Contacts of the helix formed by residues 462 - 475 (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 ARG 462 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458J ILE* 5.3 4.0 - - + -
459J GLU* 3.0 46.4 + - + +
460J LEU 3.1 0.4 - - - -
461J SER* 1.3 82.7 + - - +
463J ILE* 1.3 60.3 + - - +
464J GLY 3.2 1.8 - - - -
465J GLU* 3.1 34.4 + - + +
466J PHE* 2.8 28.7 + - - +
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Residues in contact with ILE 463 (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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425J ARG* 3.7 44.0 - - + +
428J GLN* 4.4 19.3 - - + +
429J LEU* 4.8 15.9 - - + -
455J LEU* 5.6 10.1 - - + +
458J ILE* 4.1 12.6 - - + +
459J GLU 3.4 14.4 - - - +
460J LEU* 3.2 26.6 + - + +
462J ARG* 1.3 79.0 - - - +
464J GLY* 1.3 62.9 + - - +
466J PHE* 3.1 23.2 + - + +
467J GLU* 3.3 14.7 + - - +
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Residues in contact with GLY 464 (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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428J GLN* 5.3 9.8 - - - +
460J LEU 4.3 3.4 + - - -
461J SER 4.6 3.4 + - - -
462J ARG* 3.2 1.8 - - - +
463J ILE* 1.3 80.7 - - - +
465J GLU* 1.3 57.1 + - - +
467J GLU* 4.1 17.1 + - - +
468J SER* 4.3 4.5 + - - -
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Residues in contact with GLU 465 (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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461J SER 4.7 4.1 + - - +
462J ARG* 3.1 48.1 - - + +
464J GLY* 1.3 75.3 - - - +
466J PHE* 1.3 60.5 + - - +
467J GLU 3.4 0.9 - - - -
468J SER* 3.4 19.5 + - - +
469J SER* 3.0 18.5 + - - -
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Residues in contact with PHE 466 (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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429J LEU* 6.3 1.6 - - + -
446J LEU* 4.8 9.0 - - + -
449J ALA* 5.3 3.4 - - + -
455J LEU* 3.3 51.1 - - + -
458J ILE* 5.4 8.7 - - + -
462J ARG 2.8 17.9 + - - +
463J ILE* 3.1 18.3 + - + +
465J GLU* 1.3 77.5 - - - +
467J GLU* 1.3 63.4 + - - +
469J SER* 2.9 7.4 + - - -
470J PHE* 2.8 61.4 + + + +
503J THR* 6.3 0.7 - - + -
506J PHE* 3.6 30.7 - + - -
507J VAL* 6.1 1.6 - - - -
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Residues in contact with GLU 467 (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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153J LYS* 3.3 29.9 + - - +
429J LEU* 5.6 2.7 - - + -
431J LYS 4.6 2.3 - - - +
432J GLN* 5.5 3.8 - - - +
438J LEU* 3.4 22.3 - - - +
446J LEU* 3.9 32.6 - - + +
463J ILE 3.3 10.6 + - - +
464J GLY* 4.2 11.0 - - - +
465J GLU 3.4 0.2 - - - -
466J PHE* 1.3 83.5 - - + +
468J SER* 1.3 61.2 + - - +
469J SER 3.2 0.4 + - - -
470J PHE 4.4 0.2 - - - -
471J LEU* 3.1 36.1 + - + +
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Residues in contact with SER 468 (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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464J GLY 4.3 3.9 + - - -
465J GLU* 3.4 22.0 + - - +
467J GLU* 1.3 81.5 - - - +
469J SER* 1.3 58.1 + - - +
471J LEU* 4.4 7.5 - - - +
472J SER* 2.9 20.7 + - - -
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Residues in contact with SER 469 (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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465J GLU 3.0 15.8 + - - -
466J PHE* 2.9 22.9 + - - -
468J SER* 1.3 78.9 - - - +
470J PHE* 1.3 59.3 + - - +
471J LEU 3.3 1.1 - - - -
472J SER* 3.1 15.6 + - - -
473J TYR* 3.1 18.4 + - - +
506J PHE* 3.6 19.0 - - - -
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Residues in contact with PHE 470 (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* 3.8 23.8 - - + -
446J LEU* 4.9 11.4 - - + -
449J ALA* 5.5 2.7 - - + -
466J PHE* 2.8 41.1 + + + +
467J GLU* 4.4 2.7 - - - +
469J SER* 1.3 76.0 + - - +
471J LEU* 1.3 65.6 + - + +
473J TYR* 3.4 8.9 - + - +
474J LEU* 3.3 50.9 + - + +
499J LEU* 6.1 0.7 - - + -
502J ALA 4.9 0.9 - - - -
503J THR* 3.8 39.0 - - + -
506J PHE* 3.3 48.9 - + + -
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Residues in contact with LEU 471 (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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438J LEU* 4.4 11.0 - - + -
442J GLU* 3.3 56.3 - - + +
445J PRO* 5.1 1.1 - - + -
446J LEU* 4.1 22.4 - - + -
467J GLU* 3.1 31.3 + - + +
468J SER* 4.8 5.2 - - - +
469J SER 3.3 0.4 - - - -
470J PHE* 1.3 77.6 - - + +
472J SER* 1.3 56.9 + - - +
473J TYR 3.0 4.7 - - - -
474J LEU* 2.9 17.5 + - + +
475J LYS* 2.8 38.8 + - + +
482J LEU* 4.9 1.3 - - + +
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Residues in contact with SER 472 (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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468J SER 2.9 21.2 + - - -
469J SER* 3.1 13.3 + - - -
471J LEU* 1.3 76.9 - - - +
473J TYR* 1.3 58.4 + - - +
475J LYS* 4.0 11.1 - - - +
476J SER* 3.6 21.3 + - - -
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Residues in contact with TYR 473 (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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469J SER 3.1 18.6 + - - +
470J PHE* 3.4 10.1 - + - +
471J LEU 3.0 0.4 - - - -
472J SER* 1.3 80.6 - - - +
474J LEU* 1.3 67.0 + - + +
476J SER* 4.3 1.1 - - - -
477J ASN* 3.1 57.6 + - - +
478J HIS* 4.1 23.1 + + - -
502J ALA 4.1 6.3 - - - -
505J SER* 2.9 30.6 + - - -
506J PHE* 3.3 39.3 - + + -
509J THR* 5.6 5.8 - - + -
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Residues in contact with LEU 474 (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* 3.9 23.1 - - + -
470J PHE* 3.3 45.3 - - + +
471J LEU* 2.9 12.8 + - + +
473J TYR* 1.3 86.0 - - + +
475J LYS* 1.3 55.1 + - - +
476J SER 2.9 8.4 + - - -
478J HIS* 3.1 34.3 + - + +
479J ASN* 2.8 32.7 + - - -
481J LEU* 6.0 1.1 - - + -
482J LEU* 3.6 22.9 - - + -
499J LEU* 5.7 7.6 - - + -
502J ALA* 5.2 7.9 - - + +
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Residues in contact with LYS 475 (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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442J GLU* 4.8 25.6 + - + +
471J LEU* 2.8 24.0 + - + +
472J SER* 3.9 8.9 + - - -
473J TYR 3.6 0.2 - - - -
474J LEU* 1.3 74.3 - - - +
476J SER* 1.3 58.5 + - - +
479J ASN* 4.1 17.4 - - - +
482J LEU* 3.7 19.3 - - + -
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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