Contacts of the helix formed by residues 39 - 50 (chain B) in PDB entry 4A12
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 SER 39 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B SER* 4.2 0.4 - - - -
38B VAL* 1.3 74.2 - - - +
40B ILE* 1.4 65.5 + - - +
41B GLN* 3.5 18.3 + - - +
42B THR* 2.9 27.4 + - - -
43B ILE* 3.2 10.7 + - - +
20F T 2.8 55.2 + - - -
21F A 4.2 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 3.9 13.9 - - + +
30B HIS* 3.7 36.6 - - + +
33B SER* 3.9 15.0 - - - +
39B SER* 1.4 70.7 - - - +
41B GLN* 1.4 76.7 + - - +
43B ILE* 3.2 5.0 + - - +
44B ARG* 3.0 74.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B SER* 3.5 17.4 - - - +
40B ILE* 1.4 90.2 - - + +
42B THR* 1.4 58.5 + - - +
44B ARG* 3.2 15.3 + - - +
45B LEU* 2.9 31.1 + - + +
20F T 3.7 22.6 - - + +
21F A 3.3 36.8 + - - +
22F G 3.1 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 3.4 35.7 - - - +
38B VAL* 4.3 8.5 - - + -
39B SER* 2.9 11.1 + - - -
41B GLN* 1.4 75.7 - - - +
43B ILE* 1.4 50.5 + - - +
45B LEU* 3.1 11.0 + - + +
46B ASP* 2.8 43.5 + - - +
19F T 3.5 24.5 - - - +
20F T 2.6 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 3.7 28.0 - - + +
29B ASP* 3.7 37.0 - - + +
32B LEU* 3.7 38.4 - - + +
33B SER* 3.6 23.8 - - - +
36B PHE* 4.5 1.6 - - + -
38B VAL* 3.8 15.7 - - + -
39B SER 3.2 8.6 + - - +
40B ILE 3.2 8.8 + - - +
42B THR* 1.4 74.6 - - - +
44B ARG* 1.3 57.5 + - - +
46B ASP* 3.2 6.7 + - - +
47B ARG* 3.0 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 3.4 16.6 + - - +
40B ILE* 3.0 58.7 + - - +
41B GLN* 3.6 13.8 - - - +
43B ILE* 1.3 74.4 - - - +
45B LEU* 1.4 52.4 - - - +
47B ARG* 3.6 16.1 + - - +
48B THR* 2.7 37.6 + - - -
15G G 5.4 1.0 - - - +
16G G 3.5 35.1 + - - -
17G T 3.5 40.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 4.3 9.8 + - - +
41B GLN* 2.9 12.2 + - + +
42B THR* 3.3 13.0 - - + +
44B ARG* 1.4 76.0 - - - +
46B ASP* 1.3 62.8 + - - +
48B THR* 3.4 11.7 + - + +
49B TYR* 3.1 23.7 + - - +
45C LEU* 3.5 32.1 - - + -
19F T 3.8 22.2 - - + -
20F T 3.8 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 2.9 36.8 + - - -
14B ARG* 2.8 45.4 + - + +
17B ILE* 3.3 21.2 - - + +
42B THR* 2.8 28.4 + - - +
43B ILE* 3.2 8.2 + - - +
45B LEU* 1.3 73.0 - - - +
47B ARG* 1.4 58.5 + - - +
49B TYR* 3.3 3.8 + - - +
50B LEU* 3.0 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 5.0 2.4 - - + +
21B ILE* 3.8 22.2 - - + -
29B ASP* 2.8 40.7 + - - -
32B LEU* 5.3 0.2 - - - -
43B ILE* 3.0 18.3 + - + +
44B ARG* 3.9 9.4 + - - +
46B ASP* 1.4 75.0 - - - +
48B THR* 1.4 57.8 + - - +
50B LEU* 3.4 4.3 + - - -
51B ASN* 2.9 8.7 + - - -
52B ILE* 2.8 64.4 + - + +
54B GLU* 3.5 16.1 - - - +
58B ARG* 3.5 23.1 - - - +
16G G 3.4 8.3 - - - -
17G T 2.8 42.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 2.7 23.3 + - - +
45B LEU* 3.5 13.8 - - + +
46B ASP 3.3 0.2 - - - -
47B ARG* 1.4 77.3 + - - +
49B TYR* 1.3 62.0 + - - +
51B ASN* 3.2 13.2 + - - +
52B ILE 5.1 1.1 - - - -
14C ARG* 5.4 8.1 - - - +
49C TYR* 3.5 35.5 - - + -
17G T 5.2 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 5.7 2.9 - - - -
11B ASP* 5.8 2.5 - - - -
14B ARG* 3.4 38.6 - - - +
45B LEU 3.1 16.1 + - - +
46B ASP 3.8 3.6 - - - +
48B THR* 1.3 77.0 - - - +
50B LEU* 1.4 62.4 + - + +
51B ASN* 3.2 13.2 + - - -
48C THR* 3.7 31.4 - - + -
49C TYR* 4.9 11.6 - + - -
51C ASN* 2.8 37.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 3.3 50.5 - - + +
15B GLU* 5.0 1.8 - - - +
17B ILE* 4.2 9.4 - - + -
18B ARG* 4.2 21.7 - - + +
46B ASP 3.0 27.2 + - - +
47B ARG 4.0 0.2 - - - +
49B TYR* 1.4 78.1 - - + +
51B ASN* 1.4 67.3 + - - +
52B ILE* 3.2 32.6 + - + +
----------------------------------------------------------
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