Contacts of the helix formed by residues 475 - 486 (chain E) in PDB entry 3DBL
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 LYS 475 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419E PRO* 4.0 25.1 + - + -
420E ASP* 3.2 38.3 + - - +
473E MET* 3.9 21.1 + - + -
474E VAL* 1.3 76.6 - - - +
476E ASP* 1.3 59.9 + - - +
477E ASP* 2.8 26.9 + - + +
478E TYR* 2.9 32.3 + - + +
479E VAL* 4.0 1.0 + - - +
30F PHE* 5.9 3.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 476 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458E LYS* 2.9 40.5 + - - +
474E VAL 3.1 4.6 + - - +
475E LYS* 1.3 70.5 - - - +
477E ASP* 1.3 63.3 + - - +
478E TYR 3.1 0.4 - - - -
479E VAL* 3.0 22.4 + - + +
480E HIS* 3.1 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 477 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475E LYS* 2.8 19.0 - - + +
476E ASP* 1.3 81.6 - - - +
478E TYR* 1.3 60.3 + - - +
480E HIS* 4.3 6.3 - - - -
481E GLU 3.4 16.1 + - - -
29F PRO* 3.4 37.7 - - + +
30F PHE* 3.4 17.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 478 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419E PRO 3.4 20.4 - - - -
420E ASP* 2.7 37.1 + - - +
424E VAL* 3.4 25.4 - - + -
425E LEU* 4.2 25.3 - - + +
428E MET* 3.7 10.4 - - + +
474E VAL* 4.0 13.7 - - + -
475E LYS* 2.9 29.6 + - + +
477E ASP* 1.3 76.2 - - - +
479E VAL* 1.3 65.7 + - - +
481E GLU* 4.4 1.8 - - + -
482E PHE* 3.1 34.2 + + - +
525E MET* 4.5 7.4 - - + -
30F PHE* 3.4 31.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 479 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428E MET* 3.9 11.4 - - + -
454E ILE* 3.5 33.4 - - + +
457E LEU* 3.6 22.9 - - + +
458E LYS* 3.9 20.0 - - + +
461E LEU* 4.1 25.8 - - + -
474E VAL* 5.1 0.4 - - + -
475E LYS 4.6 3.1 - - - +
476E ASP* 3.0 21.5 + - + +
478E TYR* 1.3 75.8 - - - +
480E HIS* 1.3 68.1 + - - +
482E PHE 3.5 0.7 + - - -
483E CYS* 3.3 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 480 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450E VAL* 5.7 0.3 - - - +
454E ILE* 3.2 44.8 - - + +
476E ASP* 3.1 34.6 + - + +
477E ASP* 3.9 9.2 - - - +
478E TYR 3.3 0.2 - - - -
479E VAL* 1.3 77.2 - - + +
481E GLU* 1.3 52.3 + - - +
483E CYS* 2.7 25.6 + - - +
484E ARG* 2.8 18.4 + - - +
28F GLY* 5.8 0.2 - - - -
29F PRO* 3.5 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 481 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477E ASP 3.4 14.4 + - - +
478E TYR* 3.9 5.8 - - + +
480E HIS* 1.3 79.7 - - - +
482E PHE* 1.3 59.3 + - + +
484E ARG* 3.3 21.9 + - - +
485E TYR* 3.1 41.1 + - + -
525E MET* 3.8 16.8 - - + -
29F PRO* 3.1 21.7 - - - +
30F PHE* 3.7 23.4 + - + -
315F TYR* 2.6 42.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 482 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E TYR* 3.8 43.3 + + - -
159E VAL* 3.8 20.4 - - + -
425E LEU* 3.6 29.6 - - + -
428E MET* 3.3 51.6 - - + -
429E LEU* 4.2 9.9 - - + -
432E VAL* 3.9 11.4 - - + -
443E PRO* 4.5 2.1 - - - +
457E LEU* 4.2 7.0 - - + -
478E TYR* 3.1 31.4 + + - +
479E VAL 4.0 2.5 - - - +
480E HIS 3.2 0.2 - - - -
481E GLU* 1.3 77.0 - - + +
483E CYS* 1.3 64.5 + - - +
485E TYR* 3.4 28.3 - + - +
486E GLY 3.9 2.3 + - - -
525E MET* 5.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 483 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443E PRO* 4.3 17.0 - - - -
444E GLY* 3.6 11.3 - - - -
450E VAL* 4.3 11.9 - - + +
453E ASP* 4.2 7.0 - - - -
454E ILE* 3.8 41.3 - - + -
457E LEU* 3.9 15.5 - - - -
479E VAL 3.3 17.7 + - - +
480E HIS 2.7 12.0 + - - +
482E PHE* 1.3 69.6 - - - +
484E ARG* 1.3 66.5 + - - +
485E TYR 3.1 0.2 - - - -
486E GLY 3.1 7.1 + - - -
26F ARG* 3.1 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 484 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450E VAL* 4.8 5.8 - - + +
480E HIS 2.8 11.3 + - - +
481E GLU* 3.3 43.4 + - - +
483E CYS* 1.3 78.5 - - - +
485E TYR* 1.3 63.0 + - - +
22F LYS* 4.0 13.2 + - - +
23F PHE* 3.1 28.6 + - + +
26F ARG* 3.1 53.9 + - + +
27F SER 3.4 24.9 + - - +
28F GLY* 4.0 3.7 - - - -
31F THR* 4.1 13.1 + - - +
35F PHE* 4.0 7.1 - - - -
314F ALA* 3.5 22.0 + - - +
315F TYR* 3.4 23.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 485 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E TYR* 4.2 10.3 - + + -
157E GLY* 3.6 21.5 - - - -
158E LEU* 3.4 27.0 - - + +
159E VAL* 4.3 6.7 - - + -
481E GLU* 3.1 29.3 + - + -
482E PHE* 3.4 42.0 - + - +
484E ARG* 1.3 77.2 - - + +
486E GLY* 1.3 63.9 + - - +
487E ALA 4.1 4.9 - - - +
488E ALA* 3.0 24.1 + - - +
525E MET* 3.0 39.3 - - - +
22F LYS* 3.2 5.7 - - - +
23F PHE* 3.6 13.9 - + - -
315F TYR* 3.0 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 486 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443E PRO 3.8 9.2 - - - -
444E GLY 3.4 25.4 - - - -
445E VAL* 3.9 9.7 - - - +
482E PHE 3.9 1.4 + - - -
483E CYS 3.1 7.1 + - - -
484E ARG 3.1 2.0 + - - -
485E TYR* 1.3 78.7 - - - +
487E ALA* 1.3 69.4 + - - +
488E ALA* 3.0 1.6 + - - -
22F LYS* 3.3 23.0 + - - -
26F ARG* 3.9 0.4 - - - -
----------------------------------------------------------
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