Contacts of the helix formed by residues 418 - 434 (chain J) in PDB entry 5G04
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 TRP 418 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412J ALA 4.8 0.4 + - - -
413J PHE* 3.7 38.8 - + - +
416J GLY* 3.1 32.6 + - - -
417J GLU* 1.3 73.2 - - - +
419J LYS* 1.3 61.9 + - + +
420J THR* 3.3 1.1 + - - -
421J ALA* 3.3 12.8 + - - +
422J GLU* 2.9 31.2 + - - +
454J VAL* 4.8 2.8 - - - +
457J LYS* 3.5 56.8 - - + -
458J LEU* 4.5 20.0 - - + +
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Residues in contact with LYS 419 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417J GLU 2.6 13.7 + - - +
418J TRP* 1.3 77.2 - - + +
420J THR* 1.3 62.3 + - + +
422J GLU* 3.5 11.7 + - - +
423J LYS* 3.1 21.8 + - - +
458J LEU* 4.1 24.9 - - + +
460J LYS* 4.8 8.7 - - - +
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Residues in contact with THR 420 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412J ALA* 3.8 8.3 - - - +
417J GLU* 2.8 45.0 + - + +
419J LYS* 1.3 77.3 - - + +
421J ALA* 1.3 58.4 + - - -
423J LYS* 3.2 9.2 + - + +
424J TRP* 2.9 42.0 + - - -
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Residues in contact with ALA 421 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409J GLY* 3.5 24.0 - - - +
412J ALA* 3.9 8.4 - - + +
413J PHE* 3.9 25.6 - - + +
418J TRP* 3.3 12.6 + - - +
420J THR* 1.3 80.5 + - - +
422J GLU* 1.3 62.6 + - - +
424J TRP* 3.1 3.1 + - - +
425J PHE* 2.9 40.3 + - + -
454J VAL* 4.4 1.1 - - + -
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Residues in contact with GLU 422 (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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418J TRP 2.9 19.2 + - - +
419J LYS* 3.9 10.6 + - - +
421J ALA* 1.3 72.2 - - - +
423J LYS* 1.3 57.8 + - - +
425J PHE* 3.3 2.5 + - - +
426J LEU* 2.9 53.3 + - + +
451J LEU* 6.3 0.9 - - + -
454J VAL* 3.9 27.3 - - + +
455J CYS* 4.4 4.2 - - - -
458J LEU* 3.4 19.4 - - + +
460J LYS* 2.9 35.8 + - - +
463J GLU* 4.2 10.2 - - - +
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Residues in contact with LYS 423 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419J LYS 3.1 15.1 + - - +
420J THR* 3.2 12.5 + - + +
422J GLU* 1.3 78.0 + - - +
424J TRP* 1.3 83.4 + - + +
426J LEU* 3.9 7.0 - - - +
427J ASP* 3.0 42.0 + - - +
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Residues in contact with TRP 424 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395J LEU* 4.2 26.2 - - + -
405J MET* 3.7 39.7 - - + +
408J VAL* 3.3 34.1 - - + +
409J GLY* 3.7 19.3 - - - -
412J ALA* 4.6 4.3 - - + -
420J THR* 2.9 30.1 + - - -
421J ALA 3.1 6.5 + - - +
423J LYS* 1.3 99.5 - - + +
425J PHE* 1.3 58.0 + - - +
427J ASP* 3.4 24.9 + - - +
428J ALA* 2.9 28.8 + - - +
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Residues in contact with PHE 425 (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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9G LEU* 4.2 6.1 - - + -
406J HIS* 3.4 53.6 - + - -
409J GLY* 3.5 21.8 - - - -
410J VAL* 3.7 11.9 - - + -
413J PHE* 4.7 0.2 - + - -
421J ALA* 2.9 29.6 + - + +
422J GLU* 3.8 3.4 - - - +
424J TRP* 1.3 78.4 - - - +
426J LEU* 1.3 57.2 + - - +
428J ALA* 3.2 4.7 + - - +
429J LEU* 2.9 29.1 + - - +
447J LEU* 3.8 6.3 - - + +
450J ASN* 3.9 16.8 - - + -
451J LEU* 3.9 24.4 - - + +
454J VAL* 3.3 35.4 - - + -
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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
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422J GLU* 2.9 47.2 + - + +
423J LYS* 3.9 5.4 - - - +
425J PHE* 1.3 76.7 - - - +
427J ASP* 1.3 56.7 + - - +
429J LEU* 3.3 13.6 + - + +
430J GLU* 3.0 41.8 + - + +
451J LEU* 4.8 7.6 - - + +
463J GLU* 4.9 8.7 - - - +
467J TYR* 4.1 20.2 - - - +
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Residues in contact with ASP 427 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405J MET* 3.2 22.6 - - + +
423J LYS* 3.0 31.2 + - - +
424J TRP* 3.4 25.4 - - + +
426J LEU* 1.3 77.1 - - - +
428J ALA* 1.3 63.7 + - - +
430J GLU* 3.3 16.7 + - - +
431J LYS* 3.1 35.3 + - - +
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Residues in contact with ALA 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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402J PRO* 4.0 26.5 - - + +
405J MET* 4.0 14.6 - - + -
406J HIS* 4.1 6.1 - - + +
424J TRP 2.9 14.3 + - - +
425J PHE* 3.2 9.6 + - - +
427J ASP* 1.3 77.7 - - - +
429J LEU* 1.3 57.5 + - - +
431J LYS* 3.3 4.2 + - - +
432J ILE* 2.9 31.5 + - - +
447J LEU* 3.9 18.2 - - + -
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Residues in contact with LEU 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 PHE 2.9 10.9 + - - +
426J LEU* 3.5 15.3 - - + +
428J ALA* 1.3 75.9 - - - +
430J GLU* 1.3 56.8 + - - +
432J ILE* 3.2 14.9 - - + +
433J LYS* 2.8 63.5 + - + +
439J VAL* 4.6 6.1 - - + -
447J LEU* 4.2 4.4 - - + +
448J LEU* 4.1 18.2 - - + -
451J LEU* 3.7 38.8 - - + -
467J TYR* 4.0 19.5 - - + +
470J GLN* 5.8 0.9 - - - +
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Residues in contact with GLU 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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426J LEU* 3.0 29.3 + - + +
427J ASP* 3.3 19.4 + - - +
429J LEU* 1.3 75.4 - - - +
431J LYS* 1.3 66.5 + - + +
433J LYS* 3.3 19.5 + - - +
434J ALA* 3.6 6.2 + - - +
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Residues in contact with LYS 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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214J LYS* 6.5 0.2 - - + -
215J PRO* 5.1 2.5 - - + +
216J SER* 4.0 16.8 + - - -
400J GLU* 3.9 37.5 + - + +
402J PRO* 4.2 20.1 - - + +
405J MET* 3.4 21.1 - - + -
427J ASP* 3.1 29.2 + - - +
428J ALA 3.7 6.3 - - - +
430J GLU* 1.3 80.5 - - - +
432J ILE* 1.3 62.0 - - - +
434J ALA* 3.5 17.1 + - - +
435J ILE 4.7 0.2 + - - -
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Residues in contact with ILE 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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215J PRO* 4.9 2.9 - - + -
244J ASN 4.7 0.7 - - - +
402J PRO* 4.0 17.4 - - + +
428J ALA 2.9 16.7 + - - +
429J LEU* 3.2 27.6 - - + +
431J LYS* 1.3 75.8 - - - +
433J LYS* 1.3 64.2 + - - +
434J ALA 3.3 0.9 + - - -
435J ILE* 3.4 41.3 + - + +
436J GLY 4.2 2.3 + - - +
439J VAL* 3.9 28.9 - - + +
441J VAL* 4.9 1.6 - - + -
444J TRP* 3.2 41.3 - - + +
447J LEU* 3.8 15.7 - - + -
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Residues in contact with LYS 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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429J LEU* 2.8 53.3 + - + +
430J GLU* 3.5 10.8 - - - +
431J LYS 3.3 0.4 - - - -
432J ILE* 1.3 73.2 - - - +
434J ALA* 1.3 62.4 + - - +
435J ILE 3.2 0.2 - - - -
436J GLY 2.8 25.2 + - - +
437J ASN* 2.7 36.3 + - - +
438J GLU* 4.3 16.0 + - - +
439J VAL* 5.2 7.4 - - + +
470J GLN* 5.5 7.1 + - - +
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Residues in contact with ALA 434 (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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216J SER* 3.4 42.5 - - - +
218J THR* 3.9 5.9 - - - +
430J GLU 3.6 5.9 + - - +
431J LYS* 3.5 7.7 + - - +
432J ILE 3.2 0.6 - - - -
433J LYS* 1.3 78.2 - - - +
435J ILE* 1.3 63.2 - - - +
437J ASN* 5.8 0.2 - - - +
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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