Contacts of the helix formed by residues 382 - 389 (chain L) 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 VAL 382 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147L PRO* 4.1 17.4 - - + +
149L GLN* 4.1 19.1 - - + +
381L GLN* 1.3 74.9 - - - +
383L LYS* 1.3 61.2 + - - +
384L ALA* 3.6 14.1 - - + +
385L LEU* 2.8 26.8 + - + +
386L LYS* 2.9 9.5 + - - +
440L THR* 3.9 33.2 - - + +
485L ILE 5.5 0.4 - - - +
489L GLY* 3.5 24.9 - - - +
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Residues in contact with LYS 383 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378L SER 5.6 2.8 + - - -
381L GLN 3.3 6.3 + - - +
382L VAL* 1.3 73.8 - - - +
384L ALA* 1.3 59.6 + - - +
386L LYS* 3.2 47.3 + - + +
387L GLN* 2.6 32.2 - - - +
489L GLY 3.4 12.3 + - - +
490L GLU* 3.9 24.9 - - + +
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Residues in contact with ALA 384 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382L VAL* 3.0 8.9 - - + -
383L LYS* 1.3 78.3 - - - +
385L LEU* 1.3 59.9 + - - +
387L GLN* 3.5 16.5 + - - +
388L VAL* 3.7 8.7 - - - +
440L THR* 4.8 0.4 - - + -
444L VAL* 3.8 19.8 - - + +
485L ILE* 4.2 15.3 - - + -
489L GLY 3.1 24.6 + - - +
490L GLU* 3.9 9.6 - - - +
491L LEU* 3.8 16.8 - - + +
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Residues in contact with LEU 385 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156L ASP* 3.3 37.0 - - + +
157L ALA* 4.1 4.0 - - + -
381L GLN* 3.5 18.4 - - + +
382L VAL* 2.8 17.8 + - + +
384L ALA* 1.3 75.8 - - - +
386L LYS* 1.3 60.3 + - - +
387L GLN 3.1 2.0 - - - -
388L VAL* 3.3 19.5 - - + +
389L ALA* 3.0 39.3 + - + +
440L THR* 4.8 7.0 - - + +
443L GLN* 4.2 20.9 - - + +
444L VAL* 4.0 15.4 - - + +
447L ILE* 4.2 17.9 - - + -
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Residues in contact with LYS 386 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378L SER* 3.4 37.5 + - - +
379L ALA* 6.1 0.4 - - - +
381L GLN* 3.9 13.0 + - - +
382L VAL 2.9 11.3 + - - +
383L LYS* 3.2 50.2 - - + +
384L ALA 3.3 0.2 - - - -
385L LEU* 1.3 78.4 - - - +
387L GLN* 1.3 66.6 + - - +
389L ALA 3.3 15.4 - - - +
390L GLY* 4.9 1.4 - - - -
422M GLU* 6.3 1.2 - - - +
423M VAL* 5.4 4.4 - - - +
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Residues in contact with GLN 387 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383L LYS* 2.6 28.1 + - - +
384L ALA 3.5 9.2 - - - +
385L LEU 3.1 0.6 - - - -
386L LYS* 1.3 87.1 - - - +
388L VAL* 1.3 66.8 + - + +
389L ALA 3.3 3.3 + - - -
390L GLY* 4.2 2.8 + - - -
490L GLU* 3.5 21.6 + - - +
491L LEU* 3.3 43.3 + - + +
496L LEU* 4.8 13.2 - - + -
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Residues in contact with VAL 388 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384L ALA 3.7 1.3 - - - +
385L LEU* 3.3 33.9 - - + +
387L GLN* 1.3 78.6 - - + +
389L ALA* 1.3 59.7 + - - +
390L GLY 3.5 3.3 + - - -
444L VAL* 3.4 36.3 - - + +
447L ILE* 3.6 23.3 - - + -
448L TYR* 3.6 29.8 - - + +
451L VAL* 3.2 31.4 - - - +
452L ASN* 5.4 1.5 + - - +
491L LEU* 4.0 9.0 - - + -
496L LEU* 6.1 0.2 - - + -
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Residues in contact with ALA 389 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157L ALA* 4.4 21.5 - - + +
381L GLN* 4.7 8.7 - - - +
385L LEU* 3.0 20.3 + - + +
386L LYS* 3.3 16.8 - - - +
387L GLN 3.2 0.4 - - - -
388L VAL* 1.3 76.2 - - + +
390L GLY* 1.3 66.3 + - - +
392L LEU* 5.0 11.9 - - + -
447L ILE* 4.3 11.7 - - + -
451L VAL* 4.8 2.5 - - - -
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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