Contacts of the helix formed by residues 465 - 483 (chain X) in PDB entry 3FEW
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 ILE 465 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324X TYR* 5.9 2.7 - - - -
373X ASP* 4.3 16.2 - - - +
463X PRO* 3.8 0.8 - - - +
464X ALA* 1.3 82.1 - - - +
466X ALA* 1.3 63.3 + - - +
467X VAL 3.1 2.2 - - - +
468X GLY* 3.2 18.1 + - - +
469X ILE* 3.5 16.7 + - + +
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Residues in contact with ALA 466 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373X ASP* 4.3 20.8 - - + +
377X LEU* 3.8 23.8 - - + -
463X PRO* 3.2 24.6 - - + +
465X ILE* 1.3 80.4 - - - +
467X VAL* 1.3 61.8 + - - +
469X ILE* 3.0 14.8 + - - +
470X VAL* 3.0 28.0 + - - +
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Residues in contact with VAL 467 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320X LYS* 4.5 12.6 - - + -
321X VAL* 4.0 20.8 - - + +
324X TYR* 4.0 30.7 - - + -
457X ALA 5.3 3.1 - - - +
460X LEU* 4.5 16.8 - - + +
463X PRO* 3.6 28.5 - - + +
464X ALA* 4.0 18.6 - - + +
466X ALA* 1.3 77.0 - - - +
468X GLY* 1.3 56.5 + - - +
470X VAL* 3.3 12.6 + - + +
471X GLY* 2.9 26.2 + - - -
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Residues in contact with GLY 468 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321X VAL* 4.3 12.6 - - - -
324X TYR* 5.3 5.7 - - - +
325X LEU* 4.4 18.2 - - - -
465X ILE* 3.2 13.4 + - - +
467X VAL* 1.3 78.9 - - - +
469X ILE* 1.3 56.4 + - - +
471X GLY* 3.4 0.7 + - - -
472X ILE* 2.9 38.0 + - - +
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Residues in contact with ILE 469 (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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367X PHE* 4.2 13.3 - - + -
368X LYS 5.7 0.9 - - - +
369X PHE* 3.5 59.5 - - + -
373X ASP* 3.7 16.4 - - + +
377X LEU* 4.0 14.1 - - + -
465X ILE* 3.5 26.7 + - + +
466X ALA* 3.0 17.3 + - + +
468X GLY* 1.3 76.7 - - - +
470X VAL* 1.3 58.6 + - + +
472X ILE* 3.4 4.6 + - - +
473X LEU* 3.1 34.3 + - + +
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Residues in contact with VAL 470 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321X VAL* 5.2 1.6 - - + -
377X LEU* 3.8 21.1 - - + -
420X TYR* 3.5 22.4 - - - +
456X TYR* 4.1 8.5 - - + -
457X ALA* 4.2 25.8 - - + +
460X LEU* 4.1 22.0 - - + -
466X ALA 3.0 13.7 + - - +
467X VAL* 3.4 12.8 - - + +
469X ILE* 1.3 72.9 - - - +
471X GLY* 1.3 61.9 + - - +
473X LEU* 3.6 7.2 - - - +
474X LEU* 2.8 37.9 + - + +
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Residues in contact with GLY 471 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317X ILE* 5.3 1.3 - - - -
321X VAL* 3.8 16.8 - - - -
329X TYR* 2.6 38.9 + - - -
467X VAL 2.9 17.0 + - - -
468X GLY 3.6 2.0 - - - -
469X ILE 3.2 0.2 - - - -
470X VAL* 1.3 77.7 - - - +
472X ILE* 1.3 58.6 - - - +
474X LEU* 4.2 2.0 - - - +
475X ALA* 3.3 12.1 + - - +
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Residues in contact with ILE 472 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325X LEU* 3.5 28.3 - - + -
329X TYR* 4.4 4.7 - - + -
361X VAL* 4.2 12.8 - - + -
367X PHE* 3.7 31.4 - - + -
468X GLY 2.9 18.4 + - - +
469X ILE 3.7 5.8 - - - +
471X GLY* 1.3 76.6 - - - +
473X LEU* 1.3 58.7 + - - +
475X ALA* 3.6 2.9 + - - +
476X ALA* 3.0 26.5 + - - +
490X LEU* 3.9 9.5 - - + +
494X ILE* 3.0 32.8 - - + -
495X ILE* 3.9 19.1 - - + -
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Residues in contact with LEU 473 (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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358X LEU* 4.8 5.8 - - + -
361X VAL* 6.2 0.7 - - + -
362X LEU* 4.0 26.5 - - + -
367X PHE* 4.6 6.5 - - + -
369X PHE* 4.2 17.0 - - + -
420X TYR* 3.8 21.3 - - + +
425X TRP* 3.6 40.8 - - + -
469X ILE* 3.1 20.6 + - + +
470X VAL* 3.2 6.3 + - - +
472X ILE* 1.3 75.4 - - - +
474X LEU* 1.3 60.4 + - - +
476X ALA* 3.2 4.4 + - + +
477X VAL* 2.9 43.7 + - + +
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Residues in contact with LEU 474 (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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314X ILE* 4.4 14.1 - - + -
317X ILE* 3.7 42.8 - - + -
329X TYR* 4.7 2.5 - - - +
336X ILE* 6.2 1.1 - - + -
450X SER 5.0 1.1 - - - +
453X LEU* 3.7 41.7 - - + +
454X GLY* 4.0 0.4 - - - +
457X ALA* 4.3 10.8 - - + -
470X VAL* 2.8 22.0 + - + +
471X GLY* 4.2 3.6 - - - +
473X LEU* 1.3 70.4 - - - +
475X ALA* 1.3 69.8 + - - +
477X VAL* 4.1 7.4 - - - -
478X VAL* 2.9 44.6 + - + +
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Residues in contact with ALA 475 (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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329X TYR* 4.1 12.3 - - + +
332X LEU* 4.3 4.5 - - + -
333X ALA* 6.4 0.7 - - - -
336X ILE* 3.9 25.6 - - + +
471X GLY 3.3 17.5 + - - +
472X ILE 3.8 4.0 - - - +
474X LEU* 1.3 84.2 - - + +
476X ALA* 1.3 56.9 + - - +
478X VAL* 5.0 0.2 - - - -
479X GLY* 3.0 27.4 + - - +
486X PHE* 4.7 2.9 - - - +
490X LEU* 3.9 21.5 - - + +
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Residues in contact with ALA 476 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357X SER 5.4 0.7 - - - +
358X LEU* 3.7 24.4 - - + +
361X VAL* 4.0 15.7 - - + -
472X ILE 3.0 19.7 + - - +
473X LEU* 3.4 9.6 - - + +
474X LEU 3.1 0.2 - - - -
475X ALA* 1.3 76.3 - - - +
477X VAL* 1.3 59.0 + - - +
480X ALA* 3.0 28.1 + - - +
486X PHE 6.3 0.2 - - - -
487X ALA* 6.2 0.7 - - - +
490X LEU* 3.6 17.3 - - + -
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Residues in contact with VAL 477 (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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358X LEU* 4.2 25.1 - - + -
425X TRP* 5.1 4.9 - - + -
428X LEU* 4.6 12.6 - - + -
429X MET* 3.5 28.6 - - - +
449X PHE* 3.7 9.2 - - + -
453X LEU* 3.6 29.8 - - + -
473X LEU* 2.9 32.9 + - + +
474X LEU* 3.6 7.6 - - - +
476X ALA* 1.3 72.1 - - - +
478X VAL* 1.3 69.1 + - - +
480X ALA* 3.5 14.6 + - - +
481X LEU* 3.5 6.8 - - - +
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Residues in contact with VAL 478 (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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314X ILE* 4.4 6.1 - - + -
336X ILE* 3.9 23.1 - - + -
340X VAL* 4.9 2.2 - - + -
446X LEU* 4.6 4.3 - - + -
449X PHE* 4.2 10.5 - - + -
450X SER* 3.8 28.3 - - - +
453X LEU* 4.2 13.9 - - + -
474X LEU* 2.9 32.3 + - + +
475X ALA* 4.6 0.9 - - - +
477X VAL* 1.3 81.9 - - + +
479X GLY* 1.3 59.5 + - - +
480X ALA 3.1 1.1 - - - -
481X LEU* 3.0 21.8 + - - +
482X LEU* 3.3 24.9 - - + +
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Residues in contact with GLY 479 (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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336X ILE* 4.6 3.5 - - - +
475X ALA 3.0 19.8 + - - -
476X ALA 4.1 0.2 - - - -
478X VAL* 1.3 77.5 - - - +
480X ALA* 1.3 57.1 + - - +
482X LEU* 3.8 5.8 - - - -
483X ASP 2.9 39.3 + - - +
486X PHE* 3.7 25.1 - - - -
487X ALA 5.8 0.7 - - - -
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Residues in contact with ALA 480 (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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349X ARG* 2.7 27.6 + - - +
354X ALA* 3.6 36.0 - - + +
357X SER* 4.2 14.8 - - - -
358X LEU* 4.5 4.9 - - + +
429X MET* 4.2 4.7 - - + -
476X ALA 3.0 21.4 + - - +
477X VAL* 3.5 9.6 - - - +
478X VAL 3.1 0.8 - - - -
479X GLY* 1.3 77.3 - - - +
481X LEU* 1.3 59.3 + - - +
482X LEU 3.3 0.2 - - - -
483X ASP 4.9 0.2 - - - -
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Residues in contact with LEU 481 (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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343X PHE* 5.0 1.0 - - - -
347X THR 4.9 0.2 - - - +
348X ILE* 3.6 30.8 - - + +
349X ARG* 2.8 37.4 + - - +
354X ALA* 4.3 8.1 - - + -
429X MET* 3.7 20.2 - - + +
432X VAL* 4.2 19.1 - - + -
433X GLU 6.2 0.2 - - - +
446X LEU* 4.0 17.7 - - + -
449X PHE* 3.5 36.1 - - + -
477X VAL 3.5 10.1 - - - +
478X VAL* 3.0 8.6 + - - +
480X ALA* 1.3 78.7 - - - +
482X LEU* 1.3 62.6 + - + +
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Residues in contact with LEU 482 (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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336X ILE* 3.7 33.4 - - + +
339X ASP* 4.4 9.9 - - + +
340X VAL* 3.8 14.8 - - + -
343X PHE* 4.4 22.0 - - + -
349X ARG* 3.4 13.3 - - - +
446X LEU* 3.3 36.1 - - + -
478X VAL* 3.3 17.5 - - + +
479X GLY* 3.2 5.3 + - - +
481X LEU* 1.3 82.2 - - - +
483X ASP* 1.3 64.3 + - + +
486X PHE* 4.0 17.3 - - + -
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Residues in contact with ASP 483 (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 ASP* 4.6 5.1 - - - +
349X ARG* 3.6 10.2 - - - +
357X SER* 5.6 0.2 - - - -
479X GLY 2.9 22.7 + - - +
480X ALA* 4.9 0.2 - - - -
482X LEU* 1.3 77.1 - - + +
484X ASP* 1.3 79.8 + - - +
485X LYS* 2.9 41.5 + - - +
486X PHE* 3.2 30.6 + - + +
487X ALA 4.5 0.5 + - - -
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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