Contacts of the helix formed by residues 472 - 481 (chain D) in PDB entry 1FSJ
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 ASN 472 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470D ASN 3.9 1.8 + - - -
471D LEU* 1.3 74.5 - - - +
473D PRO* 1.3 73.1 - - + +
474D SER* 3.2 11.7 + - - -
475D ASN* 2.8 35.7 + - - +
476D LYS* 2.8 28.3 + - - +
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Residues in contact with PRO 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D LEU 4.8 0.2 - - - +
472D ASN* 1.3 89.4 - - + +
474D SER* 1.3 62.1 + - - +
476D LYS* 3.3 14.7 + - + +
477D SER* 3.0 23.0 + - - -
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Residues in contact with SER 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D ASN* 3.2 12.0 + - - -
473D PRO* 1.3 78.8 - - - +
475D ASN* 1.3 58.6 + - - +
477D SER* 3.2 9.0 + - - -
478D SER* 3.0 31.8 + - - -
486D PHE* 5.0 12.1 - - - -
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Residues in contact with ASN 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D LEU* 4.0 19.9 - - + +
472D ASN* 2.8 30.6 + - - +
474D SER* 1.3 70.6 - - - +
476D LYS* 1.3 60.6 + - - +
478D SER* 3.3 7.0 + - - -
479D VAL* 2.9 33.9 + - - +
485D PRO* 3.4 18.2 - - + +
486D PHE* 2.9 59.0 + - - +
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Residues in contact with LYS 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462D SER* 4.7 0.7 - - - -
468D SER* 3.6 23.8 - - - +
469D LYS* 4.0 11.9 + - - +
471D LEU* 3.0 31.4 + - + +
472D ASN* 2.8 19.7 + - - +
473D PRO* 3.6 11.9 - - + +
474D SER 3.3 0.2 - - - -
475D ASN* 1.3 77.0 - - - +
477D SER* 1.3 63.3 + - - +
479D VAL* 3.3 10.3 - - + +
480D SER* 3.2 23.7 + - - -
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Residues in contact with SER 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473D PRO 3.0 13.1 + - - -
474D SER* 3.4 10.8 - - - -
476D LYS* 1.3 75.2 - - - +
478D SER* 1.3 61.4 + - - +
480D SER* 2.6 24.6 + - - -
481D LYS* 3.4 21.8 + - - +
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Residues in contact with SER 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474D SER* 3.0 17.1 + - - -
475D ASN* 3.5 18.4 + - - -
477D SER* 1.3 75.4 + - - +
479D VAL* 1.3 63.5 + - - +
481D LYS* 3.1 13.7 + - - +
483D TYR* 3.0 49.0 + - - +
484D SER 4.9 1.1 - - - -
485D PRO* 4.8 6.5 - - - -
486D PHE* 5.4 6.8 - - - -
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Residues in contact with VAL 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D TRP* 3.4 35.9 - - + +
459D GLU* 3.5 6.6 - - - -
461D VAL* 5.0 0.9 - - + -
462D SER* 3.5 20.2 - - - +
468D SER* 5.4 0.7 - - - -
471D LEU* 3.9 19.1 - - + -
475D ASN 2.9 22.1 + - - +
476D LYS* 3.3 17.5 - - + +
478D SER* 1.3 67.7 - - - +
480D SER* 1.3 57.2 + - - +
481D LYS 3.0 5.4 - - - -
482D GLY* 2.9 15.6 + - - -
483D TYR 3.5 17.7 - - - +
485D PRO* 3.7 27.6 - - + -
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Residues in contact with SER 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D GLU* 4.2 10.4 - - - +
462D SER* 3.4 19.4 + - - -
463D LYS* 5.5 3.3 - - - -
476D LYS 3.2 12.8 + - - -
477D SER* 2.6 25.5 + - - -
479D VAL* 1.3 77.5 - - - +
481D LYS* 1.3 63.3 + - - +
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Residues in contact with LYS 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455D LYS* 4.1 15.6 - - - -
459D GLU* 4.3 3.8 - - - +
477D SER* 3.5 27.2 + - - +
478D SER* 3.1 8.0 + - - +
479D VAL 3.0 0.6 - - - -
480D SER* 1.3 83.6 - - - +
482D GLY* 1.3 58.7 + - - +
483D TYR* 3.7 42.2 + - + +
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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