Contacts of the helix formed by residues 397 - 415 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406J ALA 4.6 6.6 + - - -
410J SER* 3.5 26.9 + - - -
396M LEU* 1.3 74.3 - - - +
398M GLU* 1.3 61.5 + - - +
399M GLN* 3.4 8.8 + - - +
400M ASP* 3.1 21.0 + - - +
401M LYS* 3.0 33.5 + - - +
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Residues in contact with GLU 398 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397M SER* 1.3 75.8 - - - +
399M GLN* 1.3 63.9 + - - +
401M LYS* 4.1 9.0 + - - +
402M LEU* 3.1 36.7 + - + +
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Residues in contact with GLN 399 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424J GLU* 4.9 11.6 + - - +
397M SER* 3.4 7.0 + - - +
398M GLU* 1.3 80.8 - - - +
400M ASP* 1.3 62.8 + - - +
402M LEU* 4.6 4.6 - - - +
403M THR* 2.8 32.5 + - - +
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Residues in contact with ASP 400 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406J ALA 5.6 3.8 - - - -
380M THR* 4.6 15.5 - - - +
384M LEU* 4.9 8.2 - - + +
396M LEU* 3.4 37.8 - - + +
397M SER* 3.1 19.1 + - - +
398M GLU 3.2 0.2 - - - -
399M GLN* 1.3 87.4 - - - +
401M LYS* 1.3 60.1 + - - +
402M LEU 3.4 0.4 - - - -
403M THR* 3.9 2.8 - - - -
404M VAL* 3.1 36.7 + - - +
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Residues in contact with LYS 401 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393M MET* 3.3 30.8 - - + +
394M ASP* 2.8 39.5 + - - +
396M LEU* 3.2 26.0 - - + +
397M SER 3.0 23.3 + - - +
398M GLU* 4.1 8.6 + - - +
400M ASP* 1.3 76.4 - - - +
402M LEU* 1.3 64.8 + - - +
404M VAL* 4.1 3.9 - - - +
405M GLU* 3.2 25.3 + - - +
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Residues in contact with LEU 402 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398M GLU* 3.1 29.5 + - + +
399M GLN* 4.6 3.8 - - - +
401M LYS* 1.3 77.4 - - - +
403M THR* 1.3 64.5 + - - +
405M GLU* 3.5 12.2 + - - +
406M ARG* 3.3 73.6 + - + +
450M ASP* 3.9 8.3 - - + +
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Residues in contact with THR 403 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377M THR* 3.7 32.8 - - + +
380M THR* 4.4 21.5 - - + -
381M TYR 5.6 0.4 - - - +
399M GLN* 2.8 26.5 + - - +
400M ASP* 3.6 5.3 + - - -
401M LYS 3.3 0.4 - - - -
402M LEU* 1.3 79.8 - - - +
404M VAL* 1.3 56.3 + - + +
406M ARG* 3.3 8.5 + - - +
407M ALA* 2.8 31.8 + - + +
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Residues in contact with VAL 404 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405L PHE* 4.9 6.5 - - + -
380M THR* 5.7 1.6 - - + -
381M TYR* 3.7 32.1 - - + -
384M LEU* 4.3 16.2 - - + -
388M ILE* 4.0 27.6 - - + -
393M MET* 5.5 5.8 - - + -
396M LEU* 5.8 0.9 - - + -
400M ASP* 3.1 20.8 + - + +
401M LYS* 4.1 4.0 - - - +
403M THR* 1.3 75.2 - - + +
405M GLU* 1.3 61.1 + - - +
407M ALA* 3.4 6.4 - - - +
408M ARG* 2.9 38.7 + - - +
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Residues in contact with GLU 405 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393M MET* 5.9 8.4 - - + +
401M LYS 3.2 16.6 + - - +
402M LEU* 3.7 13.5 - - - +
404M VAL* 1.3 80.2 - - - +
406M ARG* 1.3 61.6 + - + +
408M ARG* 3.7 7.6 + - - +
409M LYS* 3.1 56.4 + - - +
450M ASP* 3.5 17.3 - - - +
454M GLU* 5.3 0.5 - - - +
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Residues in contact with ARG 406 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377M THR* 4.8 8.5 - - + -
402M LEU* 3.3 48.6 + - + +
403M THR* 3.3 9.1 + - - +
404M VAL 3.2 0.2 - - - -
405M GLU* 1.3 78.1 - - + +
407M ALA* 1.3 55.5 + - - +
409M LYS* 3.1 10.8 + - + +
410M ILE* 2.7 45.8 + - + +
444M VAL* 4.1 17.0 - - + +
445M LEU* 2.8 25.1 + - + +
446M GLU 4.1 4.4 + - - -
447M GLY* 3.1 17.4 + - - +
450M ASP* 3.0 36.3 + - - +
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Residues in contact with ALA 407 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377M THR* 3.6 19.3 - - - +
378M LEU* 3.7 7.0 - - + +
381M TYR* 3.3 36.7 - - + -
403M THR 2.8 17.5 + - - +
404M VAL* 3.1 7.4 + - - +
406M ARG* 1.3 77.8 - - - +
408M ARG* 1.3 59.4 + - - +
409M LYS 3.1 0.2 - - - -
410M ILE* 4.5 3.8 - - - +
411M GLN* 3.3 26.7 + - - +
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Residues in contact with ARG 408 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401L GLU* 3.8 27.5 + - - +
402L VAL* 5.1 6.7 - - - +
405L PHE* 3.1 62.6 - - - +
381M TYR* 2.8 51.8 + - + +
404M VAL* 2.9 22.2 + - - +
405M GLU* 4.1 6.5 - - - +
406M ARG 3.3 0.2 - - - -
407M ALA* 1.3 76.5 - - - +
409M LYS* 1.3 58.9 + - - +
411M GLN* 4.9 3.9 - - - +
412M ARG* 3.2 37.5 + - - +
454M GLU* 2.8 42.9 + - - +
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Residues in contact with LYS 409 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405M GLU* 3.1 40.1 + - - +
406M ARG* 3.1 13.7 + - + +
408M ARG* 1.3 81.1 - - - +
410M ILE* 1.3 55.1 + - - +
411M GLN 3.4 0.2 - - - -
412M ARG* 3.2 5.5 + - - +
413M PHE* 2.7 37.3 + - - +
444M VAL* 5.3 8.7 - - + -
449M TYR 4.0 2.0 + - - +
450M ASP* 2.9 40.6 + - - +
452M ILE 3.3 19.4 + - - -
453M PRO* 5.0 3.6 - - - -
454M GLU* 4.5 15.0 - - + +
457M PHE* 3.9 33.7 - - + +
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Residues in contact with ILE 410 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374M VAL* 3.8 27.8 - - + +
377M THR* 5.3 6.3 - - + -
378M LEU* 4.2 13.5 - - + -
406M ARG* 2.7 28.3 + - + +
407M ALA* 4.1 6.1 - - - +
409M LYS* 1.3 69.4 - - - +
411M GLN* 1.3 62.1 + - - +
413M PHE* 2.8 21.3 + - + +
414M LEU* 3.0 15.8 + - + +
441M PHE* 3.6 29.5 - - + -
444M VAL* 3.5 31.2 - - + -
445M LEU* 4.6 18.4 - - + -
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Residues in contact with GLN 411 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401L GLU* 5.1 5.5 - - - +
339M ILE* 4.7 13.1 - - + +
342M LEU* 3.9 26.1 - - - +
344M ILE* 4.1 21.4 - - + +
350M PRO* 5.2 12.1 - - + +
378M LEU* 3.7 14.1 - - + +
381M TYR* 3.9 22.8 + - - -
407M ALA 3.3 14.8 + - - +
408M ARG* 4.9 3.9 - - - +
410M ILE* 1.3 79.1 - - - +
412M ARG* 1.3 63.8 + - - +
414M LEU* 3.2 28.3 + - + +
415M SER 3.8 2.9 + - - -
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Residues in contact with ARG 412 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398L GLN* 3.0 45.7 + - - +
401L GLU* 2.8 42.6 + - - -
402L VAL* 4.7 7.5 - - - +
342M LEU 4.7 2.2 + - - -
344M ILE* 4.9 11.7 - - - +
408M ARG* 3.2 33.5 + - - +
409M LYS* 3.2 8.4 + - - +
411M GLN* 1.3 81.5 - - - +
413M PHE* 1.3 57.8 + - - +
414M LEU 3.1 0.4 - - - -
415M SER* 2.7 26.0 + - - -
454M GLU* 4.0 31.8 + - + +
455M HIS* 5.9 0.4 - - - +
457M PHE* 3.0 15.7 - - + +
458M TYR* 3.7 26.2 - - + -
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Residues in contact with PHE 413 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139M LYS* 2.9 36.8 + - + +
409M LYS 2.7 20.4 + - - +
410M ILE* 2.8 10.7 + - + +
412M ARG* 1.3 72.1 - - - +
414M LEU* 1.3 57.8 + - - +
415M SER 3.4 0.2 - - - -
440M SER* 3.4 27.4 - - - -
441M PHE* 3.3 42.6 - + - -
444M VAL* 4.8 12.3 - - + -
457M PHE* 3.3 36.1 - + + -
460M VAL* 4.1 8.1 - - + -
461M GLY 4.3 3.4 - - - -
462M GLY* 4.0 4.9 - - - -
463M ILE* 3.9 16.8 - - + -
466M VAL* 3.4 23.3 - - + -
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Residues in contact with LEU 414 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139M LYS* 4.3 4.9 - - - +
140M VAL* 3.9 46.9 + - + +
143M LEU* 5.3 2.5 - - + -
144M LEU* 4.5 11.9 - - + -
344M ILE* 5.3 3.8 - - + -
346M PRO* 4.3 6.2 - - - +
350M PRO* 3.9 30.5 - - + -
374M VAL* 5.1 1.3 - - + -
378M LEU* 4.0 14.1 - - + -
410M ILE* 3.0 19.0 + - + +
411M GLN* 3.4 18.2 - - + +
412M ARG 3.1 0.6 - - - -
413M PHE* 1.3 77.5 - - - +
415M SER* 1.3 66.5 + - - +
416M GLN* 3.7 6.2 + - - +
441M PHE* 3.5 26.5 - - + -
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Residues in contact with SER 415 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M LYS* 3.0 21.7 + - - -
344M ILE* 4.1 19.2 - - - +
345M TYR 3.3 25.1 - - - -
411M GLN 3.8 2.4 + - - -
412M ARG 2.7 22.3 + - - -
413M PHE 3.8 0.9 - - - +
414M LEU* 1.3 79.6 - - - +
416M GLN* 1.3 58.7 + - - +
458M TYR* 3.9 7.0 - - - -
459M MET* 3.3 32.1 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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