Contacts of the helix formed by residues 397 - 414 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395E GLU 3.5 4.5 + - - -
396E LEU* 1.3 72.6 - - - +
398E GLU* 1.3 61.4 + - - +
399E GLN* 4.0 3.3 + - - +
400E ASP* 2.7 33.6 + - - +
401E LYS* 2.8 34.2 + - - +
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Residues in contact with GLU 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397E SER* 1.3 80.1 - - - +
399E GLN* 1.3 77.4 + - + +
401E LYS* 3.7 14.8 - - - +
402E LEU* 3.2 40.7 + - - +
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Residues in contact with GLN 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397E SER* 3.4 3.8 + - - +
398E GLU* 1.3 90.4 - - + +
400E ASP* 1.3 63.8 + - - +
401E LYS 3.4 0.2 - - - -
402E LEU* 4.1 5.4 - - - -
403E THR* 2.9 33.3 + - + +
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Residues in contact with ASP 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384E LEU* 4.4 6.9 - - + +
395E GLU 4.9 2.3 - - - +
396E LEU* 3.2 20.8 - - + +
397E SER* 2.7 41.4 + - - +
399E GLN* 1.3 84.2 - - - +
401E LYS* 1.3 57.4 + - - +
403E THR* 3.7 4.8 + - - -
404E VAL* 2.9 27.4 - - - +
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Residues in contact with LYS 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393E MET* 5.5 1.8 - - + +
396E LEU* 3.5 32.7 + - + +
397E SER 2.8 20.5 + - - +
398E GLU* 3.7 16.2 - - - +
400E ASP* 1.3 75.3 - - - +
402E LEU* 1.3 68.4 + - - +
403E THR 3.3 1.8 - - - -
404E VAL* 4.0 2.3 - - - +
405E GLU* 3.6 19.6 + - - +
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Residues in contact with LEU 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398E GLU* 3.2 37.2 + - - +
399E GLN* 4.4 5.8 - - - +
401E LYS* 1.3 82.6 - - + +
403E THR* 1.3 59.2 + - + +
405E GLU* 3.7 13.1 - - - +
406E ARG* 2.8 44.2 + - - +
450E ASP* 3.9 18.8 - - - +
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Residues in contact with THR 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377E THR* 4.0 19.0 - - + +
380E THR* 5.5 3.5 + - - -
384E LEU* 5.7 1.2 - - - +
399E GLN* 2.9 24.4 + - + +
400E ASP* 3.7 6.6 + - - -
402E LEU* 1.3 77.6 - - + +
404E VAL* 1.3 66.9 + - - +
405E GLU 3.1 2.0 - - - -
406E ARG* 3.1 25.9 + - - +
407E ALA* 2.9 20.9 + - - +
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Residues in contact with VAL 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381E TYR* 4.1 23.1 - - + -
384E LEU* 3.4 28.0 - - + -
388E ILE* 5.0 9.0 - - + -
393E MET* 5.9 5.4 - - - -
396E LEU* 3.9 17.0 - - + -
400E ASP 2.9 26.9 + - - +
401E LYS 3.8 5.8 + - - +
402E LEU 3.5 0.4 - - - -
403E THR* 1.3 77.5 + - - +
405E GLU* 1.3 57.7 + - - +
407E ALA* 3.1 7.5 + - - +
408E ARG* 2.8 35.5 + - + +
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Residues in contact with GLU 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401E LYS 3.6 11.4 + - - +
402E LEU* 3.7 17.8 - - - +
403E THR 3.1 0.4 - - - -
404E VAL* 1.3 79.9 - - - +
406E ARG* 1.3 62.9 + - - +
408E ARG* 3.3 7.1 + - - +
409E LYS* 3.2 49.6 + - + +
450E ASP* 3.3 41.2 - - - +
454E GLU* 4.9 7.4 - - - +
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Residues in contact with ARG 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377E THR* 5.1 4.0 - - + -
402E LEU* 2.8 51.9 + - - +
403E THR* 3.1 23.1 + - - +
405E GLU* 1.3 80.0 - - - +
407E ALA* 1.3 53.6 + - - +
409E LYS* 2.9 9.8 + - + +
410E ILE* 2.6 52.2 + - + +
444E VAL* 3.9 23.8 - - + +
445E LEU* 3.8 18.4 + - + -
446E GLU 4.2 2.8 + - - -
447E GLY* 3.5 21.6 - - - -
450E ASP* 3.4 28.8 + - - +
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Residues in contact with ALA 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377E THR* 4.4 11.2 - - + +
378E LEU* 4.1 13.4 - - + +
381E TYR* 3.4 38.4 - - + -
403E THR 2.9 12.1 + - - +
404E VAL* 3.1 9.8 + - - +
406E ARG* 1.3 76.0 - - - +
408E ARG* 1.3 62.9 + - - +
409E LYS 3.0 1.2 + - - -
410E ILE* 4.5 4.4 - - - +
411E GLN* 3.0 28.8 + - - +
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Residues in contact with ARG 408 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342E LEU* 6.4 0.2 - - - +
381E TYR* 3.3 32.2 + - + -
404E VAL* 2.8 27.1 + - + +
405E GLU* 3.6 3.6 - - - +
407E ALA* 1.3 71.9 - - - +
409E LYS* 1.3 58.1 + - - +
411E GLN* 4.8 8.3 + - - +
412E ARG* 2.9 60.0 + - - +
454E GLU* 3.4 32.2 - - - +
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Residues in contact with LYS 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405E GLU* 3.2 34.9 + - - +
406E ARG* 2.9 9.7 + - + +
408E ARG* 1.3 77.8 - - - +
410E ILE* 1.3 54.9 + - + +
411E GLN 3.2 1.3 - - - -
412E ARG* 2.8 9.4 + - - +
413E PHE* 2.8 35.6 + - - +
444E VAL* 5.6 7.4 - - + -
449E TYR 3.9 1.8 + - - +
450E ASP* 2.9 32.1 + - - +
452E ILE 2.8 24.9 + - - -
453E PRO* 4.3 1.1 - - - +
454E GLU* 3.6 28.9 - - + +
457E PHE* 3.5 35.8 - - + +
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Residues in contact with ILE 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374E VAL* 3.8 23.8 - - + +
377E THR* 5.0 11.0 - - + -
378E LEU* 4.6 11.0 - - + -
406E ARG* 2.6 42.0 + - + +
407E ALA* 4.1 6.3 - - - +
409E LYS* 1.3 71.8 - - - +
411E GLN* 1.3 61.8 + - - +
413E PHE* 3.0 17.5 + - + -
414E LEU* 3.2 17.3 + - + +
441E PHE* 3.8 26.2 - - + -
444E VAL* 4.5 15.7 - - + +
445E LEU* 4.1 24.9 - - + -
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Residues in contact with GLN 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339E ILE* 5.7 4.6 - - - +
342E LEU* 3.7 28.1 - - - +
344E ILE* 3.5 28.9 - - + +
350E PRO* 6.0 6.0 - - + +
378E LEU* 4.1 16.2 - - + +
381E TYR* 3.8 32.3 + - - -
407E ALA 3.0 17.1 + - - +
408E ARG* 4.8 9.2 + - - +
410E ILE* 1.3 76.5 - - - +
412E ARG* 1.3 61.0 + - + +
414E LEU* 4.3 16.3 + - + +
415E SER 4.8 0.2 + - - -
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Residues in contact with ARG 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342E LEU 5.8 1.8 + - - -
344E ILE* 5.4 4.9 - - + -
408E ARG* 2.9 55.5 + - - +
409E LYS 2.8 8.5 + - - +
411E GLN* 1.3 83.0 - - + +
413E PHE* 1.3 55.6 + - - +
414E LEU 3.2 4.9 - - - -
415E SER* 3.1 20.2 + - - -
454E GLU* 3.6 33.9 + - - +
455E HIS* 5.7 0.2 - - - +
457E PHE* 2.9 26.8 - - + +
458E TYR* 3.7 28.9 - - + +
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Residues in contact with PHE 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E LYS* 2.7 51.8 + - + +
409E LYS 2.8 13.3 + - - +
410E ILE* 3.0 8.7 + - - +
412E ARG* 1.3 77.2 - - - +
414E LEU* 1.3 57.2 + - - +
415E SER 3.5 0.4 - - - -
440E SER* 4.0 23.3 - - - -
441E PHE* 3.4 50.0 - + - -
444E VAL* 5.4 8.7 - - + -
457E PHE* 3.8 29.4 - + + -
460E VAL* 3.9 7.4 - - + -
461E GLY 3.8 0.7 - - - -
462E GLY 3.5 27.6 - - - -
463E ILE* 4.5 4.0 - - + -
466E VAL* 3.8 9.9 - - + -
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Residues in contact with LEU 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E LYS* 3.8 13.4 - - - +
140E VAL* 3.1 58.6 - - + +
143E LEU* 4.7 3.6 - - + -
144E LEU* 4.2 21.8 - - + -
344E ILE* 5.8 2.7 - - + -
346E PRO* 4.8 0.2 - - - +
350E PRO* 4.3 18.6 - - + -
374E VAL* 5.1 1.6 - - + -
378E LEU* 4.4 15.0 - - + -
410E ILE* 3.2 20.7 + - + +
411E GLN* 4.5 10.1 - - + +
412E ARG 3.2 0.6 - - - -
413E PHE* 1.3 78.5 - - - +
415E SER* 1.3 64.9 + - - +
416E GLN* 3.6 2.9 + - - +
441E PHE* 3.8 23.6 - - + -
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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