Contacts of the helix formed by residues 479 - 489 (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 ASN 479 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474K LEU 3.2 10.7 + - - +
475K LYS* 3.8 15.2 + - - +
476K SER 4.6 4.7 + - - +
477K ASN 3.7 2.8 + - - -
478K HIS* 1.3 75.0 - - - +
480K GLU* 1.3 61.7 + - - +
481K LEU 3.4 0.9 - - - -
482K LEU* 3.5 23.8 - - - +
483K THR* 2.9 25.7 + - - -
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Residues in contact with GLU 480 (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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477K ASN 5.4 5.2 - - - +
478K HIS* 3.2 2.6 - - + -
479K ASN* 1.3 80.9 - - + +
481K LEU* 1.3 69.4 + - + +
482K LEU 3.2 0.2 - - - -
483K THR* 3.4 15.3 + - - -
484K GLU* 3.4 22.7 + - - +
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Residues in contact with LEU 481 (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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470K PHE* 6.1 1.8 - - + -
474K LEU* 5.0 9.2 - - + -
478K HIS* 3.5 38.3 + - + +
479K ASN 3.4 0.2 - - - -
480K GLU* 1.3 80.4 - - + +
482K LEU* 1.3 64.4 + - + +
483K THR 3.3 0.4 + - - -
484K GLU* 3.7 12.5 + - - +
485K ILE* 3.2 34.4 + - + +
495K LEU* 3.5 30.0 - - + +
498K SER* 4.5 14.6 - - - +
499K LEU* 4.0 24.9 - - + -
502K ALA* 4.6 8.1 - - + -
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Residues in contact with LEU 482 (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* 4.0 39.8 - - + +
442K GLU* 5.2 4.5 - - + +
445K PRO* 6.2 0.7 - - + -
471K LEU* 6.2 2.5 - - + -
474K LEU* 3.4 53.6 - - + +
475K LYS* 5.4 2.5 - - + -
478K HIS 3.9 9.2 - - - +
479K ASN* 3.5 19.1 - - - +
480K GLU 3.2 0.6 - - - -
481K LEU* 1.3 79.3 - - + +
483K THR* 1.3 63.2 + - - +
485K ILE* 3.9 1.5 + - + -
486K ARG* 3.4 34.5 + - - +
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Residues in contact with THR 483 (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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479K ASN* 2.9 21.3 + - - -
480K GLU* 3.4 10.4 + - - -
481K LEU 3.3 0.6 - - - -
482K LEU* 1.3 77.7 - - - +
484K GLU* 1.3 67.0 + - + +
486K ARG* 4.1 3.7 - - - +
487K GLU* 3.1 41.9 + - + +
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Residues in contact with GLU 484 (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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480K GLU* 3.4 20.3 + - - +
481K LEU* 4.0 11.9 - - - +
482K LEU 3.4 0.2 - - - -
483K THR* 1.3 78.4 - - - +
485K ILE* 1.3 58.8 + - - +
487K GLU* 4.1 0.8 - - - +
488K LYS* 2.8 58.5 + - + +
490K GLU 5.5 0.7 - - - -
492K SER* 5.4 1.4 + - - -
495K LEU* 3.3 43.9 - - + +
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Residues in contact with ILE 485 (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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384K ALA* 4.4 17.9 - - + -
440K THR* 4.9 6.5 - - + +
441K GLU* 4.2 30.5 - - + +
444K VAL* 4.1 25.8 - - + -
445K PRO* 5.5 4.0 - - + -
481K LEU* 3.2 25.2 + - + +
482K LEU* 5.2 1.3 - - + -
483K THR 3.5 0.2 - - - -
484K GLU* 1.3 75.3 - - - +
486K ARG* 1.3 58.3 + - - +
489K GLY* 2.8 33.1 + - - +
490K GLU 4.8 4.7 - - - -
491K LEU* 4.1 16.2 - - + -
495K LEU* 4.1 18.4 - - + -
499K LEU* 5.4 7.9 - - + -
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Residues in contact with ARG 486 (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* 3.7 32.7 + - - +
479K ASN* 6.0 0.2 + - - -
482K LEU* 3.4 24.5 + - - +
483K THR* 4.1 4.4 - - - +
484K GLU 3.3 0.8 - - - -
485K ILE* 1.3 80.1 - - - +
487K GLU* 1.3 83.1 + - - +
488K LYS 4.7 0.2 - - - -
489K GLY* 4.4 3.1 + - - -
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Residues in contact with GLU 487 (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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483K THR* 3.1 30.6 + - + +
484K GLU* 4.1 1.3 - - - +
486K ARG* 1.3 101.9 + - + +
488K LYS* 1.3 68.3 + - + +
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Residues in contact with LYS 488 (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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484K GLU* 2.8 40.8 + - + +
486K ARG 4.7 0.2 - - - -
487K GLU* 1.3 82.7 - - + +
489K GLY* 1.3 57.0 + - - +
490K GLU* 3.3 29.1 + - + +
492K SER* 5.5 11.9 - - - +
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Residues in contact with GLY 489 (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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382K VAL* 3.2 22.7 - - - +
383K LYS 4.2 0.3 + - - -
384K ALA* 3.1 25.9 + - - +
440K THR* 6.3 0.4 - - - -
485K ILE* 2.8 27.1 + - - +
486K ARG 4.8 2.5 - - - -
487K GLU 3.7 0.4 - - - -
488K LYS* 1.3 73.0 - - - +
490K GLU* 1.3 61.8 + - - +
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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