Contacts of the helix formed by residues 28 - 40 (chain D) in PDB entry 4PCW
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 SER 28 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ASP* 3.3 23.6 + - - -
26D THR 4.0 0.2 + - - -
27D LEU* 1.3 76.0 - - - +
29D LYS* 1.3 59.8 + - - +
30D LYS* 3.4 9.2 + - - +
31D GLU* 2.8 36.2 + - - +
32D LEU* 2.9 26.7 + - - +
57D MET* 3.9 3.1 - - - -
66D LYS 4.8 4.7 - - - -
67D LYS* 4.9 9.4 - - - +
101D CA 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D SER* 1.3 74.7 - - - +
30D LYS* 1.3 57.7 + - - +
32D LEU* 3.9 0.8 - - - +
33D LYS* 3.0 28.4 + - - +
51D ASP* 4.0 3.0 + - - -
53D VAL* 3.6 24.7 - - + +
54D ASP* 3.3 46.5 + - - +
57D MET* 3.6 30.1 - - + +
66D LYS* 4.6 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ASP* 5.6 4.5 - - - +
28D SER* 3.2 8.4 + - - +
29D LYS* 1.3 78.4 - - - +
31D GLU* 1.3 66.1 + - + +
33D LYS* 3.3 16.5 + - - +
34D GLU* 3.1 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D TYR* 3.0 35.0 - - - +
18D SER 3.1 0.5 - - - +
20D LYS* 3.3 9.8 - - + +
21D ASP* 2.6 45.3 + - - +
26D THR 3.1 4.3 - - - +
27D LEU* 3.3 9.8 - - + -
28D SER* 2.8 34.8 + - - +
30D LYS* 1.3 75.9 - - + +
32D LEU* 1.3 65.6 + - - +
34D GLU* 3.3 10.9 + - - +
35D LEU* 3.1 21.9 + - - +
101D CA 2.4 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 4.3 24.5 - - + +
28D SER 2.9 18.1 + - - +
29D LYS 3.9 3.1 - - - +
31D GLU* 1.3 75.7 - - - +
33D LYS* 1.3 63.0 + - - +
35D LEU* 3.1 10.0 + - + +
36D LEU* 3.0 43.3 + - + +
53D VAL* 4.5 6.5 - - + +
56D PHE* 4.1 20.0 - - + -
57D MET* 3.9 33.7 - - + +
60D LEU* 5.6 1.8 - - + -
68D ILE* 4.1 13.7 - - + -
76D MET* 4.4 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LYS 3.0 19.1 + - - +
30D LYS* 3.4 17.5 - - - +
31D GLU 3.2 0.4 - - - -
32D LEU* 1.3 76.7 - - - +
34D GLU* 1.3 69.7 + - + +
36D LEU* 3.6 5.0 + - - +
37D GLU* 3.2 57.9 + - + +
53D VAL* 3.4 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D TYR* 3.8 9.4 - - + -
20D LYS* 3.1 34.4 + - - -
30D LYS* 3.1 39.0 + - + +
31D GLU* 3.8 8.3 - - - +
32D LEU 3.3 0.2 - - - -
33D LYS* 1.3 86.4 + - + +
35D LEU* 1.3 64.9 + - - +
37D GLU* 3.8 9.3 - - - +
38D LYS* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 4.9 2.0 - - + -
13D LEU* 4.8 7.0 - - + -
14D PHE* 5.1 3.4 - - - -
17D TYR* 3.5 39.6 - - + -
27D LEU* 3.9 26.5 - - + -
31D GLU 3.1 13.2 + - - +
32D LEU* 3.1 12.3 + - + +
34D GLU* 1.3 73.6 - - - +
36D LEU* 1.3 67.7 + - + +
38D LYS* 3.3 1.2 + - - +
39D GLU* 2.8 54.1 + - + +
40D PHE* 4.6 8.3 - - + -
73D PHE* 3.9 25.8 - - + -
76D MET* 5.2 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 3.0 42.2 + - + +
33D LYS* 4.1 7.2 - - - +
35D LEU* 1.3 77.3 - - + +
37D GLU* 1.3 58.4 + - + +
40D PHE* 2.8 60.8 + - + +
52D MET* 4.4 22.2 - - + +
53D VAL* 4.8 6.3 - - + -
56D PHE* 3.4 55.2 - - + -
76D MET* 4.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LYS* 3.2 51.0 + - + +
34D GLU* 3.8 9.5 - - - +
36D LEU* 1.3 80.2 - - + +
38D LYS* 1.3 62.0 + - - +
40D PHE 3.5 11.1 - - - +
41D ARG* 3.4 25.6 + - - +
42D GLN* 6.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C THR* 5.5 7.2 - - - +
13D LEU* 5.8 0.6 - - - +
16D GLN* 4.4 15.9 + - - +
17D TYR* 3.3 28.2 + - + +
34D GLU 3.1 12.6 + - - +
37D GLU* 1.3 78.0 - - - +
39D GLU* 1.3 73.2 + - + +
41D ARG* 3.5 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C SER 5.0 1.2 - - - +
2C THR* 3.3 19.4 - - - +
3C LEU* 2.7 37.0 + - + +
4C LEU* 3.5 24.4 - - - +
13D LEU* 3.1 31.7 - - + +
17D TYR* 4.2 7.8 + - - +
35D LEU* 2.8 36.4 + - + +
38D LYS* 1.3 88.4 + - - +
40D PHE* 1.3 75.4 + - + +
41D ARG* 3.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 4.1 13.5 - - + -
4C LEU* 4.2 23.8 - - + -
35D LEU* 4.6 2.7 - - + -
36D LEU* 2.8 55.9 + - + +
37D GLU* 3.5 5.2 - - - +
39D GLU* 1.3 92.7 - - + +
41D ARG* 1.3 66.0 + - - +
42D GLN* 3.2 23.0 + - - +
52D MET* 4.8 10.7 - - + +
56D PHE* 5.5 2.7 - + - -
76D MET* 4.3 9.9 - - - -
80D LEU* 3.6 41.3 - - + -
----------------------------------------------------------
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