Contacts of the helix formed by residues 481 - 489 (chain B) in PDB entry 6EBT
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 THR 481 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ASN* 3.8 23.1 - - + +
451B GLU* 4.1 26.0 - - + +
475B ALA* 4.0 2.0 - - - -
480B SER* 1.3 79.9 - - - +
482B LEU* 1.3 63.9 + - - +
483B LYS* 3.6 6.6 + - - +
484B GLU* 3.1 40.8 + - - +
485B THR* 3.0 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ASN 4.6 5.0 + - - +
452B SER 3.4 24.4 + - - +
453B LEU* 3.8 27.9 - - + +
455B LEU* 4.1 9.2 - - + +
456B VAL* 3.5 43.1 - - + +
459B LEU* 5.7 0.9 - - + -
471B ILE* 3.6 11.5 - - + +
472B ALA* 4.1 22.4 - - - -
475B ALA* 4.2 3.6 - - + -
480B SER 4.2 0.2 + - - -
481B THR* 1.3 72.8 - - - +
483B LYS* 1.3 57.7 + - - +
485B THR 3.4 0.2 + - - -
486B ALA* 2.8 34.0 + - - +
497B PHE* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ASN 5.5 0.6 + - - +
481B THR* 3.3 7.4 + - - +
482B LEU* 1.3 77.1 - - - +
484B GLU* 1.3 67.7 + - + +
486B ALA* 3.8 1.0 - - - +
487B ILE* 3.1 38.1 + - + +
494B ALA* 3.9 27.8 + - - +
497B PHE* 3.7 36.1 - - + -
498B ASP* 3.2 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B SER* 3.4 15.2 - - - -
481B THR* 3.1 40.5 + - - +
483B LYS* 1.3 79.9 - - + +
485B THR* 1.3 63.7 + - - +
487B ILE* 3.3 8.0 + - - +
488B GLU* 3.1 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ILE* 3.6 31.9 - - + +
474B THR* 3.7 26.7 - - + +
475B ALA* 3.5 8.7 + - - -
478B ASN* 5.2 0.2 + - - -
480B SER* 2.8 26.3 + - - -
481B THR 3.0 13.9 + - - -
482B LEU 3.8 2.2 - - - -
484B GLU* 1.3 76.1 - - - +
486B ALA* 1.3 64.9 + - - +
487B ILE 2.9 1.7 + - - -
488B GLU* 3.1 12.9 + - - +
489B LEU* 3.1 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ILE* 3.7 33.6 - - + +
482B LEU 2.8 23.2 + - - +
483B LYS 3.9 3.4 - - - +
485B THR* 1.3 72.7 - - - +
487B ILE* 1.3 58.2 + - - +
489B LEU* 4.1 2.4 + - - -
490B GLY 3.5 0.9 + - - -
491B TYR* 3.2 27.6 + - + +
492B LEU* 3.7 29.0 + - + -
497B PHE* 4.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LYS* 3.2 30.5 - - + +
484B GLU* 3.6 7.2 - - - +
485B THR 3.0 1.0 - - - -
486B ALA* 1.3 77.4 - - - +
488B GLU* 1.3 64.2 + - + +
489B LEU 3.2 1.3 - - - -
490B GLY* 2.8 21.1 + - - -
492B LEU* 4.0 22.6 - - + +
493B THR* 5.8 0.7 - - - -
494B ALA* 3.8 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B THR* 6.1 0.7 - - - +
478B ASN* 5.6 2.4 - - - +
480B SER* 5.4 3.1 + - - -
484B GLU* 3.1 24.0 + - - +
485B THR* 3.1 11.6 + - - +
487B ILE* 1.3 78.0 - - + +
489B LEU* 1.3 66.9 + - + +
490B GLY* 3.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B LYS* 4.2 13.0 - - + -
471B ILE* 4.3 5.4 - - + -
474B THR* 4.4 19.3 - - + +
485B THR* 3.1 31.7 + - + +
486B ALA 4.3 0.9 - - - +
488B GLU* 1.3 82.4 - - + +
490B GLY* 1.3 60.1 + - - +
491B TYR* 3.3 55.6 - - + +
----------------------------------------------------------
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