Contacts of the helix formed by residues 441 - 460 (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 ALA 441 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231X TYR 3.9 17.3 - - - +
232X GLY 4.5 3.6 - - - +
233X ASN* 2.8 18.6 - - - +
289X TYR* 4.2 24.7 - - + +
302X ILE* 6.1 0.9 - - + -
436X VAL* 4.5 0.2 - - - -
439X GLY 3.4 3.7 + - - -
440X ILE* 1.3 75.3 - - - +
442X SER* 1.3 67.2 + - - +
443X ALA* 4.3 7.4 - - + +
444X VAL* 3.0 9.4 + - + +
445X ALA* 3.0 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 442 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343X PHE* 4.1 3.6 - - - -
346X LYS 3.7 17.0 - - - -
347X THR* 3.2 12.3 - - - +
348X ILE* 2.9 40.5 + - - +
436X VAL* 4.1 17.1 - - - +
440X ILE 3.5 2.6 + - - -
441X ALA* 1.3 70.6 - - - +
443X ALA* 1.3 63.2 + - - +
445X ALA* 3.2 2.6 + - - +
446X LEU* 2.9 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 443 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289X TYR* 6.0 1.8 - - - +
302X ILE* 4.0 23.6 - - + -
306X VAL* 3.4 11.2 - - + +
307X LEU* 3.8 29.6 - - + +
343X PHE* 4.7 8.4 - - + -
344X GLN 5.7 3.8 - - - +
441X ALA* 3.2 5.9 - - + +
442X SER* 1.3 78.6 - - - +
444X VAL* 1.3 59.0 - - + +
446X LEU* 3.5 5.2 + - - +
447X GLY* 2.8 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 444 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231X TYR* 3.9 24.5 - - + +
233X ASN* 3.6 35.4 - - - +
302X ILE* 5.7 1.1 - - + -
306X VAL* 3.9 20.9 - - + -
399X ALA* 4.9 8.7 - - + +
402X PHE* 4.0 20.6 - - + -
440X ILE* 3.7 9.6 - - + -
441X ALA* 3.0 10.1 + - + +
443X ALA* 1.3 75.0 - - + +
445X ALA* 1.3 61.3 + - - +
447X GLY* 3.5 0.2 - - - -
448X VAL* 2.8 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 445 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348X ILE* 4.8 2.7 - - + -
432X VAL* 4.3 11.4 - - + -
435X TRP* 3.6 27.3 - - + -
436X VAL* 3.9 22.4 - - + -
440X ILE* 3.9 8.0 - - + +
441X ALA 3.0 11.2 + - - +
442X SER 3.5 7.2 - - - +
444X VAL* 1.3 76.3 - - - +
446X LEU* 1.3 58.4 + - - +
448X VAL* 3.4 0.4 + - - -
449X PHE* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307X LEU* 5.1 2.5 - - + -
310X ALA* 5.1 0.4 - - - -
340X VAL* 3.9 28.5 - - + -
343X PHE* 4.2 29.8 - - + -
348X ILE* 4.4 8.2 - - + +
432X VAL* 5.3 0.2 - - - +
442X SER 2.9 16.9 + - - +
443X ALA 3.7 4.7 - - - +
445X ALA* 1.3 76.2 - - - +
447X GLY* 1.3 57.4 + - - +
449X PHE* 3.8 4.8 - - + +
450X SER* 2.9 37.7 + - - +
478X VAL* 4.6 10.8 - - + +
481X LEU* 4.0 24.7 - - + -
482X LEU* 3.3 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 447 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306X VAL* 4.4 5.4 - - - -
310X ALA* 4.0 20.8 - - - +
400X PHE* 3.4 16.2 - - - -
443X ALA 2.8 17.2 + - - -
444X VAL 3.2 3.8 + - - -
446X LEU* 1.3 78.2 - - - +
448X VAL* 1.3 55.4 + - - +
450X SER* 3.9 1.4 - - - -
451X ALA* 3.1 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 448 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393X LEU* 4.8 7.6 - - + -
399X ALA 5.0 3.1 - - - +
400X PHE* 3.9 22.9 - - + -
402X PHE* 4.3 23.6 - - + -
405X VAL* 4.8 8.1 - - + -
408X LYS* 4.4 17.5 - - + -
409X VAL* 5.6 1.1 - - + -
412X VAL* 6.2 0.2 - - + -
435X TRP* 4.1 20.4 - - + -
444X VAL* 2.8 27.5 + - + +
445X ALA* 4.0 2.2 - - - +
447X GLY* 1.3 70.5 - - - +
449X PHE* 1.3 59.4 + - - +
451X ALA* 4.2 0.2 - - - +
452X THR* 2.6 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 449 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412X VAL* 4.5 12.1 - - + -
428X LEU* 4.1 28.3 - - + -
429X MET* 4.3 7.6 - - - -
432X VAL* 3.6 27.4 - - + -
435X TRP* 3.9 9.3 - + + -
445X ALA 2.9 19.4 + - - +
446X LEU* 3.8 4.9 - - + +
448X VAL* 1.3 75.0 - - - +
450X SER* 1.3 66.6 + - - +
452X THR* 3.9 2.8 - - - -
453X LEU* 3.1 47.5 + - + +
477X VAL* 3.7 34.3 - - + -
478X VAL* 4.2 6.5 - - + -
481X LEU* 3.5 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 450 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310X ALA* 4.4 15.3 - - - +
313X VAL* 4.2 4.3 - - - +
314X ILE* 3.4 32.7 - - - +
317X ILE* 4.9 0.3 - - - +
340X VAL* 5.1 1.7 - - - +
446X LEU* 2.9 27.0 + - - +
447X GLY 3.9 3.1 - - - -
449X PHE* 1.3 77.1 - - - +
451X ALA* 1.3 58.2 + - - +
453X LEU* 3.7 2.5 - - - +
454X GLY* 2.8 27.9 + - - -
474X LEU* 5.0 0.3 - - - +
478X VAL* 3.8 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 451 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310X ALA* 5.7 2.0 - - - -
313X VAL* 4.1 19.9 - - + +
393X LEU* 3.6 17.9 - - + +
396X ILE* 3.9 11.4 - - + -
400X PHE* 3.7 20.6 - - + -
447X GLY 3.1 17.5 + - - +
448X VAL 4.2 0.7 - - - +
450X SER* 1.3 80.2 - - - +
452X THR* 1.3 57.8 + - - +
454X GLY 3.8 0.2 - - - -
455X ALA* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 452 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381X TRP* 4.3 4.2 - - + -
389X MET* 3.9 24.1 - - + +
393X LEU* 3.4 21.2 - - - +
408X LYS 5.8 0.2 - - - -
409X VAL* 4.0 15.8 - - + +
412X VAL* 3.9 31.4 - - + +
448X VAL* 2.6 29.7 + - - +
449X PHE* 3.9 3.6 - - - -
451X ALA* 1.3 74.5 - - - +
453X LEU* 1.3 66.1 + - - +
455X ALA* 3.2 6.4 + - - +
456X TYR* 3.2 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 453 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381X TRP* 4.4 10.1 - - + -
412X VAL* 3.5 29.4 - - + -
416X SER* 4.7 4.5 - - - +
428X LEU* 5.2 4.5 - - + -
449X PHE* 3.1 51.9 + - + +
450X SER* 3.7 3.1 - - - +
452X THR* 1.3 77.0 - - - +
454X GLY* 1.3 63.4 + - - +
456X TYR* 3.3 10.5 + - - +
457X ALA* 3.0 22.3 + - - +
474X LEU* 3.7 20.8 - - + +
477X VAL* 3.6 18.8 - - + -
478X VAL* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 454 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313X VAL* 3.9 7.6 - - - -
317X ILE* 3.5 26.2 - - - -
450X SER 2.8 21.4 + - - -
451X ALA 3.9 1.6 - - - -
453X LEU* 1.3 73.2 - - - +
455X ALA* 1.3 55.9 + - - +
457X ALA* 3.0 3.5 + - - +
458X LEU* 2.9 38.2 + - - +
474X LEU* 4.0 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 455 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313X VAL* 5.0 0.4 - - - +
389X MET* 4.1 24.9 - - + +
392X LYS* 6.1 7.9 - - + -
393X LEU* 4.7 7.0 - - + -
451X ALA 3.0 18.9 + - - +
452X THR* 3.2 6.3 + - - +
454X GLY* 1.3 74.0 - - - +
456X TYR* 1.3 61.0 + - - +
458X LEU* 3.7 6.1 + - - +
459X SER* 3.3 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 456 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377X LEU* 2.8 40.7 + - - +
380X VAL* 3.7 23.8 - - + +
381X TRP* 3.4 58.8 - + + -
384X ILE* 3.7 16.2 - - + -
389X MET* 4.1 7.1 - - + +
420X TYR* 4.1 14.3 - - - -
452X THR 3.2 7.7 + - - +
453X LEU* 3.4 9.9 - - - +
455X ALA* 1.3 75.3 - - - +
457X ALA* 1.3 69.6 + - + +
459X SER* 2.7 23.1 + - - -
460X LEU* 3.6 19.5 + - + +
470X VAL* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 457 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317X ILE* 4.4 17.0 - - + -
320X LYS* 3.6 18.8 - - + +
321X VAL* 5.5 3.1 - - + -
453X LEU 3.0 13.8 + - - +
454X GLY 3.0 7.8 + - - +
456X TYR* 1.3 83.6 - - + +
458X LEU* 1.3 61.9 + - + +
460X LEU* 3.7 12.1 + - - +
467X VAL* 5.3 2.8 - - - +
470X VAL* 4.2 22.2 - - + +
474X LEU* 4.3 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 458 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313X VAL* 5.1 5.6 - - + +
316X ASP* 4.0 28.3 - - + +
317X ILE* 4.2 21.1 - - + -
320X LYS* 3.8 45.3 + - + +
454X GLY* 2.9 20.7 + - - +
455X ALA* 4.3 5.6 - - - +
456X TYR 3.2 0.2 - - - -
457X ALA* 1.3 75.7 - - + +
459X SER* 1.3 60.5 + - - +
460X LEU 3.3 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 459 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380X VAL* 4.9 1.7 - - - +
384X ILE* 4.6 12.8 - - - +
389X MET* 6.3 0.4 - - - -
455X ALA 3.3 15.0 + - - -
456X TYR* 2.7 22.8 + - - -
458X LEU* 1.3 75.3 - - - +
460X LEU* 1.3 66.5 + - - +
461X GLY* 3.4 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 460 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320X LYS* 2.7 35.0 + - - -
377X LEU* 4.3 10.3 - - + -
380X VAL* 3.7 31.4 - - + -
456X TYR* 3.6 27.5 + - + +
457X ALA 3.8 9.9 - - - +
458X LEU 3.3 1.4 - - - -
459X SER* 1.3 79.8 + - - +
461X GLY* 1.3 67.0 + - - +
462X ALA* 4.1 0.9 - - - -
463X PRO* 4.1 18.2 - - + -
467X VAL* 4.5 13.4 - - + +
470X VAL* 4.1 33.9 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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