Contacts of the helix formed by residues 463 - 473 (chain X) in PDB entry 3FKS
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 ILE 463 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21K VAL* 5.8 2.0 - - + -
26K ASN* 3.4 33.9 - - + +
413X PHE* 4.0 5.8 - - + -
436X ASP* 4.5 0.8 + - - +
440X SER* 2.9 41.0 + - - +
443X ALA* 5.0 2.0 - - + -
444X VAL* 4.6 8.1 - - + -
449X TYR* 3.6 54.3 - - + +
457X PHE* 4.7 3.1 - - + -
462X GLY* 1.3 68.7 - - - -
464X GLU* 1.3 64.2 + - - +
465X ASP 3.1 2.0 - - - -
466X VAL* 3.0 37.9 + - + +
467X VAL* 3.5 5.9 + - - +
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Residues in contact with GLU 464 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K VAL* 4.7 14.1 - - + +
26K ASN 3.2 24.6 - - - +
27K LEU* 3.7 0.9 - - - -
28K ASN* 3.2 17.9 + - - +
29K GLU* 2.8 35.6 + - - +
30K THR* 2.7 38.5 + - + +
436X ASP* 5.7 0.7 - - - +
462X GLY* 4.9 4.0 - - - +
463X ILE* 1.3 85.0 - - + +
465X ASP* 1.3 65.2 + - + +
466X VAL 3.1 0.2 - - - -
467X VAL* 3.0 28.1 - - + +
468X ALA* 3.4 9.7 + - - +
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Residues in contact with ASP 465 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K GLU* 5.7 5.0 - - - +
430X LYS* 3.1 43.7 + - - +
460X VAL* 4.3 10.7 - - + +
461X GLY* 3.9 14.9 + - - +
462X GLY 3.4 16.1 + - - +
463X ILE 3.1 0.6 - - - -
464X GLU* 1.3 84.4 - - + +
466X VAL* 1.3 58.4 - - - +
468X ALA* 3.6 9.6 - - - +
469X LYS* 3.1 25.6 + - - +
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Residues in contact with VAL 466 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413X PHE* 3.6 33.2 - - + -
449X TYR* 5.3 0.2 - - + -
452X ILE* 3.9 17.0 - - + -
456X ALA* 3.8 32.4 - - + +
457X PHE* 4.3 14.1 - - + -
460X VAL* 4.0 11.0 - - + -
462X GLY 3.8 2.7 - - - +
463X ILE* 3.0 23.2 + - + +
465X ASP* 1.3 75.0 - - - +
467X VAL* 1.3 57.7 + - + +
468X ALA 2.9 4.4 + - - -
469X LYS* 2.9 3.9 + - - +
470X ALA* 2.8 32.1 + - - +
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Residues in contact with VAL 467 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ILE* 3.8 22.4 - - + +
19K LYS 4.1 11.4 - - - +
20K GLY* 6.0 0.7 - - - -
21K VAL* 5.7 6.1 - - + +
30K THR* 6.5 0.7 - - + -
449X TYR* 3.4 36.6 - - + +
452X ILE* 4.9 2.0 - - + -
463X ILE 4.5 1.6 - - - +
464X GLU* 3.0 33.2 - - + +
466X VAL* 1.3 76.0 - - + +
468X ALA* 1.3 57.9 + - - +
470X ALA* 3.9 9.2 - - - +
471X GLU* 3.1 35.5 + - - +
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Residues in contact with ALA 468 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K THR* 6.4 1.6 - - + -
91K LYS* 5.4 15.6 + - - +
464X GLU 3.4 10.7 + - - +
465X ASP* 3.6 17.0 - - - +
466X VAL 2.9 0.8 - - - -
467X VAL* 1.3 80.3 - - - +
469X LYS* 1.3 65.1 + - - +
471X GLU* 3.3 9.0 + - - +
472X LYS* 3.2 19.6 + - - +
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Residues in contact with LYS 469 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427X ILE* 5.8 3.2 - - - +
455X HIS* 3.5 38.3 + - - +
456X ALA* 3.8 20.2 - - - +
458X TYR* 2.8 27.3 + - - -
459X MET* 4.7 4.0 + - - +
460X VAL* 3.8 12.9 - - + +
465X ASP* 3.1 13.7 + - - +
466X VAL 2.9 4.3 + - - +
468X ALA* 1.3 76.4 - - - +
470X ALA* 1.3 55.1 + - - +
472X LYS* 3.0 10.9 + - + +
473X LEU* 2.7 47.1 + - + +
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Residues in contact with ALA 470 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ILE* 5.1 4.5 - - + -
452X ILE* 4.4 17.5 - - + -
453X PRO* 4.6 11.8 - - + +
456X ALA* 4.3 17.2 - - + +
466X VAL 2.8 16.4 + - - +
467X VAL* 3.9 11.2 - - - +
469X LYS* 1.3 77.3 - - - +
471X GLU* 1.3 56.2 + - - +
473X LEU* 3.2 9.0 + - - +
474X ALA* 3.1 25.3 + - - +
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Residues in contact with GLU 471 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ILE* 4.6 16.4 - - + +
89K LEU* 5.3 10.2 - - - +
91K LYS* 4.4 16.2 + - - +
467X VAL* 3.1 21.3 + - - +
468X ALA* 3.3 7.7 + - - +
469X LYS 3.2 0.4 - - - -
470X ALA* 1.3 77.8 - - - +
472X LYS* 1.3 59.2 + - - +
474X ALA* 3.4 20.2 + - - +
475X ALA* 3.8 8.3 + - - +
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Residues in contact with LYS 472 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468X ALA 3.2 11.4 + - - +
469X LYS* 3.0 14.0 + - + +
471X GLU* 1.3 74.1 - - - +
473X LEU* 1.3 60.6 + - + +
474X ALA 3.1 7.8 + - - -
475X ALA* 3.6 20.1 + - + +
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Residues in contact with LEU 473 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415T SER* 6.0 2.6 - - - -
453X PRO* 5.7 9.1 - - + +
455X HIS* 3.6 39.0 - - + +
456X ALA* 4.5 9.9 - - + +
469X LYS* 2.7 37.1 + - + +
470X ALA* 3.2 9.4 + - - +
472X LYS* 1.3 78.8 - - + +
474X ALA* 1.3 58.1 + - - +
475X ALA 3.5 3.6 - - - -
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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
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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