Contacts of the helix formed by residues 42 - 51 (chain C) in PDB entry 3IO6
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 42 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASN* 5.2 8.3 + - - -
40C PRO 3.8 0.8 + - - -
41C ASP* 1.3 79.8 + - + +
43C LEU* 1.3 59.1 + - - +
44C GLU* 3.2 30.2 + - - +
45C GLU* 3.0 30.3 + - + +
46C LYS* 3.1 14.0 + - + +
62C TRP* 5.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TRP* 4.0 19.0 - - + +
11C ILE 3.3 32.1 - - - +
12C ASN* 3.7 12.8 - - - +
40C PRO* 3.4 38.6 - - + +
41C ASP 3.3 2.2 - - - -
42C LYS* 1.3 72.1 - - - +
44C GLU* 1.3 60.6 + - - +
45C GLU 3.0 5.8 - - - -
46C LYS* 3.7 9.0 - - - +
47C PHE* 2.9 33.6 + - - +
60C ILE* 3.7 30.7 - - + -
61C PHE 4.6 0.9 - - - +
62C TRP* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LYS* 3.6 28.7 + - - +
43C LEU* 1.3 89.4 + - - +
45C GLU* 1.3 66.4 + - + +
47C PHE* 5.1 0.2 - - - -
48C PRO* 3.4 6.0 - - - +
60C ILE* 5.4 0.7 - - - -
62C TRP* 3.2 52.2 - - + +
66C ARG* 3.2 35.9 + - - +
70C TYR* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LYS* 3.0 19.9 + - + +
44C GLU* 1.3 94.1 - - + +
46C LYS* 1.3 65.3 + - + +
47C PHE 3.5 0.2 - - - -
48C PRO* 3.5 9.5 - - - +
49C GLN* 3.4 19.9 - - - +
66C ARG* 3.2 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TRP* 4.1 19.3 - - + -
40C PRO* 5.9 2.7 - - + -
41C ASP 4.4 9.9 - - - +
42C LYS* 3.1 16.9 + - + +
43C LEU* 3.4 2.9 + - - +
45C GLU* 1.3 82.4 - - + +
47C PHE* 1.3 64.2 + - - +
49C GLN* 3.0 30.0 + - - +
50C VAL* 3.0 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TRP* 4.0 9.8 - - + -
43C LEU 2.9 18.6 + - - +
46C LYS* 1.3 77.7 - - - +
48C PRO* 1.4 64.6 - - + +
50C VAL* 4.2 2.2 - - - -
51C ALA* 3.0 52.8 + - + +
57C PRO* 4.0 23.6 - - + -
60C ILE* 3.7 32.8 - - + -
70C TYR* 4.0 33.0 - + + +
75C LEU* 3.9 32.3 - - + -
76C LEU* 4.1 18.8 - - + -
267C ASN* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU 3.4 21.3 - - - +
45C GLU* 3.5 14.1 - - - +
47C PHE* 1.4 94.4 - - + +
49C GLN* 1.3 65.7 + - - +
52C ALA* 3.6 19.0 + - - +
66C ARG* 4.3 8.3 - - - +
70C TYR* 3.4 26.2 - - + -
75C LEU* 3.9 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLU 3.4 18.3 - - - +
46C LYS* 3.0 26.7 + - - +
47C PHE 3.0 0.8 - - - -
48C PRO* 1.3 85.2 - - - +
50C VAL* 1.3 68.8 + - + +
52C ALA* 3.7 14.8 + - - +
53C THR* 3.8 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TRP* 4.2 14.4 - - + -
46C LYS* 3.0 28.5 + - + +
47C PHE* 4.0 4.7 - - - +
49C GLN* 1.3 77.2 - - + +
51C ALA* 1.3 66.5 + - - +
52C ALA 3.2 0.4 - - - -
53C THR* 2.7 23.2 + - - +
55C ASP* 2.9 33.2 + - + +
56C GLY* 3.7 21.5 - - - +
57C PRO* 4.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A THR* 4.3 5.0 + - - -
47C PHE* 3.0 49.8 + - + +
50C VAL* 1.3 79.0 - - + +
52C ALA* 1.3 60.2 + - - +
54C GLY* 3.1 12.8 + - - -
55C ASP 3.5 11.4 - - - -
75C LEU* 3.6 19.4 - - + +
267C ASN* 3.9 15.4 - - - +
269C ALA* 4.8 1.9 - - - +
----------------------------------------------------------
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