Contacts of the helix formed by residues 413 - 435 (chain J) in PDB entry 5FUR
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 SER 413 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410J PRO* 4.6 7.2 - - - +
411J VAL 3.9 0.6 + - - -
412J LEU* 1.3 91.0 - - - +
414J ASN* 1.3 63.2 + - - +
415J ILE* 2.8 18.5 + - - -
416J ASP 2.9 13.5 + - - -
417J ARG* 3.0 8.3 + - - +
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Residues in contact with ASN 414 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413J SER* 1.3 80.6 + - - +
415J ILE* 1.3 69.5 + - + +
417J ARG* 2.8 51.1 + - - +
418J ILE* 2.9 29.1 + - - +
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Residues in contact with ILE 415 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323J VAL* 3.5 31.9 - - + -
327J TRP* 6.1 0.9 - - + -
370J TRP* 3.2 57.3 - - + +
374J TYR* 5.6 3.4 - - + -
407J LEU* 3.5 2.8 - - - +
411J VAL 5.1 1.8 - - - +
412J LEU 2.8 13.9 + - - +
413J SER* 2.8 8.2 + - - -
414J ASN* 1.3 90.1 - - + +
416J ASP* 1.3 55.0 + - - -
418J ILE* 4.8 5.4 - - + -
419J GLY* 3.1 31.7 + - - +
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Residues in contact with ASP 416 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370J TRP* 3.7 0.2 - - - -
404J ARG* 5.5 1.6 - - - +
406J VAL* 3.2 27.5 - - - +
407J LEU* 3.1 28.2 + - + +
412J LEU* 3.3 25.2 + - + +
413J SER 2.9 9.5 + - - +
415J ILE* 1.3 74.8 - - - +
417J ARG* 1.3 61.3 + - - +
420J ALA* 2.8 49.7 + - - +
421J ASP 3.3 1.2 + - - -
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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
----------------------------------------------------------
413J SER 3.0 8.1 + - - +
414J ASN* 2.8 42.8 + - - +
416J ASP* 1.3 78.8 + - - +
418J ILE* 1.3 84.8 + - - +
421J ASP* 2.9 29.6 + - - +
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Residues in contact with ILE 418 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323J VAL* 4.7 20.0 - - + -
327J TRP* 5.8 2.5 - - + -
374J TYR* 5.3 2.9 - - - +
414J ASN* 2.9 29.8 + - - +
415J ILE* 4.7 7.0 - - + -
417J ARG* 1.3 106.4 - - - +
419J GLY* 1.3 59.7 + - - +
421J ASP* 3.8 8.7 - - - +
422J HIS* 2.9 56.0 + - + +
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Residues in contact with GLY 419 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374J TYR* 3.2 31.0 - - - -
407J LEU* 4.0 3.8 - - - -
415J ILE* 3.1 24.7 + - - +
418J ILE* 1.3 78.8 - - - +
420J ALA* 1.3 57.9 + - - +
423J VAL* 3.0 31.9 + - - +
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Residues in contact with ALA 420 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407J LEU* 4.5 7.6 - - + -
416J ASP* 2.8 43.2 + - - +
419J GLY* 1.3 75.8 - - - +
421J ASP* 1.3 58.0 + - - -
423J VAL* 3.9 11.2 - - + -
424J GLN* 2.9 45.0 + - + +
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Residues in contact with ASP 421 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416J ASP 3.3 0.6 + - - -
417J ARG* 2.9 29.5 + - - +
418J ILE* 3.9 10.7 - - + +
419J GLY 3.6 0.2 - - - -
420J ALA* 1.3 72.4 - - - +
422J HIS* 1.3 77.2 + - - +
424J GLN* 2.9 9.9 + - - +
425J SER* 2.8 39.4 + - - -
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Residues in contact with HIS 422 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327J TRP* 3.4 42.7 + + - -
374J TYR* 3.1 23.3 + - + -
418J ILE* 2.9 45.2 + - + +
419J GLY 3.9 4.9 - - - +
420J ALA 3.6 0.2 - - - -
421J ASP* 1.3 80.2 - - - +
423J VAL* 1.3 58.4 + - - +
425J SER* 4.1 7.2 - - - -
426J LEU* 2.9 48.2 + - + +
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Residues in contact with VAL 423 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363J TRP* 4.2 17.5 - - + -
374J TYR* 4.0 12.1 - - + -
377J ILE* 3.5 41.9 - - + +
378J ALA* 5.3 2.5 - - + +
407J LEU* 5.6 2.9 - - + -
419J GLY 3.0 23.9 + - - +
420J ALA* 4.0 10.5 - - + +
421J ASP 3.2 0.2 - - - -
422J HIS* 1.3 73.7 - - - +
424J GLN* 1.3 59.5 + - + +
426J LEU* 3.9 6.4 - - + +
427J LEU* 2.9 52.6 + - + +
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Residues in contact with GLN 424 (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 LEU* 6.1 1.1 - - + -
420J ALA* 2.9 34.4 + - + +
421J ASP* 2.9 11.7 + - - +
423J VAL* 1.3 74.7 - - + +
425J SER* 1.3 54.4 + - - +
427J LEU* 3.7 14.1 - - + +
428J LEU* 2.9 29.5 + - - +
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Residues in contact with SER 425 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421J ASP* 2.8 34.2 + - - -
422J HIS* 3.6 9.4 - - - -
424J GLN* 1.3 70.8 - - - +
426J LEU* 1.3 61.1 + - - +
428J LEU* 3.2 3.7 + - - +
429J LYS* 2.9 66.1 + - - +
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Residues in contact with LEU 426 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331J ASP* 6.1 0.4 - - - +
335J ARG* 5.3 5.6 - - - +
374J TYR* 6.1 1.3 - - + -
377J ILE* 6.0 2.2 - - + -
378J ALA* 5.2 14.8 - - + -
381J ALA* 4.6 18.6 - - + -
382J GLU* 4.1 21.5 - - + +
388J ILE* 4.5 3.7 - - - +
422J HIS* 2.9 35.7 + - + +
423J VAL* 4.1 6.1 - - + +
425J SER* 1.3 73.2 - - - +
427J LEU* 1.3 58.5 + - - +
429J LYS* 4.5 5.4 - - + +
430J HIS* 3.0 46.1 + - + +
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Residues in contact with LEU 427 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363J TRP* 5.8 2.7 - - + -
377J ILE* 4.5 8.3 - - + +
388J ILE* 5.2 4.6 - - + +
392J ILE* 3.3 37.5 - - + +
393J LEU* 5.8 1.1 - - + -
396J LEU* 3.3 46.2 - - + +
423J VAL* 2.9 46.7 + - + +
424J GLN* 3.7 12.8 - - + +
426J LEU* 1.3 73.9 - - - +
428J LEU* 1.3 59.5 + - - +
429J LYS 3.2 0.2 - - - -
431J CYS* 2.9 33.2 + - - +
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Residues in contact with LEU 428 (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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424J GLN 2.9 20.9 + - - +
425J SER* 3.2 6.7 + - - +
427J LEU* 1.3 74.9 - - - +
429J LYS* 1.3 76.0 + - + +
430J HIS 3.5 0.2 - - - -
431J CYS* 3.8 6.8 - - + +
432J ALA* 3.0 33.7 + - + +
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Residues in contact with LYS 429 (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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425J SER* 2.9 47.9 + - - +
426J LEU* 3.7 6.1 - - + +
428J LEU* 1.3 92.5 - - + +
430J HIS* 1.3 69.0 + - + +
432J ALA* 4.6 2.7 - - + -
433J PRO* 3.0 24.4 - - - +
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Residues in contact with HIS 430 (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 ALA* 3.8 27.1 + - + -
382J GLU* 4.7 17.1 + - - -
385J HIS* 3.1 30.8 + + + -
388J ILE* 3.5 30.5 - - + -
426J LEU* 3.0 35.6 + - + +
429J LYS* 1.3 86.2 + - + +
431J CYS* 1.3 56.3 + - - +
432J ALA 3.5 0.9 - - - -
433J PRO* 3.4 3.2 - - - +
434J VAL* 3.0 35.7 + - - +
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Residues in contact with CYS 431 (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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388J ILE* 4.2 3.1 - - - +
393J LEU* 4.2 30.7 - - + -
396J LEU* 6.3 1.1 - - + -
427J LEU 2.9 20.7 + - - +
428J LEU* 3.8 9.6 - - + +
430J HIS* 1.3 72.0 - - - +
432J ALA* 1.3 63.6 + - - +
434J VAL* 3.3 8.1 + - - +
435J LEU* 3.0 48.5 + - - +
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Residues in contact with ALA 432 (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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428J LEU* 3.0 23.9 + - + +
429J LYS* 4.6 2.5 - - + -
431J CYS* 1.3 76.2 - - - +
433J PRO* 1.4 62.1 - - + +
435J LEU* 3.7 8.2 + - - +
436J ALA* 3.0 28.2 + - - +
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Residues in contact with PRO 433 (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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385J HIS* 3.4 35.2 + - + +
429J LYS* 3.0 31.9 - - - +
430J HIS* 3.4 8.5 - - - +
432J ALA* 1.4 89.4 - - + +
434J VAL* 1.3 61.5 + - - -
436J ALA* 3.5 23.3 + - + +
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Residues in contact with VAL 434 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385J HIS* 3.0 46.7 - - + +
386J ASP* 5.3 2.2 - - - +
388J ILE* 3.9 8.3 - - + -
389J LYS* 3.2 50.8 + - + +
393J LEU* 4.7 6.3 - - + -
430J HIS 3.0 25.5 + - - +
431J CYS* 3.4 12.6 - - - +
433J PRO* 1.3 73.0 - - - +
435J LEU* 1.3 67.6 + - + +
436J ALA 4.8 0.7 - - - -
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Residues in contact with LEU 435 (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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389J LYS* 3.9 22.6 + - - +
393J LEU* 5.4 4.5 - - + -
431J CYS* 3.0 40.3 + - - +
432J ALA* 3.7 6.5 - - - +
434J VAL* 1.3 80.0 - - + +
436J ALA* 1.3 63.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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