Contacts of the helix formed by residues 38 - 48 (chain A) in PDB entry 2PWZ
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 VAL 38 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 3.7 27.4 - - + +
14A GLN* 5.0 4.9 - - - +
36A ALA* 3.1 9.5 + - + +
37A PRO* 1.3 78.3 - - - +
39A THR* 1.3 55.1 + - - +
40A PRO 3.5 0.2 - - - -
41A GLY* 2.9 28.2 + - - -
42A VAL* 3.2 20.0 + - + -
216C ALA 3.9 1.6 - - - +
217C LYS* 3.5 46.2 + - + +
220C GLY* 3.9 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 4.2 6.7 - - + -
9A ALA* 3.6 7.8 - - - +
32A LEU* 4.0 22.0 - - + +
33A TYR 4.0 4.7 - - - -
34A ASP* 3.0 30.3 + - + +
36A ALA 2.7 20.9 + - - -
37A PRO 3.2 0.4 - - - -
38A VAL* 1.3 76.2 - - - +
40A PRO* 1.4 66.5 - - - +
41A GLY 3.3 0.7 + - - -
42A VAL* 3.3 18.3 + - + +
43A ALA 3.3 9.0 + - - -
57A GLY* 3.8 4.2 - - - -
58A PHE 3.3 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO 3.3 17.3 - - - +
38A VAL 3.6 0.9 - - - -
39A THR* 1.4 93.9 - - - +
41A GLY* 1.3 54.2 + - - +
43A ALA* 3.5 6.4 - - - +
44A VAL* 3.1 28.9 + - + +
57A GLY* 3.6 26.9 + - - +
58A PHE* 4.3 2.2 - - - +
59A SER* 4.0 16.4 - - - +
216C ALA* 4.1 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL 2.9 10.5 + - - -
40A PRO* 1.3 74.4 - - - +
42A VAL* 1.3 55.7 + - - +
43A ALA 3.2 1.1 - - - -
44A VAL* 3.6 2.4 - - - +
45A ASP* 2.8 32.6 + - - +
213C VAL* 4.1 3.3 - - - +
216C ALA* 3.2 32.5 + - - -
217C LYS* 3.7 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA 4.0 13.2 - - - +
9A ALA* 4.8 2.9 - - - -
14A GLN* 3.9 28.3 - - + +
32A LEU* 3.8 18.6 - - + -
38A VAL* 3.2 32.5 + - + +
39A THR* 3.3 11.9 + - + +
41A GLY* 1.3 73.9 - - - +
43A ALA* 1.3 57.0 + - - +
45A ASP* 3.1 9.0 - - - +
46A LEU* 3.0 29.5 + - + +
217C LYS* 4.1 8.0 - - - +
225C LEU* 3.9 22.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
32A LEU* 4.0 9.8 - - + +
39A THR 3.3 3.2 + - - +
40A PRO 3.5 3.6 - - - +
41A GLY 3.2 0.4 - - - -
42A VAL* 1.3 76.2 - - - +
44A VAL* 1.3 55.6 + - + +
46A LEU* 3.1 3.1 + - - +
47A SER* 2.8 35.3 + - - -
55A ILE* 3.7 15.7 - - + +
56A LYS* 3.4 12.6 - - - +
57A GLY* 3.1 39.5 - - - +
----------------------------------------------------------
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 PRO* 3.1 18.4 + - + +
41A GLY 3.4 4.6 + - - +
43A ALA* 1.3 73.0 - - + +
45A ASP* 1.3 64.3 + - - +
47A SER* 2.5 26.7 + - - +
48A HIS* 3.4 11.6 - - - +
212C GLU* 3.8 43.1 - - + +
213C VAL* 4.2 6.3 - - + -
216C ALA* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLY 2.8 21.4 + - - +
42A VAL* 3.1 9.6 - - - +
44A VAL* 1.3 73.9 - - - +
46A LEU* 1.3 62.9 + - - +
47A SER 3.3 0.2 + - - -
48A HIS* 3.3 7.1 + - - +
213C VAL* 4.0 17.3 - - + +
217C LYS* 3.1 14.1 + - - -
223C ALA* 4.1 5.4 - - - -
224C THR* 3.0 25.7 + - - -
225C LEU* 3.3 15.6 + - - +
226C SER* 2.7 57.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 3.6 37.5 - - + +
18A LEU* 3.7 20.9 - - + -
21A LYS* 3.3 15.4 - - + -
32A LEU* 4.2 3.6 - - + -
42A VAL* 3.0 21.5 + - + +
43A ALA 3.1 3.8 + - - +
45A ASP* 1.3 72.8 - - - +
47A SER* 1.3 57.3 + - - +
48A HIS 3.1 0.4 - - - -
49A ILE* 2.9 53.3 + - + +
55A ILE* 3.7 22.9 - - + -
225C LEU* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 4.2 4.9 + - - +
43A ALA 2.8 16.9 + - - -
44A VAL* 2.5 28.1 + - - +
46A LEU* 1.3 72.4 - - - +
48A HIS* 1.3 66.3 + - - +
49A ILE 3.1 6.3 + - - +
55A ILE* 3.7 23.1 - - - +
156C THR* 3.2 21.8 - - - +
205C ARG* 5.5 1.6 + - - -
212C GLU* 5.0 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 3.4 7.8 + - - +
45A ASP 3.6 8.9 + - - +
46A LEU 3.1 1.2 + - - -
47A SER* 1.3 89.5 - - - +
49A ILE* 1.3 58.8 + - - +
50A PRO* 3.6 1.7 - - - +
149C LEU* 5.0 0.2 - - + -
152C ILE* 3.5 19.9 - - - +
153C ARG* 3.2 36.6 + - + +
156C THR* 2.9 18.0 + - - -
157C PHE* 3.7 17.7 - + - -
205C ARG* 4.8 0.9 - - - -
209C ALA* 3.6 32.1 - - + -
212C GLU* 2.9 26.0 + - - -
213C VAL* 3.7 19.8 - - + +
226C SER* 4.3 9.7 + - - -
----------------------------------------------------------
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