Contacts of the helix formed by residues 35 - 46 (chain A) in PDB entry 2D8R
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 ASP 35 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO* 3.0 1.0 - - - +
34A LEU* 1.3 80.1 - - - +
36A PRO* 1.3 66.2 - - - +
37A LYS* 3.4 30.5 - - - +
38A ARG* 4.4 7.0 - - + +
39A ARG* 2.7 41.6 + - - +
80A MET* 4.3 24.5 - - + +
81A ASP* 4.3 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU 3.9 3.3 - - - +
35A ASP* 1.3 98.7 - - - +
37A LYS* 1.3 77.3 + - + +
39A ARG* 4.0 15.0 - - + +
40A LYS* 3.2 50.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP* 3.7 21.5 - - - +
36A PRO* 1.3 93.6 - - + +
38A ARG* 1.3 78.5 + - + +
40A LYS* 4.6 2.7 - - - +
41A GLU* 3.3 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO* 3.1 22.7 - - + -
35A ASP* 3.6 10.2 + - + +
37A LYS* 1.3 97.7 + - + +
39A ARG* 1.3 59.0 + - - +
40A LYS 3.1 2.0 - - - -
41A GLU* 2.6 35.0 + - - +
42A TRP* 2.8 15.5 + - - +
80A MET 3.3 21.1 - - - +
81A ASP* 3.6 29.4 + - - +
82A ALA 3.2 22.2 - - - +
83A VAL* 3.3 25.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 4.4 1.4 - - + -
33A PRO* 3.2 23.6 + - - +
34A LEU 5.0 7.7 + - - -
35A ASP 2.7 27.2 + - - +
36A PRO* 4.0 14.2 - - + +
38A ARG* 1.3 74.2 - - - +
40A LYS* 1.3 78.8 + - - +
42A TRP* 3.5 2.9 + - - +
43A VAL* 3.3 26.1 + - + +
52A VAL* 5.4 10.3 - - - +
53A PRO* 4.1 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 3.2 39.2 + - - +
37A LYS* 4.6 2.7 - - - +
38A ARG 3.1 0.8 - - - -
39A ARG* 1.3 97.5 - - - +
41A GLU* 1.3 51.8 + - - +
43A VAL* 3.3 6.1 + - - +
44A ARG* 2.6 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS 3.3 18.1 + - - +
38A ARG* 2.6 26.4 + - - +
40A LYS* 1.3 71.7 - - + +
42A TRP* 1.3 56.7 + - - +
44A ARG* 2.8 16.6 + - - +
45A LEU* 2.6 62.9 + - - +
83A VAL* 3.3 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A HIS* 3.5 11.4 - - + -
31A ARG 3.1 27.4 - - - -
32A PHE* 3.5 25.1 - + + -
33A PRO* 3.2 28.0 - - + +
38A ARG 2.8 16.6 + - - -
39A ARG 3.8 3.8 - - - +
41A GLU* 1.3 71.4 - - - +
43A VAL* 1.3 57.8 + - - +
45A LEU* 3.8 0.9 - - - +
46A VAL* 2.8 33.2 + - - +
59A LEU* 3.5 24.0 - - + +
64A PHE* 3.0 40.6 - + - -
78A LEU* 3.9 26.2 - - + -
82A ALA 2.9 21.8 + - - -
83A VAL* 3.1 19.8 - - + +
84A PRO* 3.6 11.6 - - + +
87A PHE* 4.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 3.6 19.5 - - + -
39A ARG* 3.3 15.5 + - + +
40A LYS* 3.3 8.9 + - - +
41A GLU 3.1 0.6 - - - -
42A TRP* 1.3 74.8 - - - +
44A ARG* 1.3 62.4 + - - +
46A VAL* 3.0 20.4 - - - +
47A ARG* 3.7 4.9 + - - -
48A ARG 4.2 5.0 + - - -
49A LYS 4.1 11.9 - - - +
50A ASN* 4.7 3.6 - - - +
51A PHE* 3.1 40.2 - - + +
52A VAL* 5.6 0.9 - - + -
53A PRO* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 2.6 24.9 + - + +
41A GLU* 3.5 21.8 - - - +
43A VAL* 1.3 75.2 - - - +
45A LEU* 1.3 62.5 - - + +
47A ARG* 4.2 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU* 2.6 46.8 + - + +
42A TRP 3.8 0.2 - - - +
44A ARG* 1.3 75.6 - - + +
46A VAL* 1.3 55.2 + - - +
47A ARG* 2.7 25.6 + - - +
83A VAL* 4.2 4.9 - - + -
84A PRO* 3.3 46.0 - - + +
85A THR* 5.2 5.4 - - - +
86A ILE 5.2 0.9 - - - +
87A PHE* 3.2 27.0 - - + -
89A PHE* 3.7 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA* 3.5 13.2 - - + +
14A ALA* 3.4 32.8 - - - +
15A ALA* 3.7 12.3 + - - +
32A PHE* 5.0 2.2 - - + -
42A TRP 2.8 26.4 + - - +
43A VAL* 3.0 26.0 - - - +
45A LEU* 1.3 70.5 - - - +
47A ARG* 1.3 69.4 + - - +
48A ARG* 3.8 14.1 - - + +
51A PHE* 3.9 16.2 - - + -
59A LEU* 4.8 4.3 - - + -
87A PHE* 3.1 21.5 - - + -
89A PHE* 5.4 1.3 - - - +
----------------------------------------------------------
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