Contacts of the helix formed by residues 430 - 441 (chain B) in PDB entry 1BPO
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 TYR 430 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B THR 5.5 0.2 - - - -
395B PRO* 3.5 43.5 + - + +
398B ILE* 3.8 18.3 - - + +
399B ARG* 3.4 31.6 + - - +
402B GLN* 5.5 1.4 + - - -
428B ASN* 4.1 10.4 - - - +
429B LYS* 1.3 81.6 - - - +
431B GLU* 1.3 57.5 - - + +
433B LEU* 3.3 9.6 + - + +
434B GLU* 2.9 66.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ARG* 2.3 47.7 + - - +
394B THR 5.7 0.7 - - - -
398B ILE* 3.5 28.0 - - + +
417B TYR* 3.5 10.9 + - - -
418B PHE* 4.0 4.6 - - + -
421B LEU* 3.4 15.9 - - + +
427B LEU* 3.8 16.1 - - + +
428B ASN* 2.1 42.3 + - - +
429B LYS 3.3 0.2 - - - -
430B TYR* 1.3 77.0 - - + +
432B SER* 1.3 66.6 + - - +
434B GLU* 3.4 1.2 + - - +
435B LEU* 2.9 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 3.5 11.0 + - - +
428B ASN 2.6 25.5 + - - -
429B LYS 3.4 4.2 + - - -
430B TYR 3.3 0.4 - - - -
431B GLU* 1.3 78.7 - - - +
433B LEU* 1.3 58.9 + - - +
435B LEU* 3.3 5.6 + - - +
436B CYS* 2.9 36.6 + - - +
457B LEU* 3.6 23.3 - - - -
458B GLU 3.2 18.1 + - - -
463B LEU* 4.2 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LYS* 3.1 21.2 + - + +
430B TYR* 3.5 9.9 - - + +
432B SER* 1.3 79.3 - - - +
434B GLU* 1.3 58.0 + - - +
436B CYS* 4.1 1.7 - - - +
437B ARG* 2.9 53.5 + - - +
460B SER* 4.9 2.5 - - - +
462B GLU* 3.1 38.8 - - + +
463B LEU* 3.3 38.1 - - + +
466B LEU* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ILE* 4.1 11.7 - - + -
402B GLN* 4.3 19.0 + - - +
414B LEU* 5.1 3.6 - - - +
418B PHE* 3.9 22.3 - - + -
430B TYR* 2.9 58.8 + - + +
431B GLU 3.9 3.1 - - - +
433B LEU* 1.3 77.3 - - - +
435B LEU* 1.3 63.1 + - - +
437B ARG* 2.9 32.9 + - - +
438B PRO* 3.4 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B LEU* 4.6 12.6 - - + -
418B PHE* 4.1 30.7 - - + -
422B LEU* 4.2 7.6 - - + -
427B LEU* 3.9 20.4 - - + -
431B GLU 2.9 18.3 + - - +
432B SER* 3.5 3.4 - - - +
434B GLU* 1.3 76.7 - - - +
436B CYS* 1.3 63.6 + - - +
437B ARG 3.6 0.2 - - - -
438B PRO* 3.4 15.3 - - - +
439B VAL* 3.9 8.8 - - + +
451B TRP* 3.5 43.1 - - + -
457B LEU* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B SER 2.9 22.6 + - - +
433B LEU 4.1 0.4 - - - +
435B LEU* 1.3 79.8 - - - +
437B ARG* 1.3 65.6 + - - +
438B PRO 3.3 0.3 - - - -
439B VAL* 3.3 7.0 + - - +
440B LEU* 2.9 36.4 + - + +
448B LEU* 4.2 12.1 - - - -
451B TRP* 4.6 8.3 - - - -
457B LEU* 3.8 32.8 - - - -
463B LEU* 3.5 30.1 - - + -
466B LEU* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU* 2.9 37.3 + - - +
434B GLU* 2.9 41.7 + - - +
436B CYS* 1.3 76.2 - - - +
438B PRO* 1.4 67.6 - - + +
440B LEU* 3.5 2.8 + - - +
441B GLN* 2.9 36.4 + - - +
462B GLU* 4.5 7.7 + - - -
466B LEU* 3.5 46.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B LEU* 6.3 3.8 - - + -
434B GLU 3.4 16.4 - - - +
435B LEU* 3.4 13.2 - - - +
436B CYS 3.5 0.4 - - - -
437B ARG* 1.4 94.5 - - + +
439B VAL* 1.3 62.2 + - + +
441B GLN* 2.4 38.6 + - + +
442B GLN* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B LEU* 6.3 2.7 - - + -
435B LEU* 3.9 10.1 - - + +
436B CYS 3.3 7.4 + - - +
438B PRO* 1.3 82.1 - - + +
440B LEU* 1.3 62.6 + - + +
442B GLN* 2.9 15.8 + - - +
444B ARG* 3.1 65.8 + - + +
447B LEU* 3.7 16.4 - - + -
448B LEU* 4.7 6.5 - - + -
451B TRP* 3.6 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B CYS* 2.9 40.8 + - + +
437B ARG 3.6 4.3 - - - +
438B PRO 2.9 0.6 + - - -
439B VAL* 1.3 69.9 - - + +
441B GLN* 1.3 69.2 + - - +
443B GLY* 3.5 9.4 + - - -
444B ARG 5.0 5.4 - - - +
445B LYS* 6.1 0.7 - - - -
448B LEU* 3.3 37.7 - - + -
463B LEU* 4.6 0.7 - - + -
466B LEU* 3.6 33.2 - - + +
467B VAL* 3.8 24.5 - - + +
470B VAL* 3.8 36.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B ARG* 2.9 29.2 - - + +
438B PRO* 2.4 20.8 + - + +
440B LEU* 1.3 72.6 - - - +
442B GLN* 1.3 53.9 + - + +
443B GLY* 2.7 17.0 + - - -
466B LEU* 5.7 3.3 - - - +
470B VAL* 5.2 5.5 - - - +
----------------------------------------------------------
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