Contacts of the helix formed by residues 492 - 509 (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 SER 492 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484J GLU* 5.3 4.4 + - - -
488J LYS* 6.0 2.1 - - - +
490J GLU* 4.1 5.3 + - - +
491J LEU* 1.3 75.5 + - - +
493J LYS* 1.3 59.9 + - - +
494J GLU* 3.0 19.7 - - - -
495J LEU* 2.9 13.7 + - - +
496J LEU* 2.7 32.2 + - - +
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Residues in contact with LYS 493 (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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491J LEU 5.4 1.3 - - - +
492J SER* 1.3 78.0 - - - +
494J GLU* 1.3 70.4 + - - +
496J LEU* 4.0 6.0 - - - +
497J ALA* 3.1 28.4 + - - +
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Residues in contact with GLU 494 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492J SER* 3.3 19.0 - - - -
493J LYS* 1.3 89.6 + - - +
495J LEU* 1.3 59.2 + - - +
497J ALA* 4.1 4.2 - - - +
498J SER* 3.2 23.6 + - - -
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Residues in contact with LEU 495 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481J LEU* 3.7 27.6 - - + +
484J GLU* 3.3 47.3 - - + +
485J ILE* 3.7 16.8 - - + -
488J LYS* 6.0 0.2 - - + -
490J GLU 3.6 23.8 - - - +
491J LEU* 3.9 13.9 - - + -
492J SER* 2.9 17.7 + - - +
494J GLU* 1.3 79.6 - - - +
496J LEU* 1.3 59.5 + - - +
497J ALA 3.3 0.2 - - - -
498J SER* 3.4 3.0 + - - -
499J LEU* 2.9 31.9 + - + +
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Residues in contact with LEU 496 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387J GLN* 5.8 6.7 - - + +
448J TYR* 3.5 31.9 + - + +
452J ASN* 5.4 0.4 - - - +
491J LEU* 4.9 28.4 - - + +
492J SER 2.7 16.3 + - - +
493J LYS* 4.4 4.3 - - - +
495J LEU* 1.3 76.5 - - - +
497J ALA* 1.3 60.8 + - - +
499J LEU* 4.0 6.0 - - + +
500J LYS* 3.1 29.1 + - + +
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Residues in contact with ALA 497 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493J LYS 3.1 22.7 + - - +
494J GLU* 4.3 4.7 - - - +
496J LEU* 1.3 77.6 - - - +
498J SER* 1.3 63.1 + - - +
500J LYS* 3.7 12.6 + - - +
501J SER* 3.7 13.3 + - - -
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Residues in contact with SER 498 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478J HIS* 5.5 0.3 - - - -
481J LEU* 3.2 32.9 - - - +
494J GLU 3.2 19.4 + - - -
495J LEU* 3.5 6.5 - - - -
496J LEU 3.2 0.6 - - - -
497J ALA* 1.3 80.6 - - - +
499J LEU* 1.3 61.7 + - - +
501J SER* 3.7 3.0 + - - -
502J ALA* 3.2 21.9 + - - +
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Residues in contact with LEU 499 (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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388J VAL* 5.1 5.8 - - + -
444J VAL* 5.0 4.0 - - + +
445J PRO* 4.8 22.7 - - + -
448J TYR* 3.5 42.6 - - + -
470J PHE* 6.1 0.7 - - + -
474J LEU* 5.7 8.3 - - + -
481J LEU* 5.0 10.9 - - + +
482J LEU* 6.6 0.2 - - + -
491J LEU* 5.3 11.2 - - + -
495J LEU* 2.9 24.1 + - + +
496J LEU* 4.0 7.0 - - + +
498J SER* 1.3 75.3 - - - +
500J LYS* 1.3 65.8 + - - +
502J ALA* 3.0 9.7 + - + +
503J THR* 2.9 37.2 + - - +
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Residues in contact with LYS 500 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448J TYR* 3.5 26.0 - - - +
452J ASN* 5.5 3.1 - - - -
454J HIS* 3.7 13.3 + - + +
496J LEU* 3.1 23.3 + - + +
497J ALA* 4.0 9.4 - - - +
498J SER 3.4 0.2 - - - -
499J LEU* 1.3 77.2 - - - +
501J SER* 1.3 59.2 + - - +
504J GLU* 3.3 46.4 + - - +
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Residues in contact with SER 501 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497J ALA 3.7 11.5 + - - -
498J SER* 3.7 3.7 + - - -
499J LEU 3.1 0.4 - - - -
500J LYS* 1.3 75.7 - - - +
502J ALA* 1.3 66.0 + - - +
503J THR 3.2 2.5 + - - -
504J GLU* 3.4 13.8 + - - +
505J SER* 3.3 21.1 + - - -
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Residues in contact with ALA 502 (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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470J PHE* 4.9 1.4 - - - -
473J TYR* 4.1 11.4 - - - -
474J LEU* 5.2 5.3 - - + +
478J HIS* 3.6 38.1 - - + +
481J LEU* 4.5 4.5 - - + -
498J SER 3.2 19.2 + - - +
499J LEU* 3.0 13.1 + - + +
501J SER* 1.3 77.1 - - - +
503J THR* 1.3 58.5 + - - +
505J SER* 2.6 24.2 + - - -
506J PHE* 4.0 0.9 + - - +
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Residues in contact with THR 503 (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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445J PRO* 5.5 2.0 + - - +
448J TYR* 4.2 6.8 - - - +
449J ALA* 4.2 12.8 - - + +
454J HIS* 3.4 39.3 - - + +
466J PHE* 6.3 0.9 - - + -
470J PHE* 3.8 30.3 - - + -
499J LEU* 2.9 28.8 + - - +
502J ALA* 1.3 74.3 - - - +
504J GLU* 1.3 58.4 + - - +
505J SER 2.9 4.9 - - - -
506J PHE* 2.9 22.9 + - - +
507J VAL* 3.4 8.6 + - + +
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Residues in contact with GLU 504 (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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454J HIS* 3.6 17.3 - - + +
500J LYS* 3.3 42.3 + - - +
501J SER* 3.4 15.0 + - - +
503J THR* 1.3 78.5 - - - +
505J SER* 1.3 61.4 + - - +
506J PHE 3.3 0.2 - - - -
507J VAL* 3.4 24.9 + - + +
508J ALA* 4.1 5.0 + - - +
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Residues in contact with SER 505 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473J TYR* 2.9 22.7 + - - -
478J HIS* 4.9 1.0 + - - -
501J SER 3.3 11.4 + - - -
502J ALA* 2.6 24.4 + - - -
503J THR 2.9 0.4 + - - -
504J GLU* 1.3 80.3 - - - +
506J PHE* 1.3 56.3 + - - +
507J VAL 3.2 1.0 + - - -
508J ALA* 4.0 3.3 + - - +
509J THR* 3.1 25.8 + - - +
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Residues in contact with PHE 506 (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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466J PHE* 3.6 30.9 - + - -
469J SER* 3.6 29.2 - - - -
470J PHE* 3.3 39.9 - + + -
473J TYR* 3.3 52.5 - + + -
503J THR 2.9 4.8 + - - +
505J SER* 1.3 78.3 + - - +
507J VAL* 1.3 64.7 - - - +
508J ALA 3.6 0.2 - - - -
509J THR* 3.6 30.0 - - + -
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Residues in contact with VAL 507 (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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454J HIS* 3.4 39.0 - - + +
455J LEU* 6.1 1.1 - - + -
458J ILE* 5.1 13.4 - - + +
466J PHE* 6.1 2.0 - - - -
503J THR* 3.4 14.6 + - + +
504J GLU* 3.4 19.5 - - + +
505J SER 3.2 0.4 - - - -
506J PHE* 1.3 77.0 - - - +
508J ALA* 1.3 71.7 + - - +
509J THR 4.3 1.2 - - - -
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Residues in contact with ALA 508 (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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504J GLU 4.1 4.3 + - - +
505J SER 4.0 5.0 + - - +
506J PHE 3.6 0.2 - - - -
507J VAL* 1.3 84.4 - - - +
509J THR* 1.3 61.4 + - - +
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Residues in contact with THR 509 (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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473J TYR* 5.6 6.7 - - + +
505J SER 3.1 20.9 - - - +
506J PHE* 3.6 36.4 - - + -
507J VAL 4.3 1.1 - - - -
508J ALA* 1.3 83.9 - - - +
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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