILE* 4.0 19.5 - - + -
394A LEU* 4.2 23.8 - - + -
409A ASP 3.4 14.5 + - - +
410A CYS 3.0 8.1 + - - +
412A ASN* 1.3 74.7 - - + +
414A TYR* 1.3 64.9 + - - +
416A LEU* 3.1 25.7 + - + +
428A ALA* 3.7 10.9 - - + +
431A PHE* 3.3 42.8 - - + -
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Residues in contact with TYR 414 (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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410A CYS* 3.0 33.3 + - + +
411A GLU* 3.2 34.5 + - - +
413A VAL* 1.3 78.7 - - - +
415A HIS* 1.3 66.0 + - + +
417A VAL* 3.1 26.4 + - - +
418A TYR* 4.4 3.0 - - - -
428A ALA 5.6 0.2 - - - -
431A PHE* 4.1 17.5 - + - -
432A LEU* 3.5 32.8 - - + -
435A LYS* 3.1 27.7 + - + +
436A LEU* 3.6 24.3 - - + +
467A PHE* 3.7 29.3 - + + -
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Residues in contact with HIS 415 (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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411A GLU* 3.2 44.4 + - + +
412A ASN* 3.5 24.7 + - - +
413A VAL 3.2 0.6 - - - -
414A TYR* 1.3 79.5 - - + +
416A LEU* 1.3 61.1 + - + +
417A VAL 3.1 0.2 - - - -
418A TYR* 3.0 34.8 + + - +
471A SER* 6.5 0.7 - - - -
473A LEU* 3.9 29.9 - - + +
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Residues in contact with LEU 416 (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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379A THR* 3.5 41.1 - - - +
380A LEU* 3.8 30.5 - - + -
391A ILE* 3.6 17.7 - - + -
412A ASN 3.8 8.7 - - - +
413A VAL* 3.4 19.5 - - - +
414A TYR 3.1 1.4 - - - -
415A HIS* 1.3 75.3 - - + +
417A VAL* 1.3 56.2 + - - +
418A TYR 2.9 5.4 - - - -
419A SER* 2.9 30.4 + - - +
424A VAL* 4.0 11.9 - - + -
425A ALA* 3.4 9.7 - - - -
428A ALA* 3.6 10.3 - - + -
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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