Contacts of the helix formed by residues 31 - 46 (chain A) in PDB entry 1WDR
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 31 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL 4.9 1.2 + - - -
29A PHE* 3.5 6.7 - - - -
30A GLU* 1.3 85.5 - - + +
32A PRO* 1.3 62.6 - - - +
33A ASP* 3.7 6.1 + - - +
34A GLY* 3.0 31.3 + - - -
35A LEU* 3.1 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.5 45.3 - - + +
30A GLU 3.4 8.1 - - - +
31A ASP* 1.3 90.9 - - - +
33A ASP* 1.4 65.4 + - - +
36A LYS* 2.8 31.1 + - - +
78A LEU* 3.7 7.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 3.3 5.4 + - - +
32A PRO* 1.4 84.1 - - - +
34A GLY* 1.4 63.7 + - - +
36A LYS* 3.3 12.4 + - - +
37A GLU* 3.2 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 3.0 26.6 + - - -
33A ASP* 1.4 79.1 - - - +
35A LEU* 1.3 62.1 + - - +
37A GLU* 3.3 8.3 + - - +
38A GLN* 3.3 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.4 6.7 - - + -
19A PRO* 4.3 14.4 - - + -
22A VAL* 3.5 17.3 - - + -
29A PHE* 3.9 9.0 - - + -
31A ASP* 3.1 17.8 + - - +
32A PRO 3.9 2.9 - - - +
34A GLY* 1.3 73.2 - - - +
36A LYS* 1.4 68.3 + - - +
38A GLN* 3.0 23.2 + - - +
39A LEU* 2.8 43.9 + - + +
75A LEU* 3.5 31.9 - - + -
78A LEU* 4.2 2.0 - - + -
421A LEU* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO 2.8 18.4 + - - +
33A ASP* 3.6 12.1 - - - +
35A LEU* 1.4 76.0 - - - +
37A GLU* 1.3 73.4 + - - +
39A LEU* 3.8 4.2 - - - +
40A LEU* 3.0 45.9 + - + +
78A LEU* 3.9 30.9 - - + +
81A GLU* 5.9 1.2 + - - -
82A CYS* 4.3 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASP 3.2 11.0 + - - +
34A GLY* 3.8 9.4 - - - +
35A LEU 3.2 0.8 - - - -
36A LYS* 1.3 98.1 - - - +
38A GLN* 1.3 63.3 + - + +
40A LEU* 3.4 17.7 + - - +
41A GLN* 3.2 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PRO* 4.5 7.9 - - - +
34A GLY 3.3 12.5 + - - +
35A LEU* 3.0 23.1 + - - +
37A GLU* 1.3 80.5 - - + +
39A LEU* 1.3 62.0 + - - +
41A GLN* 3.2 14.6 + - - +
42A LEU* 3.1 24.8 + - - +
421A LEU* 3.6 34.3 - - + +
422A SER* 4.5 7.5 - - - +
423A ASP* 3.7 20.8 + - - -
426A LEU* 3.7 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.8 27.8 - - + -
35A LEU* 2.8 39.7 + - + +
36A LYS 3.8 3.4 - - - +
38A GLN* 1.3 75.4 - - - +
40A LEU* 1.4 58.3 + - - +
42A LEU* 3.1 12.1 + - + +
43A ARG* 2.9 29.0 + - - +
50A VAL* 4.0 9.0 - - + -
78A LEU* 4.1 24.5 - - + -
79A VAL* 4.2 20.4 - - + -
82A CYS* 3.9 16.2 - - + -
84A LEU* 3.8 22.1 - - + +
421A LEU* 4.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 3.0 47.0 + - + +
37A GLU* 3.8 20.0 - - - +
38A GLN 3.3 0.2 - - - -
39A LEU* 1.4 76.9 - - - +
41A GLN* 1.3 60.7 + - + +
43A ARG* 3.4 8.6 + - + +
44A ALA* 3.0 24.4 + - - +
81A GLU 5.4 1.1 - - - +
82A CYS* 4.0 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLU* 3.2 21.1 + - - +
38A GLN* 3.2 9.7 + - - +
40A LEU* 1.3 76.6 - - - +
42A LEU* 1.3 62.5 + - - +
44A ALA* 3.4 7.0 + - - +
45A ALA* 3.0 23.6 + - - +
426A LEU* 3.4 42.6 - - + +
431A PHE* 3.6 23.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
16A VAL* 3.9 33.0 - - + -
38A GLN 3.1 15.8 + - - +
39A LEU* 3.1 17.5 + - + +
41A GLN* 1.3 76.8 - - - +
43A ARG* 1.3 60.9 + - - +
45A ALA* 3.1 11.1 + - - +
46A GLY 3.2 0.2 + - - -
47A VAL* 3.1 45.3 + - + +
50A VAL* 4.0 19.3 - - + -
84A LEU* 4.7 4.0 - - + -
421A LEU* 4.3 24.9 - - + -
425A LEU* 4.5 4.3 - - + -
426A LEU* 4.4 1.1 - - + -
431A PHE* 3.9 23.8 - - + -
434A PHE* 4.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 2.9 14.1 + - - +
40A LEU* 3.6 13.7 - - + +
42A LEU* 1.3 76.2 - - - +
44A ALA* 1.3 61.9 + - - +
46A GLY* 3.1 9.5 + - - -
47A VAL 2.8 29.3 + - - -
48A ASP 4.1 1.8 + - - -
82A CYS 3.3 27.6 - - - +
83A GLY* 2.9 33.1 + - - -
84A LEU* 3.6 12.7 - - + +
447A TYR* 3.3 50.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
40A LEU 3.0 16.7 + - - +
41A GLN* 3.8 7.2 - - - +
43A ARG* 1.3 77.0 - - - +
45A ALA* 1.3 60.0 + - - +
46A GLY* 3.4 1.0 + - - -
435A LYS* 5.8 0.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
41A GLN 3.0 17.6 + - - +
42A LEU* 3.1 7.3 + - - +
44A ALA* 1.3 76.8 - - - +
46A GLY* 1.3 56.9 + - - +
47A VAL* 3.5 7.2 - - + -
431A PHE* 3.6 23.8 - - + -
434A PHE* 4.8 3.1 - - + -
435A LYS* 3.7 30.9 - - + +
438A VAL* 3.6 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 3.1 20.3 + - - -
44A ALA 3.2 2.0 + - - -
45A ALA* 1.3 79.1 - - - +
47A VAL* 1.3 66.9 + - - +
48A ASP 3.4 0.2 + - - -
438A VAL* 3.8 7.0 - - - -
442A HIS* 3.0 24.2 - - - -
447A TYR* 3.5 20.1 - - - -
----------------------------------------------------------
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