Contacts of the helix formed by residues 397 - 414 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406U ALA 5.1 5.9 + - - -
407U GLN* 5.2 4.6 + - - -
408U PHE 4.8 8.8 + - - -
396X LEU* 1.3 75.7 - - - +
398X GLU* 1.3 58.2 + - - +
399X GLN* 3.2 3.1 - - - -
400X ASP* 2.8 26.1 + - - +
401X LYS* 2.7 35.6 + - - +
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Residues in contact with GLU 398 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396X LEU 5.1 3.3 - - - +
397X SER* 1.3 73.6 - - - +
399X GLN* 1.3 64.0 + - + +
401X LYS* 3.5 17.5 + - - +
402X LEU* 3.4 19.9 + - - +
113Y LYS* 5.3 6.8 + - - +
116Y MET 5.4 7.4 - - - +
117Y GLN* 4.6 24.1 - - - +
120Y ARG* 3.2 33.7 + - - +
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Residues in contact with GLN 399 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397X SER* 3.2 3.2 - - - -
398X GLU* 1.3 79.2 - - + +
400X ASP* 1.3 68.3 + - - +
401X LYS 3.3 0.2 - - - -
402X LEU* 3.7 7.5 + - - +
403X THR* 2.9 25.1 + - - -
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Residues in contact with ASP 400 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407U GLN* 4.0 21.5 + - - +
380X THR* 5.6 4.6 - - + +
384X LEU* 4.3 20.8 - - + +
396X LEU* 4.5 7.2 - - + -
397X SER* 2.8 30.6 + - - +
399X GLN* 1.3 83.2 - - - +
401X LYS* 1.3 64.3 + - - +
403X THR* 3.4 8.1 + - - -
404X VAL* 3.2 28.6 + - - +
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Residues in contact with LYS 401 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393X MET* 4.8 24.0 - - + +
394X ASP* 5.6 9.7 - - - +
396X LEU* 4.5 15.5 - - + +
397X SER 2.7 20.8 + - - +
398X GLU* 3.9 19.5 + - - +
400X ASP* 1.3 74.7 - - - +
402X LEU* 1.3 60.1 + - - +
404X VAL* 3.6 3.3 + - - +
405X GLU* 3.1 51.0 + - + +
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Residues in contact with LEU 402 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398X GLU 3.4 14.9 + - - +
399X GLN* 4.0 7.9 - - - +
400X ASP 3.2 0.6 - - - -
401X LYS* 1.3 78.5 - - - +
403X THR* 1.3 62.4 + - - +
405X GLU* 3.7 15.8 + - + +
406X ARG* 3.3 54.4 + - - +
450X ASP* 4.3 10.1 - - + +
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Residues in contact with THR 403 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377X THR* 3.6 25.7 - - + +
380X THR* 4.3 27.3 - - + +
381X TYR* 5.8 0.7 - - - +
399X GLN 2.9 16.8 + - - -
400X ASP* 3.4 9.8 + - - -
401X LYS 3.3 0.2 - - - -
402X LEU* 1.3 77.4 - - - +
404X VAL* 1.3 59.6 + - - +
406X ARG* 3.9 3.9 - - - +
407X ALA* 2.9 28.7 + - + +
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Residues in contact with VAL 404 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380X THR* 6.1 0.4 - - + -
381X TYR* 3.5 34.5 - - + -
384X LEU* 4.2 16.6 - - + -
388X ILE* 5.0 4.5 - - + -
393X MET* 4.2 25.6 - - + -
396X LEU* 4.0 18.8 - - + -
400X ASP 3.2 17.5 - - - +
401X LYS* 3.9 5.6 - - - +
402X LEU 3.3 0.8 - - - -
403X THR* 1.3 77.4 - - + +
405X GLU* 1.3 63.4 + - - +
407X ALA* 2.9 6.8 + - - +
408X ARG* 2.8 35.5 + - + +
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Residues in contact with GLU 405 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393X MET* 5.6 7.4 - - - -
401X LYS* 3.1 48.1 + - + +
402X LEU* 4.1 16.4 - - + +
403X THR 3.6 0.2 - - - -
404X VAL* 1.3 79.2 - - + +
406X ARG* 1.3 60.5 + - - +
408X ARG* 3.7 7.2 + - - +
409X LYS* 3.4 37.2 + - - +
450X ASP 5.6 1.4 - - - +
454X GLU* 5.1 1.4 - - - +
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Residues in contact with ARG 406 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377X THR* 5.2 4.3 - - + -
402X LEU* 3.3 43.0 + - + +
403X THR* 4.1 5.2 - - - +
404X VAL 3.2 0.8 - - - -
405X GLU* 1.3 78.8 - - - +
407X ALA* 1.3 63.9 + - - +
409X LYS* 3.5 11.6 + - + +
410X ILE* 3.1 39.3 + - + +
444X VAL* 3.4 27.1 - - + +
445X LEU* 3.3 26.4 + - - +
446X GLU 5.0 0.2 - - - -
447X GLY* 4.1 10.9 - - - +
450X ASP* 2.7 37.8 + - - +
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Residues in contact with ALA 407 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377X THR* 3.8 19.5 - - + +
378X LEU* 3.9 6.0 - - + +
381X TYR* 3.7 31.9 - - + -
403X THR 2.9 21.7 + - - +
404X VAL 2.9 7.2 + - - +
406X ARG* 1.3 74.6 - - - +
408X ARG* 1.3 60.4 + - - +
410X ILE* 3.0 7.6 + - - +
411X GLN* 2.8 30.6 + - - +
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Residues in contact with ARG 408 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401T GLU* 3.3 30.3 + - - -
402T VAL* 5.4 5.1 - - - +
381X TYR* 3.5 35.8 + - + +
393X MET* 4.8 16.9 - - - +
404X VAL* 2.8 27.6 + - + +
405X GLU* 4.0 5.6 - - - +
407X ALA* 1.3 72.2 - - - +
409X LYS* 1.3 60.6 + - - +
411X GLN* 3.4 12.3 + - - +
412X ARG* 2.9 46.9 + - + +
454X GLU* 3.2 32.5 + - - +
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Residues in contact with LYS 409 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405X GLU* 3.4 24.8 + - - +
406X ARG* 3.5 12.2 + - + +
407X ALA 3.2 0.4 - - - -
408X ARG* 1.3 77.2 - - - +
410X ILE* 1.3 52.3 + - - +
412X ARG* 3.0 5.1 + - - +
413X PHE* 2.7 37.2 + - - +
444X VAL* 5.0 5.2 - - + -
449X TYR 3.5 1.3 + - - +
450X ASP* 2.7 45.5 + - - +
452X ILE 3.2 21.2 + - - -
453X PRO 4.6 1.1 - - - -
454X GLU* 4.2 21.7 - - + +
457X PHE* 3.5 41.9 - - + +
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Residues in contact with ILE 410 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374X VAL* 4.1 27.8 - - + -
377X THR* 4.3 21.5 - - + -
378X LEU* 4.3 11.7 - - + -
406X ARG* 3.1 22.4 + - + +
407X ALA* 3.0 7.1 + - - +
409X LYS* 1.3 75.6 - - - +
411X GLN* 1.3 64.6 + - - +
413X PHE* 3.0 18.8 + - - +
414X LEU* 3.2 14.9 + - + +
441X PHE* 4.3 15.9 - - + -
444X VAL* 4.2 18.8 - - + +
445X LEU* 3.9 29.2 - - + -
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Residues in contact with GLN 411 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339X ILE* 4.9 7.1 - - - +
342X LEU* 3.3 32.3 - - - +
344X ILE* 3.9 21.8 - - + +
350X PRO* 5.6 7.8 - - + +
378X LEU* 3.7 19.9 - - + +
381X TYR* 3.5 29.0 + - - -
385X GLN* 5.8 1.4 - - - +
407X ALA 2.8 18.6 + - - +
408X ARG* 3.6 10.7 + - - +
409X LYS 3.3 0.2 - - - -
410X ILE* 1.3 73.8 - - - +
412X ARG* 1.3 67.1 + - + +
414X LEU* 3.8 17.7 - - - +
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Residues in contact with ARG 412 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398T GLN* 2.7 42.2 + - - +
401T GLU* 3.5 32.1 + - - -
342X LEU* 3.8 12.7 + - - +
344X ILE* 4.0 21.5 - - + +
408X ARG* 2.9 35.7 - - - +
409X LYS 3.0 4.8 + - - +
411X GLN* 1.3 82.7 + - + +
413X PHE* 1.3 58.8 + - - +
414X LEU 3.1 5.4 - - - -
415X SER* 2.9 25.8 + - - -
454X GLU* 3.9 32.2 + - - -
455X HIS* 5.7 1.4 - - - +
457X PHE* 3.0 15.9 - - + +
458X TYR* 3.9 18.9 - - + +
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Residues in contact with PHE 413 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139X LYS* 2.8 35.2 + - + -
409X LYS 2.7 16.3 + - - +
410X ILE* 3.0 10.3 + - - +
412X ARG* 1.3 75.9 - - - +
414X LEU* 1.3 56.8 + - - +
415X SER 3.2 0.2 - - - -
440X SER* 3.7 31.2 - - - -
441X PHE* 3.2 47.9 - + + -
444X VAL* 4.5 9.0 - - + -
457X PHE* 3.4 36.3 - + + -
460X VAL* 4.2 1.3 - - + -
461X GLY 3.7 18.6 - - - -
462X GLY* 3.8 12.1 - - - -
463X ILE* 3.9 6.1 - - + -
466X VAL* 3.6 21.8 - - + -
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Residues in contact with LEU 414 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139X LYS* 4.4 3.6 - - - +
140X VAL* 3.1 58.1 - - + +
143X LEU* 4.4 11.9 - - + -
144X LEU* 4.6 7.4 - - + -
344X ILE* 4.9 2.9 - - + -
346X PRO* 4.2 1.8 - - - +
350X PRO* 3.8 34.1 - - + -
374X VAL* 5.3 1.6 - - + -
378X LEU* 4.0 13.7 - - + -
410X ILE* 3.2 16.7 + - + +
411X GLN* 3.8 12.3 - - - +
412X ARG 3.1 0.6 - - - -
413X PHE* 1.3 77.5 - - - +
415X SER* 1.3 63.6 + - - +
416X GLN* 3.4 6.4 + - - +
441X PHE* 3.9 21.8 - - + -
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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