Contacts of the helix formed by residues 38 - 47 (chain A) in PDB entry 3PII
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 CYS 38 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 1.3 71.4 - - - +
39A HIS* 1.3 67.0 + - - +
40A THR* 3.1 17.0 - - - -
41A ASP* 3.0 26.6 + - - +
42A LEU 3.6 2.6 + - - -
61A HIS* 3.3 9.2 - - - -
148A CYS* 3.8 4.0 - - - -
176A PHE* 5.7 4.7 - - + -
323A MET* 3.8 16.0 - - - +
331A ARG* 3.2 30.3 - - - +
340A ZN 2.0 35.9 - - - -
600A BMD 4.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A CYS* 1.3 74.5 - - - +
40A THR* 1.3 62.5 + - - +
42A LEU* 3.1 15.1 + - + +
43A HIS* 3.1 43.7 + + + -
323A MET* 3.7 42.9 + - + +
324A LEU* 5.7 1.8 - - - -
326A GLY* 6.1 0.9 - - - -
342A SO4 4.5 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A CYS* 3.0 4.3 + - - -
39A HIS* 1.3 77.0 - - - +
41A ASP* 1.3 64.8 + - - +
43A HIS* 3.1 14.6 + - - +
44A ALA* 3.1 10.4 + - - +
49A TRP* 3.6 30.5 - - + -
61A HIS* 3.3 27.8 - - + +
87A TRP* 3.9 21.1 - - + -
113A GLY 6.1 0.7 - - - +
114A TYR* 5.0 4.0 - - + -
262A LEU* 4.3 3.3 - - - +
600A BMD 2.7 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY 3.6 6.1 - - - +
37A VAL* 3.3 4.3 - - - -
38A CYS 3.0 29.1 + - - +
40A THR* 1.3 76.8 - - - +
42A LEU* 1.3 55.3 + - - +
44A ALA* 2.8 33.7 + - - +
45A ALA* 3.1 6.4 + - - +
59A PRO* 3.7 8.9 - - + +
60A GLY* 3.1 24.7 + - - -
61A HIS* 3.5 20.5 + - - -
113A GLY 4.7 1.8 - - - +
120A TYR* 3.1 30.0 + - + +
320A PHE* 3.9 10.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A CYS 3.6 1.0 + - - -
39A HIS* 3.1 19.1 + - + +
41A ASP* 1.3 78.7 - - - +
43A HIS* 1.3 83.4 + - + +
45A ALA* 3.0 8.8 + - + +
46A HIS* 2.9 44.2 + - + +
320A PHE* 3.7 49.5 - - + +
323A MET* 4.1 22.0 - - + -
324A LEU* 4.1 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A HIS* 3.1 31.5 + + + -
40A THR 3.1 9.6 + - - +
42A LEU* 1.3 89.9 - - + +
44A ALA* 1.3 57.2 + - - +
46A HIS* 4.5 0.9 - - - -
47A GLY* 3.2 21.3 + - - -
48A ASP* 2.9 37.4 + - - +
49A TRP* 3.4 49.1 + + + +
53A PRO* 5.3 0.5 - - - +
114A TYR* 4.8 6.9 + - - -
262A LEU* 5.1 6.3 + - + -
264A PRO* 6.4 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 4.2 8.0 - - - +
9A PHE* 3.7 18.0 - - - -
40A THR* 3.1 6.6 + - + +
41A ASP* 2.8 16.1 + - - +
43A HIS* 1.3 78.1 - - - +
45A ALA* 1.3 63.6 + - - +
53A PRO* 3.8 8.1 - - + +
57A LEU* 4.0 20.8 - - + +
59A PRO* 5.2 2.2 - - + -
113A GLY 4.4 5.2 - - - +
114A TYR* 3.8 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 4.0 15.8 - - + +
9A PHE* 3.1 19.4 - - - -
10A LYS* 3.2 15.2 + - - +
11A GLU 5.5 1.8 - - - +
13A LEU* 4.1 25.8 - - + -
41A ASP 3.1 6.7 + - - +
42A LEU* 3.0 13.1 + - - +
44A ALA* 1.3 76.7 - - - +
46A HIS* 1.3 65.7 + - + +
47A GLY 3.0 6.6 + - - -
59A PRO* 6.2 0.2 - - + -
320A PHE* 4.7 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.9 6.5 - - - +
10A LYS* 3.7 55.9 + - + +
42A LEU* 2.9 35.3 + - + +
43A HIS* 4.5 1.7 + - - +
45A ALA* 1.3 76.2 - - + +
47A GLY* 1.3 62.0 + - - +
48A ASP* 3.4 29.3 + - - +
324A LEU* 3.5 35.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.3 32.8 - - - -
43A HIS 3.2 11.5 + - - -
44A ALA 4.3 0.4 - - - -
45A ALA 3.0 5.3 + - - -
46A HIS* 1.3 76.9 - - - +
48A ASP* 1.3 57.3 + - - +
49A TRP 3.6 4.9 + - - -
52A LYS* 3.8 26.2 - - - +
53A PRO* 5.0 1.8 - - - -
114A TYR* 6.2 0.2 - - - -
----------------------------------------------------------
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