Contacts of the helix formed by residues 456 - 463 (chain B) in PDB entry 3BJT
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 ASN 456 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LYS* 3.3 32.5 + - - +
434B SER* 5.6 0.2 - - - +
454B THR* 3.2 18.0 + - - +
455B ARG* 1.3 77.5 - - - +
457B PRO* 1.3 69.5 - - - +
458B GLN* 2.9 23.0 + - - +
459B THR* 3.1 27.3 + - - +
460B ALA* 3.2 14.9 + - - +
473B LEU* 3.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ARG 3.4 10.1 - - - +
456B ASN* 1.3 84.7 - - - +
458B GLN* 1.3 66.7 + - + +
460B ALA* 3.0 12.7 + - + +
461B ARG* 3.1 37.5 + - - +
473B LEU* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ASP* 4.5 15.0 + - - -
237B VAL 3.9 19.0 + - - -
238B ASP* 3.5 15.0 + - - +
264B ASN* 3.6 25.1 - - - +
265B ILE* 4.8 8.5 - - - +
456B ASN* 2.9 12.0 + - - +
457B PRO* 1.3 75.9 - - + +
459B THR* 1.3 61.5 + - + +
461B ARG* 3.0 20.2 + - - +
462B GLN* 2.8 52.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LYS 3.2 19.8 + - - +
434B SER* 3.5 26.4 - - - +
435B GLY* 4.5 4.8 + - - -
439B HIS* 5.9 0.9 - - - -
454B THR* 3.4 19.3 + - - +
456B ASN* 3.1 27.8 + - - +
458B GLN* 1.3 77.6 - - + +
460B ALA* 1.3 66.1 + - - +
462B GLN* 4.0 14.8 - - - +
463B ALA* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PRO* 4.1 20.8 - - + +
454B THR* 4.1 14.6 - - + -
456B ASN 3.2 11.5 + - - +
457B PRO* 3.0 18.1 + - + +
458B GLN 3.0 0.4 - - - -
459B THR* 1.3 83.6 + - - +
461B ARG* 1.3 59.1 + - - +
463B ALA* 3.5 3.0 - - - +
464B HIS* 4.2 0.2 - - - -
471B PRO* 3.2 35.1 - - + +
473B LEU* 4.2 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 6.0 7.3 - - - +
96B GLU* 5.9 0.6 + - - -
105B TYR* 5.3 7.0 + - - +
107B PRO* 4.0 16.6 - - + -
108B VAL 2.9 28.3 - - - +
109B ALA* 3.5 18.9 - - + +
110B VAL* 4.8 2.9 - - - +
236B ASP* 4.0 20.3 + - - -
238B ASP* 2.8 33.4 + - - +
239B MET* 4.8 0.3 - - - +
457B PRO* 3.1 30.2 + - - +
458B GLN* 3.0 30.9 + - - +
460B ALA* 1.3 75.2 - - - +
462B GLN* 1.3 63.1 + - - +
463B ALA 3.3 0.5 + - - -
464B HIS* 3.3 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ASP* 3.2 34.0 + - + +
239B MET* 4.4 9.6 - - + -
264B ASN* 3.1 25.9 + - - +
266B LYS* 3.3 33.1 - - + +
434B SER 5.2 2.3 - - - +
439B HIS* 5.3 3.1 - - + -
458B GLN* 2.8 39.8 + - + +
459B THR* 4.0 19.7 + - - +
461B ARG* 1.3 68.2 - - - +
463B ALA* 1.3 62.6 + - - +
464B HIS 2.9 6.8 + - - -
465B LEU* 3.0 21.7 + - - +
466B TYR* 4.0 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ALA* 6.2 0.4 - - + -
439B HIS* 4.8 7.4 - - + -
452B ALA* 5.3 3.1 - - + -
459B THR 3.0 13.4 + - - +
460B ALA* 3.5 14.1 - - - +
461B ARG 3.2 0.6 - - - -
462B GLN* 1.3 75.4 - - - +
464B HIS* 1.3 61.8 + - - +
465B LEU 3.1 0.4 - - - -
466B TYR* 3.1 27.3 + - - +
469B ILE* 3.7 30.3 - - + +
471B PRO* 3.6 17.3 - - + -
----------------------------------------------------------
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