Contacts of the helix formed by residues 38 - 46 (chain C) in PDB entry 3PTZ
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 ASN 38 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ASP* 2.9 18.5 + - - +
37C VAL* 1.3 77.7 - - + +
39C GLU* 1.3 61.5 + - - +
40C SER* 3.0 16.3 + - - -
41C ARG* 3.0 39.5 + - + +
42C ILE* 3.1 22.7 + - - +
500C NAD 4.0 10.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL 3.2 7.5 + - - +
38C ASN* 1.3 70.4 + - - +
40C SER* 1.3 60.5 + - - +
42C ILE* 3.3 0.5 + - - +
43C ASN* 2.8 51.0 + - - +
73C THR* 3.7 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN* 3.0 12.2 + - - -
39C GLU* 1.3 76.6 - - - +
41C ARG* 1.3 57.1 + - - +
43C ASN* 3.4 8.3 + - - +
44C ALA* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA* 3.8 10.3 - - + +
13C GLY* 3.4 11.3 - - - -
14C TYR* 4.3 16.0 - - - -
36C ASP* 4.5 1.3 - - - +
38C ASN* 3.0 29.3 + - + +
40C SER* 1.3 81.3 + - - +
42C ILE* 1.3 64.5 + - + +
44C ALA* 3.2 4.5 + - - +
45C TRP* 3.0 42.9 + - + +
51C PRO* 4.0 19.3 + - + +
52C ILE* 4.6 8.3 - - - +
500C NAD 3.0 66.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA* 4.0 13.9 - - + -
34C VAL 3.8 14.1 - - - +
36C ASP* 3.8 23.6 - - + -
38C ASN 3.1 13.1 + - - +
39C GLU 3.9 4.9 - - - +
41C ARG* 1.3 77.5 - - - +
43C ASN* 1.3 71.3 + - - +
45C TRP* 3.0 16.5 + - - +
46C ASN* 3.1 15.2 + - - +
71C PHE* 3.3 33.0 - - + +
72C SER* 3.2 35.0 - - - +
73C THR* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLU* 2.8 43.9 + - - +
40C SER* 3.6 7.6 - - - +
42C ILE* 1.3 75.8 - - - +
44C ALA* 1.3 62.7 + - - +
46C ASN* 3.0 20.7 + - - +
47C SER* 3.3 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C SER 2.8 21.0 + - - +
41C ARG 3.2 5.6 + - - +
43C ASN* 1.3 71.7 - - - +
45C TRP* 1.3 54.2 + - - +
47C SER* 2.7 39.9 + - - +
49C THR 3.5 20.8 - - - +
50C LEU* 4.0 0.7 - - - -
51C PRO* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA* 3.0 29.8 + - + +
13C GLY 3.8 6.1 - - - -
17C GLY* 3.4 33.2 - - - -
18C PRO* 3.8 10.8 - - + -
41C ARG* 3.0 34.3 + - + +
42C ILE* 3.0 9.2 + - - +
44C ALA* 1.3 75.2 - - - +
46C ASN* 1.3 58.7 + - - +
47C SER 3.3 0.4 - - - -
50C LEU* 3.9 22.7 - - + +
51C PRO* 3.5 24.7 - - + +
52C ILE* 4.3 9.4 - - + -
57C LEU* 4.1 23.8 - - + -
61C VAL* 4.4 10.9 - - + +
65C ARG* 2.9 25.3 + - - -
71C PHE* 3.4 53.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ILE* 3.1 17.1 + - - +
43C ASN* 3.0 15.2 + - - +
45C TRP* 1.3 76.9 - - - +
47C SER* 1.3 57.0 + - - +
65C ARG* 3.6 31.0 + - - +
71C PHE* 2.7 42.1 + - - +
----------------------------------------------------------
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