Contacts of the helix formed by residues 41 - 52 (chain D) in PDB entry 2P82
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 GLU 41 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLN 4.5 2.6 - - - +
36D HIS* 3.6 10.6 + - + -
37D LEU* 2.8 60.7 + - + +
40D THR* 1.3 88.6 - - + +
42D LYS* 1.3 63.9 + - - +
43D SER 3.4 2.5 - - - -
44D LYS* 3.2 31.6 + - + +
45D LEU* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU 3.5 2.0 + - - -
38D LEU* 3.3 22.7 - - + +
39D LYS* 3.4 14.6 + - - +
40D THR 3.6 0.2 - - - -
41D GLU* 1.3 75.8 - - - +
43D SER* 1.3 59.7 + - - +
45D LEU* 3.1 8.9 + - + +
46D LEU* 2.9 60.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLU 3.4 1.0 - - - -
42D LYS* 1.3 81.0 - - - +
44D LYS* 1.3 64.5 + - - +
46D LEU* 3.4 8.0 + - - +
47D SER* 2.9 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D HIS* 3.7 15.5 - - + +
41D GLU* 3.2 35.7 + - + +
43D SER* 1.3 81.8 + - - +
45D LEU* 1.3 59.4 + - - +
47D SER* 3.5 5.9 + - - -
48D ASP* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D VAL* 3.8 24.9 - - + -
31D ILE* 3.8 28.9 - - + -
36D HIS* 3.8 22.8 + - + -
37D LEU 5.1 0.2 - - - +
38D LEU* 4.0 35.9 - - + +
41D GLU 3.0 12.7 + - - +
42D LYS* 3.1 10.3 + - + +
44D LYS* 1.3 77.4 - - - +
46D LEU* 1.3 69.9 + - + +
48D ASP* 3.3 3.8 + - - +
49D ILE* 3.2 34.1 + - + +
276D ILE* 5.6 0.7 - - + -
306D PRO* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D LYS* 2.9 52.6 + - + +
43D SER* 4.0 6.5 - - - +
45D LEU* 1.3 88.3 - - + +
47D SER* 1.3 57.0 + - - +
49D ILE* 3.5 5.3 + - - +
50D SER* 3.0 29.9 + - - -
306D PRO* 3.8 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D SER* 2.9 23.9 + - - -
44D LYS* 3.8 6.7 - - - -
46D LEU* 1.3 74.1 - - - +
48D ASP* 1.3 58.9 + - - +
50D SER* 3.0 8.8 + - - -
51D ALA* 2.8 33.5 + - - +
100D SER* 5.1 9.4 + - - -
101D TRP 5.8 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ILE* 4.0 7.5 - - + +
34D LYS* 4.4 2.2 - - - +
36D HIS* 2.8 31.0 + - + +
44D LYS 3.0 18.3 + - - +
45D LEU 3.3 3.3 + - - +
47D SER* 1.3 77.4 - - - +
49D ILE* 1.3 58.1 + - + +
51D ALA* 3.6 5.1 - - - +
52D ARG* 2.7 39.4 + - - -
97D ARG* 2.7 45.9 + - - -
100D SER* 5.7 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ILE* 4.0 21.1 - - + -
45D LEU* 3.2 35.8 + - + +
46D LEU* 3.9 4.7 - - - +
48D ASP* 1.3 75.5 - - - +
50D SER* 1.3 65.1 + - - +
52D ARG* 3.2 22.0 + - - +
268D ILE* 4.0 20.6 - - + -
276D ILE* 4.3 7.0 - - + -
278D LEU* 4.1 26.3 - - + +
302D CYS* 4.8 5.6 + - + +
304D GLN 5.7 2.7 - - - +
306D PRO* 3.8 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LEU 3.0 19.9 + - - -
47D SER* 3.0 16.1 + - - -
49D ILE* 1.3 77.9 - - - +
51D ALA* 1.3 50.7 + - - +
52D ARG 3.4 2.8 + - - +
101D TRP* 3.9 8.8 - - - -
301D HIS* 2.8 37.9 + - - +
302D CYS 3.3 25.3 + - - +
303D LEU* 4.2 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D SER 2.8 19.3 + - - +
48D ASP* 3.6 2.7 - - - +
49D ILE 3.2 0.2 - - - -
50D SER* 1.3 74.8 + - - +
52D ARG* 1.3 86.2 + - - +
53D LEU 3.6 0.3 + - - -
99D TRP* 3.2 18.3 - - + +
100D SER* 4.5 5.8 - - - +
101D TRP* 3.9 30.1 - - - +
301D HIS* 3.1 17.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ILE* 5.1 4.0 - - - -
32D LEU* 3.5 28.5 - - + -
48D ASP* 2.7 41.1 + - - -
49D ILE* 3.2 15.3 + - - +
50D SER 3.2 4.8 - - - +
51D ALA* 1.3 102.7 - - - +
53D LEU* 1.3 64.3 + - - +
54D TRP* 3.3 5.7 + - - +
88D GLN* 2.6 52.5 + - + +
91D ILE* 4.4 13.9 - - - +
92D CYS* 5.6 0.4 - - - -
97D ARG* 3.6 14.2 + - - +
99D TRP* 3.8 19.2 + - - -
266D TYR* 5.4 3.4 - - + -
268D ILE* 5.5 2.2 - - - -
278D LEU* 4.0 20.8 - - + +
300D PHE 3.6 1.0 - - - +
301D HIS* 3.3 13.4 + - - -
302D CYS 4.7 0.9 + - - -
----------------------------------------------------------
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