Contacts of the helix formed by residues 464 - 476 (chain K) 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 GLY 464 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428K GLN* 4.1 11.2 - - - +
429K LEU* 5.2 3.8 - - - -
461K SER 5.3 0.4 + - - -
462K ARG* 3.1 1.0 - - - +
463K ILE* 1.3 77.1 - - - +
465K GLU* 1.3 63.3 + - - +
466K PHE 3.3 0.9 - - - -
467K GLU* 3.2 27.4 + - - +
468K SER* 3.7 5.9 + - - -
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Residues in contact with GLU 465 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461K SER 4.7 2.5 - - - +
462K ARG* 2.9 53.5 + - + +
464K GLY* 1.3 76.2 - - - +
466K PHE* 1.3 57.8 + - - +
468K SER* 2.7 28.0 + - - -
469K SER* 2.9 22.5 + - - +
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Residues in contact with PHE 466 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429K LEU* 6.2 0.4 - - + -
446K LEU* 4.9 13.7 - - + -
449K ALA* 5.8 3.4 - - + -
455K LEU* 3.8 33.7 - - + -
458K ILE* 4.1 23.1 - - + -
462K ARG* 3.4 4.7 + - - +
463K ILE 3.8 10.8 - - - +
464K GLY 3.3 0.6 - - - -
465K GLU* 1.3 78.0 - - - +
467K GLU* 1.3 59.7 + - - +
469K SER* 3.6 9.2 - - - -
470K PHE* 2.8 80.4 + + + +
503K THR* 5.5 8.1 - - - -
505K SER 6.5 0.4 - - - -
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Residues in contact with GLU 467 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K LYS* 3.0 32.0 + - - -
429K LEU* 3.8 17.1 - - + +
432K GLN* 5.9 0.3 - - - +
438K LEU* 4.0 18.7 - - + +
446K LEU* 3.9 34.7 - - + +
463K ILE 4.1 1.9 + - - +
464K GLY* 3.2 21.8 + - - +
465K GLU 3.1 0.4 - - - -
466K PHE* 1.3 81.6 - - - +
468K SER* 1.3 55.5 - - - +
470K PHE* 5.1 0.8 - - - +
471K LEU* 3.4 24.3 + - - +
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Residues in contact with SER 468 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464K GLY 3.7 3.4 + - - -
465K GLU* 2.7 33.8 + - - -
467K GLU* 1.3 78.5 - - - +
469K SER* 1.3 63.5 + - - +
471K LEU* 3.7 11.2 - - - +
472K SER* 3.5 21.0 + - - -
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Residues in contact with SER 469 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465K GLU* 2.9 20.4 + - - +
466K PHE* 3.2 12.0 + - - -
468K SER* 1.3 75.9 + - - +
470K PHE* 1.3 62.1 + - - +
471K LEU 3.0 5.0 + - - -
472K SER* 3.2 16.2 + - - -
473K TYR* 3.3 10.9 + - - +
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Residues in contact with PHE 470 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445K PRO* 4.5 20.4 - - + -
446K LEU* 6.1 3.6 - - + -
466K PHE* 2.8 59.5 + + + +
467K GLU* 5.1 1.3 - - - +
469K SER* 1.3 73.6 - - - +
471K LEU* 1.3 59.2 + - - +
472K SER 3.4 0.2 - - - -
473K TYR* 3.4 25.7 + + + +
474K LEU* 3.1 63.3 + - + +
481K LEU* 6.1 1.6 - - + -
502K ALA* 3.5 34.5 - - + -
503K THR* 4.9 9.4 - - + -
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Residues in contact with LEU 471 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438K LEU* 5.9 2.2 - - + -
442K GLU* 3.6 38.6 - - + +
467K GLU 3.4 21.6 + - - +
468K SER* 3.7 12.1 - - - +
469K SER 3.0 0.4 - - - -
470K PHE* 1.3 77.8 - - - +
472K SER* 1.3 64.2 + - - +
473K TYR 3.1 0.2 - - - -
474K LEU* 3.1 26.8 + - + +
475K LYS* 3.2 31.9 + - - +
482K LEU* 6.2 2.9 - - + -
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Residues in contact with SER 472 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468K SER 3.5 11.2 + - - -
469K SER* 3.2 10.6 + - - -
471K LEU* 1.3 77.2 - - - +
473K TYR* 1.3 61.9 + - - +
475K LYS* 3.2 27.3 + - - +
476K SER* 3.8 9.4 + - - -
477K ASN* 5.3 0.2 - - - +
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Residues in contact with TYR 473 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469K SER 3.3 10.7 + - - +
470K PHE* 3.4 35.2 - + + +
471K LEU 3.1 0.4 - - - -
472K SER* 1.3 79.7 - - - +
474K LEU* 1.3 49.1 + - - +
477K ASN* 3.3 34.3 + - + +
478K HIS* 2.7 79.5 + + + -
502K ALA* 4.3 13.0 - - + +
505K SER* 4.7 10.0 + - - -
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Residues in contact with LEU 474 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441K GLU 5.8 0.2 - - - +
442K GLU* 6.0 3.6 - - - -
445K PRO* 5.4 8.3 - - + -
470K PHE* 3.1 50.3 - - + +
471K LEU* 3.1 22.8 + - + +
473K TYR* 1.3 76.6 - - + +
475K LYS* 1.3 64.8 + - - +
476K SER 3.5 0.4 - - - -
478K HIS* 3.1 46.8 - - + +
479K ASN* 3.2 12.8 - - - +
481K LEU* 5.0 9.4 - - + -
482K LEU* 3.4 35.4 - - + +
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Residues in contact with LYS 475 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471K LEU* 3.2 34.8 + - - +
472K SER* 3.2 21.0 + - - +
474K LEU* 1.3 81.3 - - - +
476K SER* 1.3 61.6 + - - +
479K ASN* 3.8 14.6 + - - +
482K LEU* 5.4 2.9 - - + -
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Residues in contact with SER 476 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472K SER 3.8 7.7 + - - -
475K LYS* 1.3 81.3 - - - +
477K ASN* 1.3 78.8 + - - +
478K HIS 3.6 0.4 - - - -
479K ASN* 4.6 6.0 + - - +
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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