Contacts of the helix formed by residues 32 - 47 (chain A) in PDB entry 4WNF
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 32 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 2.9 29.7 + - + +
30A SER* 3.3 5.8 + - - +
31A GLY* 1.3 71.4 - - - +
33A CYS* 1.3 61.1 + - - +
34A ARG* 4.5 10.1 - - - +
35A ALA* 3.2 31.1 + - + +
36A GLY 3.3 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A CYS* 2.1 56.2 - - - -
31A GLY 3.2 8.1 + - - +
32A ASP* 1.3 71.9 - - - +
34A ARG* 1.3 57.2 + - - +
35A ALA 3.2 0.4 - - - -
36A GLY* 3.4 0.4 - - - +
37A VAL* 2.8 38.7 + - - +
64A ALA* 4.6 17.7 - - + +
67A TYR* 5.8 8.3 - - + -
68A LEU* 4.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP* 3.4 11.6 - - - +
33A CYS* 1.3 79.2 - - - +
35A ALA* 1.3 58.6 + - - +
37A VAL* 3.6 14.8 - - - +
38A SER* 3.6 13.7 + - - -
68A LEU* 4.2 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.1 10.8 - - + -
32A ASP* 3.2 24.2 + - + +
33A CYS 3.2 0.4 - - - -
34A ARG* 1.3 76.9 - - - +
36A GLY* 1.3 66.5 + - - +
37A VAL 3.2 0.4 - - - -
38A SER* 3.0 17.5 + - - -
39A PHE* 3.0 26.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLY* 4.0 9.6 - - - -
27A LEU* 3.8 24.6 - - - +
28A CYS* 4.6 1.6 - - - -
32A ASP 3.3 7.5 + - - -
33A CYS* 3.1 8.2 + - - -
35A ALA* 1.3 76.1 - - - +
37A VAL* 1.3 64.6 + - - +
39A PHE* 3.1 4.2 + - - +
40A PHE* 2.9 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A CYS* 5.1 0.4 - - - -
33A CYS 2.8 22.3 + - - +
34A ARG 3.6 9.2 - - - +
36A GLY* 1.3 70.8 - - - +
38A SER* 1.3 57.4 + - - +
40A PHE* 2.9 10.9 + - - +
41A GLU* 2.8 48.5 + - + +
61A LEU* 4.0 3.6 - - + -
64A ALA* 3.7 24.2 - - + -
65A TYR* 3.4 39.9 - - + +
68A LEU* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG 3.6 9.5 + - - -
35A ALA* 3.0 14.2 + - - -
37A VAL* 1.3 82.1 - - - +
39A PHE* 1.3 63.4 + - - +
41A GLU* 3.5 8.8 + - - +
42A ALA* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.5 46.3 - - + +
23A GLU* 3.8 25.6 - - + -
24A GLY* 4.0 8.7 - - - -
27A LEU* 3.4 18.4 - - + -
35A ALA* 3.0 33.7 + - + +
36A GLY 3.1 5.1 + - - +
38A SER* 1.3 81.4 - - - +
40A PHE* 1.3 57.7 + - - +
42A ALA* 3.4 6.0 - - + +
43A ALA* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 3.4 32.3 - - + -
24A GLY* 3.5 26.5 - - - -
25A GLU* 3.6 5.4 - - + -
28A CYS* 4.4 12.8 - - + -
36A GLY 2.9 27.3 + - - -
37A VAL* 3.4 8.5 - - - +
39A PHE* 1.3 73.9 - - - +
41A GLU* 1.3 67.5 + - - +
43A ALA* 2.9 7.2 + - - +
44A VAL* 2.9 22.9 + - - +
57A ILE* 3.9 17.1 - - + +
60A GLN* 3.5 48.7 - - + -
61A LEU* 3.5 28.0 - - + -
64A ALA* 5.3 0.9 - - + -
1007B VAL* 5.8 0.7 - - + -
----------------------------------------------------------
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 VAL* 2.8 30.8 + - + +
38A SER* 3.7 8.0 + - - +
40A PHE* 1.3 71.1 - - - +
42A ALA* 1.3 57.9 + - - +
44A VAL* 3.0 14.5 + - - +
45A GLN* 2.8 28.9 + - - +
61A LEU* 3.8 13.4 - - + +
65A TYR* 3.0 23.8 + - - -
73A LYS* 6.0 0.3 + - - -
77A TYR* 3.7 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.5 15.3 - - + -
38A SER 2.9 20.3 + - - +
39A PHE* 3.4 9.6 - - + +
41A GLU* 1.3 76.0 - - - +
43A ALA* 1.3 58.2 + - - +
45A GLN* 2.9 26.2 + - - +
46A VAL* 2.9 17.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A CYS* 3.6 33.9 - - - +
20A LEU* 3.7 17.4 - - + +
21A ALA* 4.0 10.5 - - + +
39A PHE 2.9 14.8 + - - +
40A PHE* 2.9 11.2 + - - +
42A ALA* 1.3 75.3 - - - +
44A VAL* 1.3 52.5 + - - +
46A VAL* 3.6 3.1 - - - +
47A GLY* 2.7 32.4 + - - -
54A LEU* 5.3 0.5 - - - +
57A ILE* 4.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE 2.9 15.5 + - - +
41A GLU* 3.1 13.9 - - - +
43A ALA* 1.3 76.3 - - - +
45A GLN* 1.3 62.1 + - - +
46A VAL 3.6 0.2 - - - -
47A GLY* 3.1 15.8 + - - -
54A LEU* 4.6 12.0 - - + +
57A ILE* 4.0 18.2 - - + -
58A TYR* 4.2 24.2 - - + +
61A LEU* 4.2 12.1 - - + -
77A TYR* 5.4 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU 2.8 15.2 + - - +
42A ALA* 2.9 15.7 + - - +
44A VAL* 1.3 75.3 - - - +
46A VAL* 1.3 60.8 + - + +
----------------------------------------------------------
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 MET* 3.4 46.6 - - + +
16A SER* 4.3 8.3 - - - -
17A CYS* 3.9 11.2 - - + +
20A LEU* 3.6 24.5 - - + -
42A ALA* 2.9 13.8 + - + +
43A ALA 3.6 4.9 - - - +
44A VAL 3.6 0.2 - - - -
45A GLN* 1.3 81.5 - - + +
47A GLY* 1.3 61.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
13A MET* 3.3 28.1 - - - +
17A CYS* 3.5 2.7 - - - +
43A ALA 2.7 19.6 + - - -
44A VAL* 3.1 13.0 + - - -
46A VAL* 1.3 77.6 - - - +
48A THR* 1.3 67.7 + - - -
54A LEU* 5.1 4.9 - - - -
----------------------------------------------------------
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