Contacts of the helix formed by residues 397 - 414 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409L GLY* 6.4 2.7 - - - -
395O GLU 4.1 0.6 + - - -
396O LEU* 1.3 72.2 - - - +
398O GLU* 1.3 54.6 + - - +
399O GLN* 3.6 17.0 + - - +
400O ASP* 3.1 20.4 + - - +
401O LYS* 2.6 36.0 + - - +
116P MET* 5.8 6.9 - - - +
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Residues in contact with GLU 398 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394O ASP 5.1 2.4 - - - +
396O LEU 3.4 6.1 + - - +
397O SER* 1.3 73.3 + - - +
399O GLN* 1.3 63.6 + - - +
401O LYS* 3.5 32.4 + - - +
402O LEU* 3.2 21.5 + - - +
89P SER* 4.9 7.5 + - - -
93P LYS* 6.1 0.7 - - - -
116P MET* 5.5 7.9 - - + +
117P GLN* 3.5 35.1 + - - +
120P ARG* 4.0 39.8 + - - +
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Residues in contact with GLN 399 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397O SER* 3.2 7.2 + - - +
398O GLU* 1.3 81.4 - - - +
400O ASP* 1.3 73.0 + - - +
402O LEU* 3.6 12.9 + - - +
403O THR* 3.4 10.9 + - - -
120P ARG* 5.6 5.1 - - - +
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Residues in contact with ASP 400 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380O THR* 5.0 10.4 - - + +
384O LEU* 4.4 24.2 - - + +
396O LEU* 5.2 2.0 - - + -
397O SER* 3.1 21.9 + - - +
399O GLN* 1.3 90.2 + - - +
401O LYS* 1.3 61.3 + - - +
402O LEU 3.1 2.5 - - - -
403O THR* 2.9 26.8 + - - -
404O VAL* 3.1 17.2 + - - +
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Residues in contact with LYS 401 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393O MET* 3.7 34.6 + - + +
394O ASP* 4.3 17.5 + - - +
396O LEU* 4.3 11.0 - - + +
397O SER 2.6 22.2 + - - +
398O GLU* 3.2 35.8 + - - +
400O ASP* 1.3 73.6 - - - +
402O LEU* 1.3 57.5 + - - +
404O VAL* 3.1 16.5 - - + +
405O GLU* 3.0 48.4 - - + +
89P SER* 4.3 15.6 + - - -
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Residues in contact with LEU 402 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398O GLU 3.2 10.0 + - - +
399O GLN* 3.7 11.7 - - - +
400O ASP 3.1 0.2 - - - -
401O LYS* 1.3 76.9 - - - +
403O THR* 1.3 64.8 + - - +
405O GLU* 3.3 12.0 + - + +
406O ARG* 3.2 49.3 + - + +
450O ASP* 3.7 22.9 - - + +
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Residues in contact with THR 403 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377O THR* 3.9 23.5 - - + +
380O THR* 4.4 27.4 - - + +
381O TYR 5.8 0.2 - - - +
399O GLN 3.4 12.0 + - - -
400O ASP* 2.9 15.8 + - - -
402O LEU* 1.3 78.5 - - - +
404O VAL* 1.3 57.5 + - + +
406O ARG* 3.3 18.8 + - - +
407O ALA* 2.9 27.5 + - - +
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Residues in contact with VAL 404 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380O THR* 4.9 1.6 - - + -
381O TYR* 3.7 40.3 - - + +
384O LEU* 4.2 19.5 - - + -
388O ILE* 4.3 6.1 - - + -
393O MET* 3.5 23.8 - - + -
396O LEU* 3.9 7.9 - - + -
400O ASP 3.4 10.5 - - - +
401O LYS* 3.1 26.5 - - - +
403O THR* 1.3 76.1 - - - +
405O GLU* 1.3 59.7 + - - +
407O ALA* 3.5 6.8 - - - +
408O ARG* 2.9 35.3 + - - +
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Residues in contact with GLU 405 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393O MET* 4.0 17.2 - - + +
401O LYS* 3.0 48.7 - - - +
402O LEU* 3.3 13.0 + - + +
403O THR 3.3 0.4 - - - -
404O VAL* 1.3 78.0 - - - +
406O ARG* 1.3 62.1 + - + +
408O ARG* 3.9 9.3 + - - +
409O LYS* 3.5 22.6 + - - +
454O GLU* 4.3 5.7 - - - +
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Residues in contact with ARG 406 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377O THR* 5.3 2.6 - - + +
402O LEU* 3.2 44.3 + - + +
403O THR* 3.7 17.7 + - - +
405O GLU* 1.3 77.2 - - + +
407O ALA* 1.3 61.4 + - - +
409O LYS* 3.1 19.3 + - - +
410O ILE* 3.0 37.5 + - + +
444O VAL* 4.0 13.6 - - + +
445O LEU* 3.1 25.0 + - - +
446O GLU 4.5 1.6 + - - -
447O GLY* 4.2 7.3 - - - +
450O ASP* 3.2 39.0 + - - +
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Residues in contact with ALA 407 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377O THR* 3.8 22.2 - - + +
378O LEU* 4.2 6.7 - - + +
381O TYR* 3.7 31.2 - - + -
403O THR 2.9 16.8 + - - +
404O VAL* 3.2 6.3 + - - +
406O ARG* 1.3 73.1 - - - +
408O ARG* 1.3 57.3 + - - +
409O LYS 2.9 10.4 + - - -
410O ILE* 3.1 5.4 + - - +
411O GLN* 2.9 29.3 + - - +
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Residues in contact with ARG 408 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401K GLU* 3.8 24.7 + - - +
405K PHE* 6.2 5.2 - - - -
381O TYR* 3.6 38.8 + - + -
393O MET* 4.5 22.6 - - - -
404O VAL 2.9 18.4 + - - +
405O GLU* 4.1 4.0 - - - +
406O ARG 3.3 0.4 - - - -
407O ALA* 1.3 75.5 - - - +
409O LYS* 1.3 57.8 + - - +
411O GLN* 4.3 7.9 - - - +
412O ARG* 2.9 44.4 + - - +
454O GLU* 3.1 39.4 + - - +
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Residues in contact with LYS 409 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405O GLU 3.5 20.9 - - - +
406O ARG* 3.1 16.9 + - - +
407O ALA 2.9 0.8 - - - -
408O ARG* 1.3 78.2 - - - +
410O ILE* 1.3 54.9 + - + +
411O GLN 3.2 1.3 - - - -
412O ARG* 3.0 7.0 + - - +
413O PHE* 2.7 37.4 + - - +
444O VAL* 5.4 8.1 - - + +
449O TYR 3.2 8.7 + - - -
450O ASP* 3.2 43.6 + - - +
452O ILE 3.5 19.0 + - - +
453O PRO 4.5 0.4 - - - +
454O GLU* 3.7 22.2 - - + -
457O PHE* 3.6 33.3 - - + +
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Residues in contact with ILE 410 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374O VAL* 3.9 19.1 - - + -
377O THR* 4.0 22.2 - - + -
378O LEU* 4.6 10.1 - - + -
406O ARG* 3.0 19.4 + - + +
407O ALA* 3.1 5.4 + - - +
409O LYS* 1.3 74.8 - - - +
411O GLN* 1.3 62.5 + - - +
413O PHE* 3.1 17.0 + - - +
414O LEU* 3.2 18.1 + - + +
441O PHE* 3.7 26.0 - - + -
444O VAL* 4.0 23.1 - - + +
445O LEU* 3.9 29.2 - - + +
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Residues in contact with GLN 411 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339O ILE* 5.1 11.8 - - + +
342O LEU* 4.5 14.9 - - - +
344O ILE* 3.3 41.4 - - + +
350O PRO* 5.8 6.6 - - + +
378O LEU* 4.0 16.6 - - + +
381O TYR* 3.5 30.7 + - - -
407O ALA 2.9 17.0 + - - +
408O ARG* 4.7 7.2 - - - +
410O ILE* 1.3 77.7 - - - +
412O ARG* 1.3 62.2 + - + +
414O LEU* 4.1 17.7 - - + +
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Residues in contact with ARG 412 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398K GLN* 3.0 37.3 + - - +
401K GLU* 3.2 32.3 + - - -
342O LEU* 4.2 7.9 + - - +
344O ILE* 4.7 18.2 - - + +
408O ARG* 2.9 36.5 - - - +
409O LYS* 3.0 6.6 + - - +
411O GLN* 1.3 80.8 + - + +
413O PHE* 1.3 56.6 + - - +
414O LEU 3.2 5.8 - - - -
415O SER* 3.3 23.8 - - - +
454O GLU* 4.6 24.9 + - - +
455O HIS* 5.7 1.2 - - - +
457O PHE 2.8 14.9 - - - +
458O TYR* 3.5 34.7 - - + +
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Residues in contact with PHE 413 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139O LYS* 2.8 30.4 + - + -
409O LYS 2.7 15.3 + - - +
410O ILE* 3.1 9.4 + - - +
412O ARG* 1.3 76.3 - - - +
414O LEU* 1.3 59.4 + - - +
415O SER 3.3 1.1 - - - -
440O SER* 3.9 13.0 - - - -
441O PHE* 3.3 50.3 - + - -
444O VAL* 4.8 6.3 - - + -
457O PHE* 3.3 35.2 - + + -
460O VAL* 4.1 1.8 - - + -
461O GLY 3.5 18.8 - - - -
462O GLY* 3.5 3.8 - - - -
463O ILE* 3.5 31.9 - - + -
466O VAL* 3.5 21.5 - - + -
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Residues in contact with LEU 414 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139O LYS* 4.0 9.1 - - - +
140O VAL* 3.1 56.1 + - + +
143O LEU* 5.5 2.0 - - + -
144O LEU* 4.0 13.0 - - + -
344O ILE* 5.2 4.3 - - + -
346O PRO* 4.4 2.5 - - - +
348O VAL 5.7 0.4 - - - +
350O PRO* 3.5 31.9 - - + -
374O VAL* 5.8 1.3 - - + -
378O LEU* 4.5 8.1 - - + -
410O ILE* 3.3 17.5 - - + +
411O GLN* 4.1 17.3 - - + +
412O ARG 3.2 0.4 - - - -
413O PHE* 1.3 78.5 - - - +
415O SER* 1.3 64.0 + - - +
416O GLN* 3.4 4.9 + - - +
441O PHE* 3.7 23.3 - - + -
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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