Contacts of the helix formed by residues 45 - 51 (chain B) in PDB entry 3DLX
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 ASP 45 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR* 3.9 6.8 - - - +
44B THR* 1.3 77.3 + - - +
46B PRO* 1.4 63.6 - - - +
47B VAL* 3.0 35.8 + - - +
48B GLU* 3.0 23.4 + - + +
49B ALA 3.0 22.2 + - - -
270B ILE* 4.5 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B THR 3.6 9.6 - - - +
45B ASP* 1.4 86.1 - - - +
47B VAL* 1.3 62.7 + - + +
49B ALA* 3.7 11.4 - - + +
50B VAL* 3.1 15.9 + - - +
72B ASN* 4.1 18.8 - - + +
73B LEU* 4.2 4.0 - - + +
76B ALA* 3.0 25.2 - - + +
270B ILE* 4.3 26.4 - - + -
271B LYS 6.1 0.2 - - - +
272B GLY* 5.9 0.2 - - - -
273B GLU* 5.8 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 3.0 18.1 + - - +
46B PRO* 1.3 78.3 - - + +
48B GLU* 1.3 60.0 + - - +
50B VAL* 3.2 3.1 + - - -
51B LYS* 2.9 31.3 + - + +
76B ALA* 3.9 15.3 - - + +
79B LYS* 4.3 25.1 - - + +
80B THR* 3.8 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR* 3.6 29.5 + - + -
45B ASP* 3.0 26.5 + - + +
47B VAL* 1.3 75.6 - - - +
49B ALA* 1.3 65.7 + - - +
50B VAL 3.4 0.3 + - - -
51B LYS* 3.8 13.5 + - + +
52B ASP* 5.0 1.0 - - - +
268B ARG* 4.9 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR* 3.8 26.4 - - + -
45B ASP 3.0 12.2 + - - +
46B PRO* 3.7 13.0 - - + +
47B VAL 3.3 0.2 - - - -
48B GLU* 1.3 78.3 - - - +
50B VAL* 1.3 58.5 + - - +
73B LEU* 4.2 6.7 - - + -
242B VAL* 3.7 27.6 - - + +
268B ARG* 3.0 29.6 + - - -
269B LEU 6.1 0.2 - - - +
270B ILE* 4.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO 3.1 16.8 - - - +
47B VAL* 3.2 6.7 + - - +
49B ALA* 1.3 81.4 - - - +
51B LYS* 1.3 63.1 + - - +
52B ASP* 3.2 5.8 + - - -
53B ILE* 3.5 24.1 + - + +
73B LEU* 4.1 16.2 - - + +
76B ALA* 3.4 17.7 - - + -
77B LEU* 4.0 18.3 - - + +
80B THR* 4.0 16.6 - - + +
82B VAL* 5.8 0.9 - - - +
207B PHE* 5.8 0.4 - - - -
209B LEU* 3.9 28.5 - - + -
242B VAL* 4.6 5.2 - - + -
268B ARG* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 2.9 21.6 + - + +
48B GLU* 3.8 11.6 + - + +
49B ALA 3.8 1.6 - - - -
50B VAL* 1.3 74.4 - - - +
52B ASP* 1.3 62.0 + - + +
53B ILE 3.5 5.5 + - - +
80B THR* 4.6 11.5 - - - +
----------------------------------------------------------
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