Contacts of the helix formed by residues 478 - 489 (chain J) 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 HIS 478 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473J TYR* 4.1 27.1 + + - -
474J LEU* 3.1 30.4 + - + +
477J ASN* 1.3 92.2 + - + +
479J ASN* 1.3 64.7 + - - +
480J GLU* 3.0 4.3 - - - -
481J LEU* 2.9 45.9 + - + +
482J LEU* 3.4 5.7 + - - +
502J ALA* 3.6 26.2 - - + +
505J SER* 4.9 0.8 + - - -
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Residues in contact with ASN 479 (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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474J LEU 2.8 13.5 + - - +
475J LYS* 4.1 20.7 + - - +
476J SER 4.4 5.4 - - - +
477J ASN 3.4 4.0 + - - -
478J HIS* 1.3 75.8 - - - +
480J GLU* 1.3 62.3 + - + +
482J LEU* 3.3 16.3 + - - +
483J THR* 2.8 31.9 + - - -
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Residues in contact with GLU 480 (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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477J ASN 6.0 0.9 - - - +
478J HIS* 2.9 2.1 + - - -
479J ASN* 1.3 78.8 - - + +
481J LEU* 1.3 64.6 + - + +
483J THR* 3.2 18.5 + - - -
484J GLU* 3.2 14.0 + - - +
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Residues in contact with LEU 481 (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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474J LEU* 6.0 1.1 - - + -
478J HIS* 2.9 42.6 + - + +
480J GLU* 1.3 78.0 - - + +
482J LEU* 1.3 64.7 + - + +
484J GLU* 3.5 17.1 + - - +
485J ILE* 3.3 22.1 + - - +
495J LEU* 3.7 28.5 - - + +
498J SER* 3.2 33.7 - - - +
499J LEU* 5.0 10.3 - - + +
502J ALA* 4.5 9.9 - - + -
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Residues in contact with LEU 482 (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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441J GLU* 3.7 41.6 - - + +
442J GLU* 5.2 6.5 - - + -
445J PRO* 4.4 4.7 - - + -
471J LEU* 6.1 0.9 - - + -
474J LEU* 3.5 57.0 - - + +
475J LYS* 3.7 22.4 - - + -
478J HIS 3.8 8.7 - - - +
479J ASN* 3.3 14.3 + - - +
480J GLU 3.2 0.2 - - - -
481J LEU* 1.3 79.8 - - + +
483J THR* 1.3 62.1 + - - +
485J ILE* 3.4 6.2 + - + +
486J ARG* 3.2 22.0 + - - +
499J LEU* 6.6 0.2 - - + -
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Residues in contact with THR 483 (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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479J ASN* 2.8 22.8 + - - -
480J GLU* 3.2 14.3 + - - -
482J LEU* 1.3 76.2 - - - +
484J GLU* 1.3 62.8 + - - +
486J ARG* 3.5 23.5 + - - +
487J GLU* 3.1 47.7 + - - +
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Residues in contact with GLU 484 (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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480J GLU 3.2 11.3 + - - +
481J LEU* 3.5 16.8 + - - +
482J LEU 3.3 0.2 - - - -
483J THR* 1.3 74.4 - - - +
485J ILE* 1.3 61.2 + - - +
487J GLU* 4.7 5.2 - - - -
488J LYS* 2.8 60.5 + - + +
490J GLU 5.2 0.2 + - - -
492J SER* 5.3 4.7 + - - -
495J LEU* 3.3 36.9 - - + +
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Residues in contact with ILE 485 (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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382J VAL* 6.2 0.4 - - + -
384J ALA* 4.4 13.7 - - + -
440J THR* 4.2 6.1 - - + +
441J GLU* 3.8 16.4 - - - +
444J VAL* 3.8 30.7 - - + -
481J LEU 3.3 15.9 - - - +
482J LEU* 3.4 9.2 + - + +
483J THR 3.3 0.4 - - - -
484J GLU* 1.3 73.2 - - - +
486J ARG* 1.3 67.2 + - - +
487J GLU 3.0 1.3 - - - -
489J GLY* 2.9 27.0 + - - +
490J GLU 3.8 5.6 - - - +
491J LEU* 3.5 33.0 - - + -
495J LEU* 3.7 19.1 - - + -
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Residues in contact with ARG 486 (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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199J LYS* 5.5 4.7 + - - -
441J GLU* 3.1 35.6 + - - +
482J LEU 3.2 12.0 + - - +
483J THR* 3.7 19.9 - - - +
484J GLU 3.4 0.2 - - - -
485J ILE* 1.3 80.0 - - - +
487J GLU* 1.3 87.3 + - - +
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Residues in contact with GLU 487 (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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199J LYS* 5.5 5.3 + - - +
483J THR* 3.1 29.7 + - - +
484J GLU* 4.1 4.0 - - - +
485J ILE 3.0 0.4 - - - -
486J ARG* 1.3 107.5 + - - +
488J LYS* 1.3 67.9 + - + +
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Residues in contact with LYS 488 (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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484J GLU* 2.8 48.1 + - + +
487J GLU* 1.3 79.4 - - + +
489J GLY* 1.3 62.7 + - - +
490J GLU* 3.2 18.8 + - + +
492J SER* 6.0 2.0 - - - +
495J LEU* 6.0 0.2 - - + -
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Residues in contact with GLY 489 (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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382J VAL* 3.9 12.0 - - - +
383J LYS* 3.5 6.9 + - - +
384J ALA* 2.8 32.0 + - - -
484J GLU 3.7 1.8 + - - -
485J ILE* 2.9 22.3 + - - -
487J GLU 3.5 0.6 - - - -
488J LYS* 1.3 78.8 - - - +
490J GLU* 1.3 62.7 + - - +
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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