Contacts of the helix formed by residues 447 - 464 (chain I) 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 447 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401I LYS* 6.5 0.7 - - - -
402I ILE* 3.9 13.6 - - - +
405I TYR* 4.2 19.4 - - - -
445I TYR 3.9 1.9 + - - -
446I TYR* 1.3 95.8 - - - +
448I MET* 1.3 64.9 + - - +
450I GLN* 4.6 5.4 - - - +
451I CYS* 3.1 24.1 + - - +
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Residues in contact with MET 448 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402I ILE* 4.7 8.7 - - + +
405I TYR* 3.9 32.8 - - + +
406I GLU* 4.0 27.1 - - + -
413I LEU 4.8 4.3 - - - +
414I LEU* 4.0 13.5 - - + -
415I HIS* 3.8 41.5 - - + +
417I ILE* 3.9 13.0 - - + +
446I TYR* 3.2 20.9 - - + -
447I SER* 1.3 80.0 + - - +
449I PHE* 1.3 68.6 + - + +
452I LYS* 3.0 36.1 + - + +
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Residues in contact with PHE 449 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368I TRP* 5.6 0.2 - - - +
371I LYS* 4.7 3.6 - - - -
415I HIS* 4.4 20.6 - + + -
416I PRO 3.4 24.9 - - - -
417I ILE* 3.9 24.5 - - + +
431I LEU* 6.5 1.1 - - + -
433I PHE* 6.3 2.9 - - + -
443I TRP* 3.6 15.9 - - + -
444I GLU* 3.2 63.7 - - + +
446I TYR* 2.8 22.6 + + + +
448I MET* 1.3 80.5 - - + +
450I GLN* 1.3 64.5 + - - +
453I ALA* 3.2 22.6 + - - +
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Residues in contact with GLN 450 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344I ARG* 5.8 2.2 - - - +
348I GLN* 3.6 25.7 + - - +
371I LYS* 3.4 50.6 + - + +
375I GLY* 5.6 7.0 - - - -
398I GLU* 4.8 4.2 + - - -
444I GLU 4.6 1.0 + - - -
445I TYR* 4.9 8.4 - - - +
446I TYR 3.2 10.5 + - - +
447I SER* 4.1 7.9 - - - +
449I PHE* 1.3 81.6 - - - +
451I CYS* 1.4 82.0 + - - +
452I LYS 3.2 2.2 - - - -
453I ALA* 3.4 2.9 - - - +
454I HIS* 2.8 22.9 + - + +
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Residues in contact with CYS 451 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398I GLU* 4.0 40.4 - - + +
399I LEU* 5.6 1.4 - - - +
402I ILE* 3.6 21.0 - - + +
447I SER* 3.1 15.2 + - - +
450I GLN* 1.4 108.0 - - - +
452I LYS* 1.3 55.6 + - - +
454I HIS* 3.6 16.3 - - + +
455I LEU* 3.1 21.8 + - - +
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Residues in contact with LYS 452 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402I ILE* 3.9 17.1 - - + +
406I GLU* 2.6 39.0 + - - +
417I ILE* 3.9 19.2 - - + +
448I MET* 3.0 28.2 + - + +
451I CYS* 1.3 76.3 - - - +
453I ALA* 1.4 56.8 + - - +
454I HIS 3.3 0.7 - - - -
455I LEU* 3.2 11.6 + - + +
456I VAL* 2.9 49.1 + - + +
522I TRP* 3.1 48.4 + - - +
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Residues in contact with ALA 453 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368I TRP* 3.9 26.7 - - + +
371I LYS* 4.3 1.8 - - + -
372I GLY* 3.5 25.6 - - - +
417I ILE* 5.0 5.7 - - + +
449I PHE 3.2 22.0 + - - +
450I GLN 3.4 4.0 - - - +
452I LYS* 1.4 74.6 - - - +
454I HIS* 1.4 64.7 + - - +
456I VAL* 3.0 16.9 + - - +
457I MET* 3.0 15.7 + - - +
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Residues in contact with HIS 454 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372I GLY* 3.7 11.1 - - - -
375I GLY* 3.6 15.2 - - - -
376I TYR* 3.6 41.2 + + - -
379I GLY* 5.8 4.3 - - - -
391I TYR* 6.5 0.4 - + - -
395I ILE* 4.2 24.4 - - + +
398I GLU* 4.5 19.2 + - + -
399I LEU* 6.0 6.3 - - + -
450I GLN 2.8 14.0 + - - +
451I CYS* 3.6 25.8 - - + -
453I ALA* 1.4 74.2 - - - +
455I LEU* 1.3 68.0 + - + +
457I MET* 3.4 2.6 + - - +
458I ARG* 3.1 30.5 + - + +
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Residues in contact with LEU 455 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399I LEU* 3.4 30.7 - - + -
402I ILE* 4.0 14.4 - - + -
451I CYS 3.1 15.8 + - - +
452I LYS* 3.2 16.3 + - + +
454I HIS* 1.3 85.6 - - + +
456I VAL* 1.3 76.6 + - + +
458I ARG* 3.2 14.3 + - + +
459I LEU* 3.2 46.6 + - + +
522I TRP* 5.2 4.7 - - + -
637I LEU* 5.1 8.3 - - + -
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Residues in contact with VAL 456 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368I TRP* 5.7 6.3 - - + -
417I ILE* 6.3 0.9 - - + -
452I LYS* 2.9 28.6 + - + +
453I ALA* 3.8 5.2 - - - +
455I LEU* 1.3 84.9 - - + +
457I MET* 1.4 69.7 + - + +
459I LEU* 3.0 8.6 + - + +
460I ILE* 2.9 25.6 + - + +
518I LEU* 6.5 0.4 - - + -
519I ILE* 4.8 14.6 - - + -
522I TRP* 3.6 46.0 - - + +
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Residues in contact with MET 457 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368I TRP* 3.6 34.5 - - + +
372I GLY* 3.7 31.4 - - - +
373I ILE* 3.6 29.2 - - + +
376I TYR* 4.9 7.9 - - + -
453I ALA 3.0 14.2 + - - +
454I HIS 3.9 4.3 - - - +
456I VAL* 1.4 75.8 - - + +
458I ARG* 1.3 63.6 + - - +
460I ILE* 3.1 23.2 - - + +
461I GLU* 3.1 37.1 + - + +
469I MET* 4.3 17.5 - - + -
503I PHE* 5.5 3.6 - - + -
507I ILE* 5.8 1.3 - - + -
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Residues in contact with ARG 458 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376I TYR* 4.3 25.7 - - + -
395I ILE* 5.0 19.2 - - - +
396I LYS* 5.0 18.6 - - - +
399I LEU* 5.9 1.8 - - - +
454I HIS* 3.1 29.3 + - - +
455I LEU* 3.2 19.1 + - + +
456I VAL 3.2 0.2 - - - -
457I MET* 1.3 79.5 - - - +
459I LEU* 1.3 66.3 + - + +
461I GLU* 3.6 11.2 - - - +
462I ASN* 3.5 28.9 + - - +
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Residues in contact with LEU 459 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455I LEU* 3.2 39.7 + - + +
456I VAL* 3.0 8.6 + - + +
458I ARG* 1.3 84.8 - - - +
460I ILE* 1.3 65.4 + - - +
462I ASN* 3.0 21.9 + - + +
463I ARG* 3.3 15.6 + - + +
518I LEU* 5.6 8.1 - - + -
522I TRP* 3.4 38.6 - - + +
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Residues in contact with ILE 460 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456I VAL* 2.9 14.0 + - + +
457I MET* 3.1 42.4 - - + +
459I LEU* 1.3 73.4 - - - +
461I GLU* 1.3 68.6 + - + +
463I ARG* 3.0 12.9 + - + +
464I ILE* 2.8 51.6 + - + +
469I MET* 6.2 0.2 - - - -
507I ILE* 5.6 3.4 - - + -
515I ILE* 4.1 27.4 - - + -
518I LEU* 4.7 16.6 - - + -
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Residues in contact with GLU 461 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376I TYR* 3.9 38.5 + - + +
457I MET* 3.1 26.1 + - - +
458I ARG* 3.6 9.2 - - + +
460I ILE* 1.3 75.4 - - - +
462I ASN* 1.4 58.2 + - - +
464I ILE* 2.8 9.0 + - - -
465I SER* 2.5 49.7 + - - +
466I MET* 3.8 19.1 - - + +
469I MET* 3.1 33.8 - - - +
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Residues in contact with ASN 462 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458I ARG* 3.5 33.2 + - - +
459I LEU* 3.0 16.7 + - - +
461I GLU* 1.4 81.9 - - - +
463I ARG* 1.3 66.0 + - + +
465I SER* 4.1 5.5 + - - +
466I MET* 5.3 9.7 - - - +
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Residues in contact with ARG 463 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459I LEU* 3.3 11.6 + - + +
460I ILE* 3.0 16.2 + - + +
461I GLU 2.8 0.6 + - - -
462I ASN* 1.3 84.5 - - + +
464I ILE* 1.3 62.9 + - + +
465I SER* 3.2 7.2 + - - -
511I SER* 4.1 1.7 + - - -
512I GLY* 5.4 2.5 - - - -
518I LEU* 5.2 13.0 - - + +
561I VAL* 5.3 8.9 - - - +
563I PRO* 5.2 12.1 - - - +
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Residues in contact with ILE 464 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460I ILE* 2.8 54.1 + - + +
461I GLU* 3.7 1.8 - - - +
463I ARG* 1.3 72.2 - - + +
465I SER* 1.3 80.5 + - - +
468I PHE* 3.3 14.6 - - - +
469I MET* 3.8 31.2 - - + +
472I VAL* 5.7 0.7 - - + -
507I ILE* 3.7 26.0 - - + -
511I SER* 2.7 51.4 + - - +
512I GLY* 3.8 8.1 - - - -
515I ILE* 5.7 1.6 - - + -
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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
------------------------------------------------------------
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