Contacts of the helix formed by residues 447 - 461 (chain B) in PDB entry 3RFU
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 VAL 447 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B PHE* 1.3 88.5 - - + +
448B GLU* 1.3 62.2 + - - +
449B ASP* 4.3 4.3 - - + +
450B ASN* 3.2 37.5 - - + +
451B ALA 3.4 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ILE* 3.1 42.5 + - + +
442B VAL* 4.8 0.5 - - - -
443B THR* 3.7 29.6 + - + +
447B VAL* 1.3 70.9 - - - +
449B ASP* 1.3 61.4 + - - +
451B ALA* 3.3 8.7 + - - +
452B LEU* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B VAL* 3.3 5.0 - - + +
448B GLU* 1.3 75.8 - - - +
450B ASN* 1.3 65.6 + - - +
452B LEU* 3.3 11.9 + - - +
453B ALA* 3.0 22.9 + - - +
477B LYS* 3.8 33.5 + - - +
478B GLY 4.3 13.5 - - - +
479B LEU* 5.4 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B PHE* 4.6 10.1 - - + -
447B VAL* 3.2 27.5 - - + +
448B GLU 3.4 0.4 - - - -
449B ASP* 1.3 77.6 - - - +
451B ALA* 1.3 63.9 + - - +
453B ALA* 3.0 8.2 + - - +
454B LEU* 3.0 33.1 + - - +
500B ASP* 3.7 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ILE* 4.7 4.5 - - + -
446B PHE* 3.4 23.9 - - + -
447B VAL 3.4 5.3 + - - +
448B GLU* 3.3 12.3 + - - +
449B ASP 3.2 0.4 - - - -
450B ASN* 1.3 78.6 - - - +
452B LEU* 1.3 57.6 + - - +
454B LEU* 3.2 5.3 + - - +
455B ALA* 3.0 25.0 + - - +
539B MET* 3.3 33.7 - - + +
547B ALA* 3.7 12.1 - - + -
549B LEU* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU* 4.7 5.4 - - + -
441B ILE* 3.6 31.4 - - + +
448B GLU 3.0 12.5 + - - +
449B ASP* 3.7 13.2 - - - +
451B ALA* 1.3 77.3 - - - +
453B ALA* 1.3 57.6 + - - +
455B ALA* 4.7 3.1 - - + +
456B ALA* 2.9 33.3 + - - +
470B ILE* 3.8 33.0 - - + +
473B ALA* 4.0 29.8 - - + +
474B ALA* 4.2 11.2 - - + +
477B LYS* 5.9 7.4 - - + -
478B GLY 5.7 2.0 - - - +
549B LEU* 5.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ASP* 3.0 15.0 + - - +
450B ASN* 3.0 14.5 + - - +
452B LEU* 1.3 76.7 - - - +
454B LEU* 1.3 65.1 + - + +
456B ALA* 3.8 4.3 - - - +
457B ALA* 3.0 28.4 + - - +
474B ALA* 5.5 2.9 - - - -
478B GLY 5.8 4.5 - - - +
479B LEU* 5.9 0.9 - - + +
480B SER* 3.4 37.5 - - - +
481B LEU* 5.0 1.6 - - - +
499B VAL* 5.0 0.4 - - - +
500B ASP* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B PHE* 5.0 6.3 - - + -
450B ASN* 3.0 23.5 + - - +
451B ALA* 3.6 5.2 - - - +
453B ALA* 1.3 79.4 - - + +
455B ALA* 1.3 65.7 + - - +
457B ALA* 3.0 6.2 + - - +
458B LEU* 3.0 28.1 + - - +
499B VAL* 3.4 31.0 - - + -
500B ASP* 2.8 44.2 - - - +
501B GLY* 5.1 1.1 - - - -
504B VAL* 4.3 10.1 - - + -
539B MET* 4.7 1.1 - - - -
541B VAL* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B ALA 3.0 10.3 + - - +
452B LEU* 4.3 2.2 - - - +
454B LEU* 1.3 76.1 - - - +
456B ALA* 1.3 60.9 + - - +
458B LEU* 3.2 9.8 + - - +
459B GLU* 2.9 30.7 + - + +
470B ILE* 3.9 8.3 - - + -
504B VAL* 5.1 3.1 - - - -
506B ILE* 5.3 7.9 - - + -
539B MET* 3.5 26.1 - - + -
549B LEU* 3.6 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LEU 2.9 21.4 + - - +
453B ALA* 3.8 4.5 - - - +
455B ALA* 1.3 77.3 - - - +
457B ALA* 1.3 57.7 + - - +
459B GLU 2.9 16.1 + - - -
460B HIS* 3.0 12.5 + - - +
470B ILE* 3.6 17.2 - - + +
471B VAL* 3.3 15.4 - - - +
474B ALA* 3.5 28.3 - - + -
481B LEU* 5.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B ALA 3.0 20.3 + - - +
454B LEU 3.4 5.6 - - - +
456B ALA* 1.3 76.6 - - - +
458B LEU* 1.3 58.8 + - + +
460B HIS* 3.8 6.8 + - - +
461B GLN* 3.0 23.7 + - - +
481B LEU* 4.6 9.2 - - + -
482B GLY* 3.6 29.8 - - - +
483B SER 5.3 0.9 - - - +
484B VAL* 4.2 6.8 - - + +
499B VAL* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B LEU 3.0 16.6 + - - +
455B ALA* 3.4 10.5 - - - +
456B ALA 3.1 0.2 - - - -
457B ALA* 1.3 76.0 - - - +
459B GLU* 1.3 67.1 + - + +
461B GLN* 2.9 23.6 + - - +
462B SER* 3.9 10.9 + - - -
484B VAL* 5.7 1.8 - - + -
495B VAL* 3.2 47.3 - - + +
497B GLY* 4.1 17.9 - - - +
498B GLN 4.8 3.1 - - - +
499B VAL* 4.5 8.7 - - + -
504B VAL* 3.5 42.6 - - + +
506B ILE* 4.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ALA* 2.9 18.1 - - + +
456B ALA 2.9 2.4 + - - +
458B LEU* 1.3 81.9 - - - +
460B HIS* 1.3 56.5 + - - +
461B GLN 3.4 0.2 - - - -
462B SER* 2.6 37.3 - - - +
464B HIS* 5.3 0.3 + - - -
466B LEU* 4.9 6.7 - - - +
467B ALA* 3.3 40.8 - - - +
468B ASN* 5.3 0.3 - - - +
470B ILE* 3.9 23.1 - - + +
471B VAL* 3.3 10.6 - - + +
495B VAL* 5.9 4.6 - - - +
506B ILE* 4.0 28.4 - - - +
549B LEU* 6.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ALA 3.0 12.0 + - - +
457B ALA* 4.1 6.7 - - - +
458B LEU 3.4 1.2 - - - -
459B GLU* 1.3 79.3 - - - +
461B GLN* 1.3 72.8 + - - +
462B SER 3.3 4.7 + - - +
463B GLU* 5.3 3.3 - - - +
468B ASN* 5.7 0.2 - - - +
471B VAL* 3.5 20.2 - - + -
475B LYS* 5.2 17.2 + - - -
481B LEU* 5.6 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ALA 3.0 22.8 + - - +
458B LEU* 2.9 28.6 + - - +
460B HIS* 1.3 81.4 + - - +
462B SER* 1.3 64.3 + - - +
463B GLU* 3.7 8.4 + - - +
484B VAL* 4.0 22.6 - - - +
487B PHE* 5.8 9.3 - - + +
----------------------------------------------------------
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