Contacts of the helix formed by residues 470 - 483 (chain B) in PDB entry 4Y5U
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 LEU 470 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ARG* 5.4 6.7 - - - +
468B GLY 4.7 5.8 - - - +
469B LEU* 1.3 77.9 - - - +
471B PRO* 1.3 76.5 - - + +
472B GLU* 3.2 28.9 - - + +
473B HIS* 2.9 39.6 + - + +
474B PHE* 3.1 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B LEU 4.6 0.9 - - - +
470B LEU* 1.3 93.3 - - + +
472B GLU* 1.3 71.9 + - - +
474B PHE* 3.3 16.9 + - + +
475B LEU* 3.1 22.7 + - - +
489B MET* 3.8 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B LEU* 3.3 39.4 - - + +
471B PRO* 1.3 87.0 - - - +
473B HIS* 1.3 64.4 + - + +
475B LEU* 3.7 5.0 - - - +
476B PHE* 3.0 34.4 - - + -
489B MET* 3.9 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ARG* 4.0 16.6 + - - -
468B GLY 4.4 1.1 - - - -
469B LEU* 3.5 15.8 - - + +
470B LEU* 2.9 48.7 + - + +
472B GLU* 1.3 81.6 - - + +
474B PHE* 1.3 60.0 + - - +
475B LEU 3.2 0.4 - - - -
476B PHE* 3.4 3.5 + - - +
477B LEU* 3.1 30.4 + - + +
533B TRP* 4.0 10.5 - + - -
539B ILE* 3.1 35.5 + - + +
541B PHE* 3.7 38.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B TRP* 3.8 4.5 + + - +
452B CYS* 3.2 57.7 - - + -
455B LEU* 5.2 1.3 - - + -
456B ASN* 4.1 6.7 - - + -
469B LEU* 3.6 44.6 - - + -
470B LEU 3.1 18.1 + - - -
471B PRO* 3.3 14.1 + - + +
473B HIS* 1.3 74.7 - - - +
475B LEU* 1.3 60.3 + - - +
477B LEU* 3.7 15.4 - - + +
478B ALA* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B PRO 3.1 15.7 + - - +
472B GLU* 3.7 6.7 - - - +
474B PHE* 1.3 76.1 - - - +
476B PHE* 1.3 75.2 + - + +
478B ALA* 3.5 5.0 + - - +
479B GLN* 3.2 31.2 + - - +
486B SER 3.8 14.4 - - - +
487B LEU* 4.0 28.7 - - + +
488B SER 3.8 17.3 - - - +
489B MET* 3.8 29.1 - - + +
492B PHE* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B GLU* 3.0 30.7 - - + -
473B HIS 3.4 5.0 + - - +
475B LEU* 1.3 85.4 - - + +
477B LEU* 1.3 62.6 + - - +
479B GLN* 3.3 24.4 - - - +
480B LYS* 3.7 20.3 + - - +
487B LEU* 4.1 16.2 - - + -
541B PHE* 3.3 28.7 - - + +
542B ILE* 3.7 16.8 - - + +
543B SER* 3.7 29.2 - - - +
546B TYR* 3.8 34.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B TRP* 4.1 10.8 - - + -
455B LEU* 4.4 11.4 - - + -
469B LEU* 4.6 7.6 - - + -
473B HIS 3.1 20.1 + - - +
474B PHE* 3.7 23.3 - - + +
475B LEU 3.1 0.4 - - - -
476B PHE* 1.3 78.1 - - - +
478B ALA* 1.3 59.9 + - - +
479B GLN 3.2 0.2 - - - -
480B LYS* 3.4 8.1 + - - +
481B ILE* 3.1 27.7 + - - +
514B PHE* 3.8 19.8 - - + -
517B TRP* 3.9 28.9 - - + -
518B PHE* 4.2 21.5 - - + -
541B PHE* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B TRP* 3.6 28.7 - - - +
474B PHE 3.0 18.7 + - - +
475B LEU* 3.7 5.4 - - - +
477B LEU* 1.3 73.6 - - - +
479B GLN* 1.3 63.9 + - - +
481B ILE* 3.9 4.7 - - - -
482B PHE* 3.1 29.9 + - + +
492B PHE* 3.7 28.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B LEU* 3.2 18.6 + - - +
476B PHE* 3.3 28.9 - - - +
478B ALA* 1.3 78.6 - - - +
480B LYS* 1.3 58.0 + - - +
483B ASN* 2.9 24.1 + - - -
484B ASP 3.0 31.7 + - - +
485B ASN* 3.6 19.0 + - - +
486B SER 2.8 28.4 + - - +
487B LEU* 3.9 16.8 - - - +
492B PHE* 4.1 7.4 - - + -
543B SER* 4.6 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B PHE 3.7 8.9 + - - +
477B LEU* 3.5 15.0 - - - +
478B ALA 3.3 0.2 - - - -
479B GLN* 1.3 79.3 - - - +
481B ILE* 1.3 64.1 + - - +
482B PHE 3.4 0.3 + - - -
483B ASN* 3.6 7.5 + - - +
507B LEU* 3.4 45.4 - - + +
510B ARG* 5.9 3.6 - - - +
514B PHE* 4.0 14.8 - - + -
517B TRP* 3.6 43.1 - - + +
565B ASP* 3.1 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B TRP* 3.9 15.9 - - + -
451B MET* 5.5 0.2 - - + -
477B LEU 3.1 13.7 + - - +
478B ALA* 3.7 12.6 - - - +
480B LYS* 1.3 79.4 - - - +
482B PHE* 1.3 83.2 + - + +
483B ASN* 5.2 0.5 - - - +
497B VAL* 3.7 23.8 - - + -
501B GLN* 3.7 36.2 + - + +
502B PHE* 4.2 8.1 - - + -
507B LEU* 4.6 5.2 - - - +
514B PHE* 3.6 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B TRP* 4.0 33.0 - + + -
478B ALA 3.1 21.4 + - - +
481B ILE* 1.3 93.6 - - + +
483B ASN* 1.3 69.2 + - - +
484B ASP* 4.2 2.8 - - + +
492B PHE* 3.6 21.1 - + + -
495B ARG* 3.7 61.7 + - + +
496B SER 3.6 19.7 - - - -
497B VAL* 4.2 4.0 - - + -
501B GLN* 3.6 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B GLN 2.9 11.6 + - - -
480B LYS* 3.6 6.6 + - - +
481B ILE 3.4 3.2 - - - +
482B PHE* 1.3 81.3 + - - +
484B ASP* 1.3 56.2 + - - +
485B ASN* 6.1 0.4 - - - -
508B LEU* 3.5 39.5 - - + +
----------------------------------------------------------
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