Contacts of the helix formed by residues 391 - 407 (chain J) in PDB entry 5Z58
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 TYR 391 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357J LYS* 5.8 3.1 - - - -
359J VAL* 4.2 15.2 - - + +
360J ASP* 5.4 1.4 + - - -
363J ARG* 3.9 22.7 + - - -
386J GLU* 2.9 37.6 + - - +
389J HIS* 3.2 39.9 - - + -
390J ALA* 1.3 73.4 - - - +
392J PHE* 1.3 59.1 + - - +
393J ALA 3.3 2.9 - - - -
394J HIS* 3.2 30.3 + + + +
395J ALA* 2.8 27.8 + - - +
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Residues in contact with PHE 392 (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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387J GLU* 3.5 35.0 - - + -
390J ALA* 2.9 37.7 + - + -
391J TYR* 1.3 69.8 - - - +
393J ALA* 1.3 61.1 + - - +
395J ALA* 4.1 3.1 - - - -
396J ARG* 2.9 29.5 + - - +
422J PHE* 3.4 20.0 - + + -
426J GLN* 3.6 38.6 - - - +
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Residues in contact with ALA 393 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391J TYR* 5.1 0.4 - - - -
392J PHE* 1.3 78.3 - - - +
394J HIS* 1.3 72.3 + - + +
396J ARG* 3.6 14.9 + - - +
397J LYS* 3.2 36.5 + - - +
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Residues in contact with HIS 394 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363J ARG* 4.0 20.4 + - - +
386J GLU* 4.4 6.3 - - - +
391J TYR* 3.2 37.3 + + + +
392J PHE 3.2 0.4 - - - -
393J ALA* 1.3 84.6 - - + +
395J ALA* 1.3 59.8 + - - +
397J LYS* 3.2 24.4 + - + +
398J VAL* 2.9 34.4 + - + +
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Residues in contact with ALA 395 (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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383J ALA* 3.9 20.0 - - - +
386J GLU* 3.9 10.3 - - + +
387J GLU* 3.9 9.2 - - + +
391J TYR 2.8 16.3 + - - +
392J PHE* 3.2 7.4 + - - +
394J HIS* 1.3 75.5 - - - +
396J ARG* 1.3 61.9 + - - +
398J VAL* 3.2 8.5 + - - +
399J TYR* 3.0 31.3 + - + -
422J PHE* 3.8 18.4 - - + -
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Residues in contact with ARG 396 (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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392J PHE* 2.9 25.4 + - - +
393J ALA* 3.6 15.6 - - - +
395J ALA* 1.3 76.6 - - - +
397J LYS* 1.3 58.3 + - + +
399J TYR* 3.1 8.4 + - - +
400J GLU* 2.9 41.0 + - + +
419J PHE* 4.8 2.5 - - + -
422J PHE* 3.6 13.8 - - + -
423J GLU* 2.8 40.1 + - - +
426J GLN* 3.1 33.9 + - - +
428J GLU* 4.8 5.5 - - - +
431J ARG* 5.5 5.8 - - - +
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Residues in contact with LYS 397 (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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393J ALA* 3.2 24.1 + - - +
394J HIS* 3.2 29.9 + - + +
396J ARG* 1.3 81.2 - - + +
398J VAL* 1.3 55.4 + - + +
400J GLU* 3.2 11.0 + - + +
401J ARG* 2.9 40.2 + - + +
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Residues in contact with VAL 398 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367J GLU* 5.2 0.9 - - - +
379J TRP* 4.2 15.1 - - + +
382J TYR* 3.7 47.3 - - + +
383J ALA* 3.9 21.1 - - + +
386J GLU* 4.6 8.1 - - + +
394J HIS* 2.9 22.5 + - + +
395J ALA* 3.4 11.0 - - - +
397J LYS* 1.3 75.9 - - - +
399J TYR* 1.3 58.5 + - - +
401J ARG* 3.2 15.5 + - - +
402J ALA* 2.9 27.1 + - + +
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Residues in contact with TYR 399 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380J ILE* 4.8 7.2 + - - +
383J ALA* 3.6 24.2 - - + +
384J ARG* 4.8 1.4 + - - +
387J GLU* 2.7 31.7 + - - -
395J ALA 3.0 28.9 + - - -
396J ARG 3.5 4.9 - - - +
398J VAL* 1.3 77.4 - - + +
400J GLU* 1.3 61.2 - - - +
402J ALA* 3.2 4.6 + - - +
403J VAL* 3.0 30.4 + - - +
415J LEU* 3.9 19.5 - - + -
418J ALA* 3.7 27.0 + - + +
419J PHE* 3.5 52.9 - + + -
422J PHE* 3.6 17.9 - + + -
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Residues in contact with GLU 400 (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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396J ARG* 2.9 27.2 + - + +
397J LYS* 3.2 11.4 + - - +
399J TYR* 1.3 76.9 - - - +
401J ARG* 1.3 58.4 + - + +
403J VAL* 3.2 12.2 - - - +
404J GLU* 2.9 32.3 + - - +
419J PHE* 3.3 29.0 - - - -
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Residues in contact with ARG 401 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367J GLU* 3.0 40.4 + - - -
379J TRP* 4.2 21.9 - - + -
382J TYR* 5.0 2.3 + - - -
397J LYS* 2.9 26.5 + - + +
398J VAL* 3.2 13.4 + - - +
400J GLU* 1.3 77.5 - - + +
402J ALA* 1.3 58.1 - - - +
404J GLU* 3.3 17.2 + - - +
405J PHE* 2.8 32.7 + - - +
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Residues in contact with ALA 402 (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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379J TRP* 3.7 33.0 - - + -
398J VAL* 2.9 13.5 + - + +
399J TYR* 3.2 10.3 + - - +
401J ARG* 1.3 77.8 - - - +
403J VAL* 1.3 59.7 + - - +
405J PHE* 3.4 2.1 + - - +
406J PHE* 2.9 36.1 + - + +
415J LEU* 3.9 27.1 - - + -
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Residues in contact with VAL 403 (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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399J TYR 3.4 14.1 - - - +
400J GLU* 3.2 24.7 - - - +
402J ALA* 1.3 78.7 - - - +
404J GLU* 1.3 66.3 + - - +
406J PHE* 4.9 2.0 - - - -
407J GLY* 3.1 22.5 + - - +
411J MET* 5.3 0.2 - - - -
415J LEU* 3.8 20.0 - - + -
416J TYR* 3.4 41.6 + - + +
419J PHE* 4.8 13.2 - - + -
442J ARG* 5.5 14.2 + - - +
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Residues in contact with GLU 404 (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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400J GLU* 2.9 18.4 + - - +
401J ARG* 3.5 21.3 - - - +
403J VAL* 1.3 80.5 - - + +
405J PHE* 1.3 64.7 + - - +
407J GLY* 3.7 8.5 + - - -
442J ARG* 5.8 4.5 - - - +
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Residues in contact with PHE 405 (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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371J LEU* 5.4 10.3 - - + -
374J PRO* 4.1 28.9 - - + -
379J TRP* 4.0 28.5 - + + -
401J ARG 2.8 18.4 + - - +
402J ALA* 3.7 2.9 - - - +
404J GLU* 1.3 80.1 - - - +
406J PHE* 1.3 100.9 + + - +
407J GLY* 3.4 0.5 + - - -
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Residues in contact with PHE 406 (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 PRO 3.7 17.0 - - - -
376J VAL* 3.5 28.9 - - + -
379J TRP* 4.0 17.5 - + - -
402J ALA 2.9 23.6 + - - +
403J VAL 4.4 0.4 - - - +
405J PHE* 1.3 94.9 - + - +
407J GLY* 1.3 64.9 + - - +
409J GLU* 4.2 16.1 - - - +
410J HIS* 4.3 19.7 + + + +
411J MET* 2.7 50.3 - - + -
415J LEU* 4.4 5.4 - - + -
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Residues in contact with GLY 407 (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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403J VAL 3.1 18.7 + - - -
404J GLU 3.9 8.7 - - - -
405J PHE 3.3 1.7 - - - -
406J PHE* 1.3 81.8 - - - +
408J ASP* 1.3 66.0 + - - +
409J GLU* 3.3 1.1 - - - -
411J MET* 3.8 19.8 + - - +
416J TYR* 4.4 5.2 + - - -
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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