Contacts of the helix formed by residues 40 - 55 (chain B) in PDB entry 3D0O
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 40 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP* 2.8 16.5 + - - +
39B LEU* 1.3 74.8 - - - +
41B THR* 1.3 57.7 + - - +
42B GLU* 3.6 7.4 + - - +
43B LYS* 3.2 37.4 + - + +
44B VAL* 3.1 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP 3.7 13.2 - - - +
39B LEU* 3.0 15.3 + - + +
40B ASP* 1.3 69.8 + - - +
42B GLU* 1.3 68.7 + - - +
44B VAL* 3.6 9.2 - - + +
45B ARG* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASP* 3.2 6.4 + - - +
41B THR* 1.3 85.8 + - - +
43B LYS* 1.3 66.4 + - - +
45B ARG* 2.8 48.5 + - - +
46B GLY* 3.0 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASN* 3.1 28.7 - - + +
15B GLY* 4.6 11.2 - - - -
19B SER* 4.9 4.6 + - - -
38B ASP* 6.4 1.1 - - - -
40B ASP* 3.2 33.0 + - + +
42B GLU* 1.3 77.2 - - - +
44B VAL* 1.3 57.8 + - - +
46B GLY* 3.3 1.8 + - - -
47B ASP* 2.8 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASN* 3.8 14.6 - - - +
36B ILE* 3.9 20.4 - - + +
38B ASP* 3.5 37.2 - - + +
40B ASP 3.1 15.2 + - - +
41B THR* 3.6 10.1 - - - +
42B GLU 3.2 0.2 - - - -
43B LYS* 1.3 76.4 - - - +
45B ARG* 1.3 57.2 + - - +
47B ASP* 3.3 0.7 + - - +
48B VAL* 2.8 38.3 + - + +
66B ALA* 3.5 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR 3.0 17.2 + - - +
42B GLU* 2.8 45.6 + - - +
44B VAL* 1.3 77.7 - - - +
46B GLY* 1.3 63.4 + - - +
48B VAL* 3.5 4.9 + - - +
49B MET* 3.1 51.9 + - + +
66B ALA* 5.3 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU 3.0 13.6 + - - -
43B LYS* 3.7 2.7 - - - -
45B ARG* 1.3 77.3 - - - +
47B ASP* 1.3 64.5 + - - +
49B MET* 3.4 17.0 + - - +
50B ASP* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASN* 2.8 30.8 + - - +
19B SER* 3.5 20.7 + - - -
36B ILE* 5.2 2.2 - - + -
43B LYS* 2.8 42.9 + - - +
44B VAL 3.8 1.8 - - - +
46B GLY* 1.3 70.6 - - - +
48B VAL* 1.3 60.0 + - - +
50B ASP* 3.2 9.5 + - - +
51B LEU* 2.8 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 4.0 18.6 - - + -
44B VAL* 2.8 35.4 + - + +
45B ARG* 3.9 4.9 - - - +
47B ASP* 1.3 72.2 - - - +
49B MET* 1.3 65.2 + - + +
51B LEU* 3.9 0.6 - - - +
52B LYS* 2.9 47.3 + - - +
64B VAL* 3.8 22.2 - - + +
65B LYS* 3.8 11.2 - - - +
66B ALA* 3.8 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ARG* 3.1 52.8 + - + +
46B GLY* 3.8 14.6 - - - +
47B ASP 3.3 0.2 - - - -
48B VAL* 1.3 80.0 - - + +
50B ASP* 1.3 63.0 + - - +
52B LYS* 3.2 10.0 + - + +
53B HIS* 3.1 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLY 3.1 17.6 + - - +
47B ASP* 3.6 12.3 - - - +
49B MET* 1.3 76.0 - - - +
51B LEU* 1.3 64.6 + - + +
53B HIS* 3.3 19.1 + - - +
54B ALA* 3.6 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASN* 5.9 0.4 - - - +
19B SER* 4.8 4.7 - - - +
22B ALA* 3.8 22.2 - - + -
23B PHE* 3.7 46.7 - - + +
26B VAL* 4.1 13.3 - - + +
34B LEU* 5.1 0.7 - - + -
36B ILE* 3.8 20.0 - - + -
47B ASP* 2.8 30.7 + - + +
48B VAL 3.9 2.7 - - - +
50B ASP* 1.3 76.3 - - + +
52B LYS* 1.3 66.6 + - - +
54B ALA* 2.9 22.4 + - - +
55B THR* 3.4 10.9 + - - +
64B VAL* 4.1 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL* 2.9 37.0 + - + +
49B MET* 3.5 12.6 - - + +
51B LEU* 1.3 76.5 - - - +
53B HIS* 1.3 70.7 + - + +
55B THR* 2.7 33.0 + - + +
56B PRO* 3.5 4.2 - - - +
64B VAL* 3.4 34.8 - - + +
65B LYS* 5.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B MET* 3.1 38.2 + - + +
50B ASP* 3.7 13.3 + - - +
51B LEU 3.1 1.2 - - - -
52B LYS* 1.3 87.5 - - + +
54B ALA* 1.3 56.3 + - - +
56B PRO* 3.2 15.5 - - - +
57B TYR* 5.1 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 4.3 18.6 - - + -
26B VAL* 3.7 17.8 - - + +
50B ASP 3.6 7.3 + - - +
51B LEU* 2.9 12.4 + - - +
53B HIS* 1.3 78.1 - - - +
55B THR* 1.3 59.1 + - - +
56B PRO* 3.2 2.0 - - - -
57B TYR* 2.9 30.0 + - - +
58B SER* 3.6 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 4.0 21.1 - - + -
51B LEU 3.4 16.4 - - - +
52B LYS* 2.7 22.9 + - - +
54B ALA* 1.3 76.3 - - - +
56B PRO* 1.4 67.8 - - - +
57B TYR 3.0 0.2 - - - -
58B SER* 3.0 28.0 + - - +
60B THR 5.8 0.2 - - - -
61B THR* 5.6 2.1 - - - -
62B VAL* 3.3 33.1 + - + +
64B VAL* 4.1 7.4 - - + +
----------------------------------------------------------
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