Contacts of the helix formed by residues 407 - 417 (chain J) in PDB entry 6ALG
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 VAL 407 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385J LEU* 4.8 2.0 - - + -
390J LEU* 3.7 30.5 - - + -
400J MET* 4.0 18.6 - - + -
405J GLU* 4.3 9.2 - - + +
406J ALA* 1.3 78.7 - - + +
408J VAL* 1.3 68.4 + - + +
409J TRP 3.2 3.9 + - - -
410J ASP* 3.6 8.2 + - - +
411J ILE* 3.3 22.8 + - + +
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Residues in contact with VAL 408 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374J LEU* 4.2 15.9 - - + -
381J ILE* 4.7 9.3 - - + +
385J LEU* 4.1 24.9 - - + -
400J MET* 4.3 13.7 - - + +
401J VAL* 4.2 13.9 - - + -
404J GLU* 4.5 2.9 - - - -
405J GLU* 3.3 28.0 - - + +
407J VAL* 1.3 85.2 - - + +
409J TRP* 1.3 73.5 + - + +
410J ASP 3.5 0.2 - - - -
411J ILE* 3.4 10.5 - - - +
412J LEU* 2.9 27.4 + - - +
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Residues in contact with TRP 409 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191H ARG* 4.6 14.8 - - - +
193H GLU 6.1 0.2 - - - +
370J LYS* 3.6 63.0 - - + +
371J LYS* 5.3 2.9 - - + -
374J LEU* 3.7 25.8 - - + -
404J GLU* 4.3 26.7 + - + -
405J GLU 3.4 24.0 + - - -
406J ALA* 4.0 12.6 - - - +
407J VAL 3.2 1.2 - - - -
408J VAL* 1.3 82.3 - - + +
410J ASP* 1.3 61.4 + - - +
412J LEU* 3.2 19.4 + - + +
413J ASP* 2.9 32.7 + - - -
441J LEU* 4.9 2.3 - - + +
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Residues in contact with ASP 410 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H ARG* 3.7 24.2 + - - -
406J ALA 4.8 3.9 + - - +
407J VAL* 3.6 9.8 + - - +
408J VAL 3.5 0.2 - - - -
409J TRP* 1.3 75.0 - - - +
411J ILE* 1.3 63.1 + - + +
413J ASP* 3.4 6.9 + - - +
414J GLU* 2.9 38.8 + - - +
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Residues in contact with ILE 411 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381J ILE* 4.0 28.3 - - + +
384J LYS* 3.8 32.3 - - + +
385J LEU* 4.0 21.8 - - + -
388J ARG* 3.6 35.0 - - - +
390J LEU* 5.8 2.0 - - + -
407J VAL* 3.3 16.1 + - + +
408J VAL* 3.4 10.3 - - - +
409J TRP 3.3 0.4 - - - -
410J ASP* 1.3 78.2 - - + +
412J LEU* 1.3 55.5 + - - +
414J GLU* 3.0 10.2 + - - +
415J VAL* 2.9 28.8 + - + +
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Residues in contact with LEU 412 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373J ALA* 3.7 16.6 - - + +
374J LEU* 3.7 39.3 - - + +
377J PHE* 4.8 2.5 - - + -
381J ILE* 3.8 17.9 - - + -
408J VAL 2.9 15.2 + - - +
409J TRP* 3.6 26.5 - - + +
410J ASP 3.2 0.4 - - - -
411J ILE* 1.3 77.9 - - - +
413J ASP* 1.3 57.2 + - - +
415J VAL* 3.2 9.8 + - + +
416J ILE* 2.9 53.7 + - + +
441J LEU* 3.7 19.5 - - + -
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Residues in contact with ASP 413 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H ARG* 3.6 35.9 + - - -
370J LYS* 4.9 2.4 + - - -
409J TRP* 2.9 19.3 + - - +
410J ASP* 3.9 8.6 - - - +
412J LEU* 1.3 76.7 - - - +
414J GLU* 1.3 62.0 + - + +
415J VAL 3.4 0.6 + - - -
416J ILE* 4.1 4.1 - - - +
417J ARG* 3.9 21.8 + - - +
441J LEU* 3.7 29.6 - - - +
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Residues in contact with GLU 414 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384J LYS* 4.7 11.6 + - - +
388J ARG* 2.4 39.3 + - - +
410J ASP* 2.9 24.4 + - + +
411J ILE* 3.0 12.6 + - - +
413J ASP* 1.3 79.7 - - + +
415J VAL* 1.3 59.4 + - + +
417J ARG* 4.7 5.3 - - - +
45K LYS* 3.4 14.7 + - - -
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Residues in contact with VAL 415 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377J PHE* 4.6 17.2 - - + -
380J PHE* 4.5 18.8 - - + +
381J ILE* 4.4 11.7 - - + -
384J LYS* 3.7 32.1 - - + -
411J ILE* 2.9 18.3 + - + +
412J LEU* 3.3 23.3 - - + +
414J GLU* 1.3 79.0 - - - +
416J ILE* 1.3 65.1 + - - +
417J ARG 3.4 1.3 - - - -
419J HIS* 3.7 13.5 + - - +
45K LYS* 3.3 21.8 - - - +
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Residues in contact with ILE 416 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368J LEU* 5.9 0.9 - - + -
373J ALA* 5.0 3.4 - - + -
377J PHE* 3.5 31.4 - - + -
412J LEU* 2.9 27.2 + - + +
413J ASP* 4.0 6.0 + - - +
414J GLU 3.7 0.2 - - - -
415J VAL* 1.3 77.7 - - - +
417J ARG* 1.3 60.1 - - - +
418J GLU 2.8 1.9 + - - -
419J HIS* 2.7 39.5 + - + +
439J PRO* 3.5 51.3 - - + +
441J LEU* 3.6 25.8 - - + -
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Residues in contact with ARG 417 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413J ASP 3.9 14.6 + - - +
414J GLU* 5.3 4.9 - - - +
415J VAL* 3.4 3.0 - - - +
416J ILE* 1.3 83.0 - - - +
418J GLU* 1.3 83.2 + - + +
419J HIS 3.6 0.6 + - - -
438J GLU* 4.1 13.9 - - - +
439J PRO 5.6 0.3 - - - +
2K ALA* 5.6 4.9 - - - +
42K GLU* 3.2 31.1 + - - +
43K ASN* 3.3 27.4 + - - +
44K ASP* 3.9 7.5 + - - +
45K LYS* 4.7 4.2 - - + +
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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