Contacts of the helix formed by residues 492 - 503 (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 SER 492 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484K GLU* 5.4 1.6 + - - -
488K LYS* 5.5 12.2 - - - +
490K GLU 4.2 1.4 + - - -
491K LEU* 1.3 75.3 - - - +
493K LYS* 1.3 53.1 + - - +
494K GLU* 3.0 12.8 - - - +
495K LEU* 2.9 22.6 + - - +
496K LEU* 2.8 35.3 + - - +
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Residues in contact with LYS 493 (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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492K SER* 1.3 72.8 - - - +
494K GLU* 1.3 63.3 + - - +
496K LEU* 3.2 41.2 + - + +
497K ALA* 3.6 9.7 + - - +
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Residues in contact with GLU 494 (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* 6.2 0.2 - - - +
492K SER* 3.0 13.2 + - - +
493K LYS* 1.3 81.3 - - - +
495K LEU* 1.3 58.7 + - + +
497K ALA* 4.1 1.4 + - - +
498K SER* 3.4 21.1 + - - -
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Residues in contact with LEU 495 (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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481K LEU* 3.5 32.5 - - + +
484K GLU* 3.3 32.8 - - + +
485K ILE* 4.1 18.8 - - + -
490K GLU 5.6 1.3 - - - +
491K LEU* 3.8 28.2 - - + +
492K SER* 2.9 19.6 + - - +
494K GLU* 1.3 76.8 - - + +
496K LEU* 1.3 62.7 + - - +
497K ALA 3.3 2.7 - - - -
498K SER* 3.8 15.7 - - - +
499K LEU* 3.3 29.1 + - + +
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Residues in contact with LEU 496 (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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387K GLN* 5.0 13.5 - - + +
448K TYR* 4.6 14.2 + - + +
491K LEU* 5.5 9.6 - - + -
492K SER 2.8 14.6 + - - +
493K LYS* 3.2 40.1 + - + +
495K LEU* 1.3 80.3 - - - +
497K ALA* 1.3 58.6 + - - +
499K LEU* 4.4 4.3 + - - +
500K LYS* 3.4 22.6 - - - +
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Residues in contact with ALA 497 (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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493K LYS 3.6 8.7 + - - +
494K GLU 4.9 1.6 - - - +
496K LEU* 1.3 76.6 - - + +
498K SER* 1.3 62.5 + - - +
499K LEU 3.0 6.5 + - - -
500K LYS* 3.2 32.4 + - - +
501K SER* 4.3 3.8 + - - -
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Residues in contact with SER 498 (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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481K LEU* 4.5 12.0 - - - +
494K GLU 3.4 19.6 + - - -
495K LEU* 3.7 19.9 + - - +
496K LEU 3.6 0.2 - - - -
497K ALA* 1.3 77.7 - - - +
499K LEU* 1.3 57.1 + - - +
500K LYS 3.5 0.2 - - - -
501K SER* 2.9 24.5 + - - -
502K ALA* 4.5 0.7 + - - +
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Residues in contact with LEU 499 (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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388K VAL* 6.1 1.3 - - + -
444K VAL 5.7 0.9 - - - +
445K PRO* 5.0 19.1 - - + -
448K TYR* 4.3 31.6 - - + -
481K LEU* 4.0 27.4 - - + -
485K ILE* 5.4 8.1 - - + -
491K LEU* 5.5 13.5 - - + -
495K LEU* 3.3 29.1 + - + +
496K LEU* 4.5 5.4 - - - +
497K ALA 3.0 0.8 - - - -
498K SER* 1.3 75.3 - - - +
500K LYS* 1.3 58.6 + - + +
501K SER 2.9 12.1 + - - -
502K ALA* 3.4 8.4 + - + +
503K THR* 3.2 28.2 - - + +
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Residues in contact with LYS 500 (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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448K TYR* 3.1 37.9 - - + +
454K HIS* 5.3 4.7 - - - +
496K LEU* 3.4 19.5 - - - +
497K ALA* 3.2 33.4 + - - +
499K LEU* 1.3 74.5 - - + +
501K SER* 1.3 56.7 + - - +
503K THR* 3.7 12.1 - - - +
504K GLU* 3.2 29.1 - - - +
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Residues in contact with SER 501 (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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478K HIS* 5.3 2.1 + - - -
497K ALA 4.3 2.4 + - - -
498K SER* 2.9 23.0 + - - -
499K LEU 2.9 1.0 + - - -
500K LYS* 1.3 79.0 - - - +
502K ALA* 1.3 71.0 + - - +
503K THR 3.1 5.4 + - - -
504K GLU* 3.8 10.8 + - - +
505K SER* 3.8 10.9 + - - -
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Residues in contact with ALA 502 (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* 3.5 24.8 - - + -
473K TYR* 4.3 9.4 - - + -
478K HIS* 3.3 39.9 - - + +
481K LEU* 4.6 7.2 - - + -
499K LEU* 3.4 7.0 + - + +
501K SER* 1.3 82.4 + - - +
503K THR* 1.3 60.4 + - + +
505K SER* 3.3 18.9 + - - -
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Residues in contact with THR 503 (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* 6.0 5.4 - - + +
448K TYR* 4.9 12.1 - - + -
454K HIS* 4.3 19.0 - - - -
455K LEU* 6.0 2.1 - - - +
466K PHE* 5.5 8.4 - - - -
470K PHE* 4.9 11.7 - - + -
499K LEU* 3.2 27.4 - - + +
500K LYS* 3.6 17.9 + - - +
502K ALA* 1.3 78.8 - - + +
504K GLU* 1.3 84.8 + - - +
505K SER 3.2 7.5 + - - -
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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