Contacts of the helix formed by residues 397 - 414 (chain W) 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 397 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395W GLU 3.5 5.5 + - - -
396W LEU* 1.3 74.6 - - - +
398W GLU* 1.3 60.4 + - - +
399W GLN* 3.7 6.5 + - - +
400W ASP* 2.8 38.4 + - - +
401W LYS* 2.8 29.5 + - - +
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Residues in contact with GLU 398 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 5.9 4.3 - - - +
397W SER* 1.3 74.6 - - - +
399W GLN* 1.3 74.8 + - + +
401W LYS* 3.4 29.5 - - - +
402W LEU* 3.3 34.7 - - - +
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Residues in contact with GLN 399 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397W SER* 3.2 6.8 + - - +
398W GLU* 1.3 90.1 - - + +
400W ASP* 1.3 66.1 + - - +
402W LEU* 3.3 7.3 + - - +
403W THR* 3.2 29.2 + - + +
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Residues in contact with ASP 400 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384W LEU* 4.5 18.6 - - + +
396W LEU* 3.8 17.8 - - + +
397W SER* 2.8 32.8 + - - +
399W GLN* 1.3 81.0 - - - +
401W LYS* 1.3 62.1 + - - +
403W THR* 3.0 21.7 + - - -
404W VAL* 3.0 18.0 + - - +
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Residues in contact with LYS 401 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393W MET* 5.2 10.1 - - + +
396W LEU* 3.9 26.1 - - + +
397W SER 2.8 26.1 + - - +
398W GLU* 3.4 32.4 - - - +
400W ASP* 1.3 75.0 - - - +
402W LEU* 1.3 61.9 + - + +
404W VAL* 3.8 8.0 - - - +
405W GLU* 3.1 26.9 + - - +
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Residues in contact with LEU 402 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 5.7 5.2 - - - +
398W GLU* 3.3 32.8 - - - +
399W GLN* 3.5 7.4 - - - +
400W ASP 3.1 0.8 - - - -
401W LYS* 1.3 83.2 - - + +
403W THR* 1.3 63.3 + - + +
405W GLU* 3.5 14.2 + - - +
406W ARG* 2.9 62.2 + - - +
450W ASP* 4.1 12.1 - - - +
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Residues in contact with THR 403 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377W THR* 3.4 16.5 - - + +
380W THR* 4.7 10.5 + - - -
381W TYR* 6.1 0.2 - - - -
384W LEU* 4.9 3.3 - - - +
399W GLN* 3.2 14.6 + - + +
400W ASP* 3.0 17.5 + - - -
402W LEU* 1.3 76.3 - - + +
404W VAL* 1.3 61.5 + - - +
405W GLU 3.4 0.2 - - - -
406W ARG* 4.6 11.9 - - - +
407W ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 404 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381W TYR* 4.0 24.5 - - + -
384W LEU* 3.5 28.0 - - + -
388W ILE* 4.6 9.6 - - + -
393W MET* 5.9 4.3 - - + -
396W LEU* 4.4 18.6 - - + -
400W ASP 3.0 22.5 + - - +
401W LYS* 3.8 7.6 - - - +
403W THR* 1.3 75.9 - - - +
405W GLU* 1.3 66.0 + - - +
407W ALA* 3.6 5.5 - - - +
408W ARG* 3.2 31.7 + - + +
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Residues in contact with GLU 405 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401W LYS 3.1 17.7 + - - +
402W LEU* 3.7 22.0 - - - +
404W VAL* 1.3 80.6 - - - +
406W ARG* 1.3 61.5 + - - +
408W ARG* 3.5 6.3 + - - +
409W LYS* 3.2 56.7 + - - +
450W ASP* 4.3 11.9 - - - +
454W GLU* 4.3 7.7 - - + +
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Residues in contact with ARG 406 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377W THR* 4.9 4.7 - - + -
402W LEU* 2.9 56.7 + - - +
403W THR* 4.1 12.0 - - - +
405W GLU* 1.3 80.4 - - - +
407W ALA* 1.3 53.9 + - - +
409W LYS* 2.8 12.9 + - + +
410W ILE* 2.6 44.5 + - + +
444W VAL* 4.1 17.7 - - + +
445W LEU* 3.9 20.0 + - + -
446W GLU 4.2 3.0 + - - -
447W GLY* 3.5 23.2 - - - -
450W ASP* 3.0 38.8 + - - +
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Residues in contact with ALA 407 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377W THR* 3.6 20.7 - - + +
378W LEU* 3.6 9.0 - - + +
381W TYR* 3.8 31.6 - - + -
403W THR 2.9 20.8 + - - +
404W VAL 3.6 5.2 - - - +
405W GLU 3.3 0.2 - - - -
406W ARG* 1.3 74.9 - - - +
408W ARG* 1.3 57.3 + - - +
410W ILE* 3.0 7.4 + - - +
411W GLN* 2.8 31.5 + - - +
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Residues in contact with ARG 408 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381W TYR* 3.5 33.5 + - + +
404W VAL* 3.2 23.4 + - - +
405W GLU* 3.8 2.0 - - - +
406W ARG 3.2 0.2 - - - -
407W ALA* 1.3 76.5 - - - +
409W LYS* 1.3 61.5 + - - +
411W GLN* 3.5 8.8 + - - +
412W ARG* 3.1 49.5 + - - +
454W GLU* 3.5 39.9 + - - +
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Residues in contact with LYS 409 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405W GLU* 3.2 49.9 + - - +
406W ARG* 2.8 14.6 + - + +
408W ARG* 1.3 76.3 - - - +
410W ILE* 1.3 59.1 + - - +
412W ARG* 4.7 2.9 - - - +
413W PHE* 3.1 27.9 + - - +
444W VAL* 5.1 8.3 - - + -
449W TYR 4.8 3.8 - - - +
450W ASP* 2.8 41.3 + - - +
452W ILE 3.7 16.2 - - - +
453W PRO* 5.4 0.4 - - - -
454W GLU* 4.0 23.8 - - + +
457W PHE* 3.9 31.4 - - + +
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Residues in contact with ILE 410 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374W VAL* 3.9 24.7 - - + -
377W THR* 5.1 4.0 - - + -
378W LEU* 4.4 11.0 - - + -
406W ARG* 2.6 30.0 + - + +
407W ALA* 3.3 9.9 - - - +
409W LYS* 1.3 72.7 - - - +
411W GLN* 1.3 64.7 + - - +
413W PHE* 3.0 15.1 + - + +
414W LEU* 3.1 14.8 + - + +
441W PHE* 3.6 28.2 - - + -
444W VAL* 3.5 36.6 - - + -
445W LEU* 4.5 20.0 - - + -
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Residues in contact with GLN 411 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339W ILE* 6.0 3.4 - - - +
342W LEU* 4.8 19.9 - - - +
344W ILE* 4.3 21.2 - - + +
350W PRO* 4.8 14.2 - - + +
378W LEU* 4.1 18.6 - - + +
381W TYR* 4.2 24.0 + - - -
407W ALA 2.8 19.3 + - - +
408W ARG* 3.9 7.5 - - - +
410W ILE* 1.3 73.9 - - - +
412W ARG* 1.3 61.8 + - + +
414W LEU* 3.5 28.6 - - + +
415W SER 4.0 3.1 + - - -
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Residues in contact with ARG 412 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344W ILE* 5.2 9.6 - - + -
408W ARG* 3.1 39.9 + - - +
409W LYS* 4.1 3.6 - - - +
411W GLN* 1.3 75.2 - - + +
413W PHE* 1.3 58.4 + - - +
414W LEU 3.1 5.4 - - - -
415W SER* 2.7 28.6 + - - -
454W GLU* 3.6 46.7 + - - +
455W HIS* 4.6 12.1 + - - +
457W PHE* 2.8 17.6 - - + +
458W TYR* 3.3 40.3 - - + +
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Residues in contact with PHE 413 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139W LYS* 2.7 35.1 + - + +
409W LYS 3.1 19.9 + - - +
410W ILE* 3.0 9.9 + - + +
412W ARG* 1.3 75.1 - - - +
414W LEU* 1.3 57.1 + - - +
415W SER 3.3 0.2 - - - -
440W SER* 3.7 21.8 - - - -
441W PHE* 3.3 35.8 - + - -
444W VAL* 5.4 6.1 - - + -
457W PHE* 3.4 27.8 - + + -
460W VAL* 3.9 13.0 - - + -
461W GLY 4.0 5.8 - - - -
462W GLY* 3.8 8.1 - - - -
463W ILE* 3.9 25.8 - - + -
466W VAL* 3.3 26.9 - - + -
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Residues in contact with LEU 414 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139W LYS* 4.0 8.9 - - - +
140W VAL* 3.0 47.0 - - + +
143W LEU* 4.8 2.5 - - + -
144W LEU* 4.1 20.2 - - + -
344W ILE* 5.3 3.8 - - + -
350W PRO* 4.1 27.1 - - + -
374W VAL* 5.1 0.9 - - + -
378W LEU* 4.2 15.7 - - + -
410W ILE* 3.1 19.8 + - + +
411W GLN* 3.5 21.5 - - + +
412W ARG 3.1 0.6 - - - -
413W PHE* 1.3 78.2 - - - +
415W SER* 1.3 63.6 + - - +
416W GLN* 3.5 3.3 + - - +
441W PHE* 3.5 25.4 - - + -
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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