Contacts of the helix formed by residues 416 - 437 (chain A) in PDB entry 6FWF
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 GLY 416 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A ASN* 4.1 1.6 + - - -
403A PHE 3.1 11.9 - - - -
404A TRP 3.1 13.0 - - - -
405A PHE 4.0 0.8 + - - -
406A GLY 3.4 16.7 + - - -
408A GLN* 4.0 2.7 - - - -
414A ASP 3.4 2.8 + - - -
415A LEU* 1.3 78.6 - - - +
417A ARG* 1.3 59.7 + - - -
418A PHE 3.5 0.2 - - - -
419A TRP* 3.3 17.2 + - - +
420A GLN 2.8 22.2 + - - -
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Residues in contact with ARG 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A PHE* 2.6 36.4 + - + +
404A TRP* 2.8 36.2 + - + -
408A GLN* 3.2 29.9 + - - +
416A GLY* 1.3 67.2 - - - -
418A PHE* 1.3 56.1 + - - +
419A TRP 3.2 1.3 - - - -
420A GLN* 2.4 35.1 + - - +
421A LEU* 2.8 35.7 + - + +
469A GLY 3.7 6.3 + - - -
470A LEU* 3.9 27.0 + - - -
472A TYR* 2.9 45.9 + - - +
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Residues in contact with PHE 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A TRP* 2.8 39.6 + + + +
405A PHE* 4.5 28.3 - + + +
417A ARG* 1.3 72.4 - - - +
419A TRP* 1.3 99.7 + + + +
421A LEU* 3.4 8.5 + - + +
422A LEU* 2.8 56.3 + - + +
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Residues in contact with TRP 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ILE* 3.8 28.7 - - + -
381A VAL* 3.7 13.3 - - + +
384A GLY* 3.3 27.5 + - - -
385A SER* 3.4 31.4 - - - -
388A GLY* 4.7 1.5 - - - -
404A TRP 4.0 1.6 - - - -
405A PHE* 3.0 41.9 + + + +
415A LEU* 3.9 3.5 - - + +
416A GLY* 3.3 16.3 + - - +
417A ARG 3.2 0.4 - - - -
418A PHE* 1.3 110.7 - + - +
420A GLN* 1.3 59.0 + - - +
422A LEU* 3.8 16.4 - - + -
423A LEU* 2.8 29.3 + - - +
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Residues in contact with GLN 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A GLN* 3.4 11.4 + - - +
413A LEU* 4.2 10.0 - - - +
415A LEU* 3.3 17.9 - - + +
416A GLY 2.8 11.4 + - - +
417A ARG* 2.4 41.5 + - - +
419A TRP* 1.3 69.6 - - - +
421A LEU* 1.3 57.4 + - - +
423A LEU* 3.3 3.1 + - - +
424A MET* 2.8 34.1 + - - +
466A TYR* 3.5 27.4 + - + -
469A GLY* 2.9 41.4 + - - +
470A LEU* 3.3 15.9 - - + +
488A VAL* 5.5 0.8 - - - +
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Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A TRP* 5.3 12.3 - - + -
417A ARG* 2.8 21.9 + - - +
418A PHE* 3.5 7.4 - - + +
420A GLN* 1.3 73.9 - - - +
422A LEU* 1.3 59.4 + - + +
424A MET* 3.4 9.8 + - + -
425A VAL* 2.8 44.2 + - + +
470A LEU* 3.6 27.2 - - + +
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Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ALA* 5.6 2.4 - - - +
380A ILE* 4.7 12.6 - - + -
381A VAL* 3.4 21.7 - - + +
418A PHE* 2.8 57.1 + - + +
419A TRP* 3.8 18.2 - - + +
421A LEU* 1.3 74.7 - - + +
423A LEU* 1.3 59.4 + - - +
425A VAL* 3.4 16.7 + - + +
426A GLY* 2.8 24.9 + - - -
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A ILE* 5.1 5.8 - - + -
341A PHE* 3.4 34.1 - - + -
344A ALA* 6.4 1.8 - - + -
378A LEU* 5.1 12.7 - - + +
381A VAL* 3.7 15.0 - - + +
415A LEU* 4.3 9.9 - - + -
419A TRP 2.8 20.8 + - - +
420A GLN* 3.3 5.8 + - - +
422A LEU* 1.3 72.0 - - - +
424A MET* 1.3 58.2 + - - +
426A GLY* 3.1 4.7 + - - -
427A LEU* 2.8 37.0 + - + -
466A TYR* 3.8 37.9 - - + +
492A TRP* 5.7 4.7 - - + -
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Residues in contact with MET 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A GLN 2.8 20.9 + - - +
421A LEU* 3.9 11.2 - - + +
423A LEU* 1.3 73.1 - - - +
425A VAL* 1.3 55.4 + - + +
427A LEU* 3.3 8.9 + - + +
428A LEU* 2.8 55.0 + - + +
463A GLY 4.8 1.3 - - - +
464A VAL 4.5 2.9 - - - +
466A TYR* 4.1 27.6 - - + -
467A ALA* 3.5 36.1 - - + +
470A LEU* 3.9 16.6 - - + -
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Residues in contact with VAL 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A LEU* 2.8 38.2 + - + +
422A LEU* 3.6 19.1 - - + +
424A MET* 1.3 74.1 - - + +
426A GLY* 1.3 55.0 + - - +
428A LEU* 3.3 7.8 + - + +
429A LEU* 2.8 35.8 + - + +
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Residues in contact with GLY 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A LEU* 6.0 1.1 - - - -
374A LEU* 3.8 12.5 - - - +
377A ALA* 5.3 9.6 - - - +
378A LEU* 4.3 17.3 - - - -
422A LEU 2.8 18.5 + - - -
423A LEU 3.1 5.8 + - - -
425A VAL* 1.3 73.8 - - - +
427A LEU* 1.3 49.8 + - - +
429A LEU* 3.5 6.1 + - - -
430A TRP* 2.8 34.5 + - - +
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Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A LEU* 4.1 23.5 - - + +
378A LEU* 5.3 0.2 - - - +
423A LEU* 2.8 24.3 + - + +
424A MET* 3.3 11.6 + - + +
426A GLY* 1.3 71.8 - - - +
428A LEU* 1.3 60.2 + - - +
430A TRP* 3.7 11.3 - - + -
431A LEU* 2.8 30.1 + - - +
462A VAL* 4.1 27.8 - - + +
463A GLY* 3.9 15.6 - - - +
466A TYR* 3.3 41.3 - - + -
492A TRP* 4.0 19.5 - - + +
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Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A MET* 2.8 44.1 + - + +
425A VAL* 3.3 8.9 + - + +
427A LEU* 1.3 73.1 - - - +
429A LEU* 1.3 59.4 + - - +
431A LEU* 3.8 13.9 - - + -
432A PHE* 2.8 29.1 + - - +
463A GLY 3.3 23.6 - - - +
464A VAL* 5.2 4.5 - - + -
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A GLY* 3.8 11.7 - - - +
373A PHE* 3.9 28.3 - - + -
374A LEU* 3.9 20.2 - - + +
377A ALA* 5.6 4.3 - - + -
425A VAL* 2.8 23.1 + - + +
426A GLY* 3.8 6.7 - - - +
428A LEU* 1.3 69.4 - - - +
430A TRP* 1.3 60.4 + - - +
432A PHE* 3.4 12.5 - - + +
433A LEU* 2.8 56.1 + - + +
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Residues in contact with TRP 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A LEU* 3.8 44.8 + - + +
351A GLY* 4.9 0.4 - - - -
352A LEU* 3.5 37.5 - - + +
374A LEU* 3.3 18.0 - - + +
426A GLY 2.8 21.6 + - - +
427A LEU* 3.7 17.5 - - + +
429A LEU* 1.3 73.4 - - - +
431A LEU* 1.3 84.7 + - + +
433A LEU* 3.4 2.5 + - - +
434A MET* 2.8 38.9 + - + +
459A MET* 3.3 44.6 - - + -
462A VAL* 4.2 10.3 - - + -
463A GLY* 3.9 11.0 - - - -
496A PHE* 6.2 0.2 - + - -
500A PHE* 4.0 25.4 - + - -
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Residues in contact with LEU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A LEU 2.8 22.9 + - - +
428A LEU* 4.1 15.0 - - + +
430A TRP* 1.3 82.3 - - + +
432A PHE* 1.3 58.1 + - - +
434A MET* 4.3 1.3 - - + -
435A LEU* 2.8 42.4 + - + +
459A MET* 3.3 46.9 - - + +
460A VAL* 3.9 20.6 - - + +
463A GLY* 4.0 21.5 - - - -
464A VAL* 4.3 10.1 - - + -
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Residues in contact with PHE 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A LEU* 2.8 21.4 + - - +
429A LEU* 3.4 16.8 - - + +
431A LEU* 1.3 75.0 - - - +
433A LEU* 1.3 58.5 + - + +
435A LEU* 3.7 8.1 - - + +
436A ARG* 2.8 80.7 + - + +
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Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A LEU* 4.1 9.0 - - + -
367A GLN* 3.5 28.2 + - - +
370A GLY* 4.5 10.1 - - - -
371A VAL* 3.7 34.1 - - + +
374A LEU* 3.6 17.3 - - + -
429A LEU* 2.8 44.3 + - + +
430A TRP 3.9 3.6 - - - +
432A PHE* 1.3 77.4 - - + +
434A MET* 1.3 57.2 + - - +
436A ARG* 3.5 18.4 - - - +
437A CYS* 2.8 35.3 + - - -
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Residues in contact with MET 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A GLY 3.2 36.1 - - - +
352A LEU* 3.9 6.7 - - + +
355A ALA* 3.6 21.5 - - + -
358A VAL* 5.0 0.9 - - + -
430A TRP* 2.8 38.1 + - + +
431A LEU* 4.0 6.7 - - + +
433A LEU* 1.3 70.9 - - - +
435A LEU* 1.3 61.3 + - - +
437A CYS* 3.2 4.1 + - - +
438A THR* 2.8 37.2 + - + +
455A PHE* 3.6 36.6 - - + -
459A MET* 3.4 19.1 - - - -
500A PHE* 4.0 10.3 - - + -
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Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A LEU* 2.8 28.4 + - + +
432A PHE* 3.8 7.6 - - + +
434A MET* 1.3 72.9 - - - +
436A ARG* 1.3 51.9 + - - +
438A THR* 3.2 8.4 + - - +
439A VAL* 2.8 43.0 + - + +
442A PHE* 5.5 13.9 - - + -
456A VAL* 5.8 1.3 - - + -
459A MET* 3.7 20.5 - - + +
460A VAL* 5.4 8.1 - - + -
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Residues in contact with ARG 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A ASN* 4.2 3.8 + - - -
362A LYS* 4.7 5.9 - - - +
364A PRO* 3.4 45.9 - - + +
365A LYS* 3.6 18.8 + - - +
366A PHE 5.4 1.2 + - - -
367A GLN* 3.8 13.1 + - - +
432A PHE* 2.8 73.4 + - + +
433A LEU* 3.5 13.5 - - - +
434A MET 3.3 0.2 - - - -
435A LEU* 1.3 74.5 - - - +
437A CYS* 1.3 58.7 + - - +
438A THR 3.5 0.5 + - - -
439A VAL* 3.7 20.9 + - + +
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Residues in contact with CYS 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A SER* 5.7 2.0 - - - -
352A LEU* 5.0 2.2 - - - -
355A ALA* 3.6 35.2 - - + +
356A PRO* 5.1 4.9 - - - -
359A ASN* 3.1 43.2 + - - +
362A LYS 5.2 0.2 - - - -
364A PRO* 4.7 5.2 - - - -
367A GLN* 3.4 26.9 - - - -
433A LEU 2.8 27.4 + - - +
434A MET* 3.2 5.3 + - - +
436A ARG* 1.3 72.3 - - - +
438A THR* 1.3 60.6 + - - +
439A VAL 3.8 0.2 - - - -
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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