Contacts of the helix formed by residues 25 - 38 (chain D) in PDB entry 4PAR
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 TYR 25 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C THR* 3.8 31.7 - - + +
11C ASP* 5.7 0.7 + - - -
14C ILE* 4.5 20.9 - - + -
24D ARG* 1.3 110.4 + - + +
26D GLU* 1.3 64.6 + - - +
27D ALA 3.4 2.2 - - - -
28D TYR* 3.4 7.5 + + + +
29D VAL* 3.0 36.1 + - + +
73D VAL* 4.7 7.0 - - + -
75D GLU* 2.9 25.6 + - + +
79D PHE* 4.7 13.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LYS* 3.6 21.9 + - + +
22D ASN* 2.8 31.7 + - - +
23D LYS* 3.1 28.2 + - + +
24D ARG 3.4 2.0 - - - -
25D TYR* 1.3 74.6 - - - +
27D ALA* 1.3 66.2 + - - +
30D VAL* 2.9 42.3 + - + +
46D THR* 5.3 1.0 - - - -
47D GLN* 3.4 28.5 + - - +
61D ASP* 4.1 24.9 - - - +
73D VAL* 4.3 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 5.5 7.6 - - + +
18C GLY* 6.4 1.6 - - - -
21D LYS* 4.1 34.7 - - + +
23D LYS 4.6 1.0 + - - -
24D ARG 4.9 4.2 + - - +
25D TYR 3.4 0.2 - - - -
26D GLU* 1.3 78.8 - - - +
28D TYR* 1.3 52.0 + - - +
30D VAL* 4.1 0.8 - - - +
31D SER* 2.7 42.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C VAL* 3.6 25.6 - - + -
14C ILE* 3.5 28.5 - - + +
17C LEU* 3.8 20.0 - - + -
34C ILE* 5.5 0.4 - - + -
35C HIS* 3.3 25.0 + + - -
40C PHE* 3.5 26.2 - + - -
24D ARG 5.5 0.2 + - - -
25D TYR* 3.4 8.8 + + + +
26D GLU 3.3 0.4 - - - -
27D ALA* 1.3 79.0 - - - +
29D VAL* 1.3 67.9 + - + +
31D SER* 2.9 5.4 + - - -
32D ARG* 2.9 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D TYR* 3.0 29.3 + - + +
28D TYR* 1.3 86.8 - - + +
30D VAL* 1.3 64.9 + - + +
32D ARG* 3.3 3.4 + - - +
33D ILE* 3.0 45.8 + - + +
71D ILE* 5.3 2.5 - - + -
73D VAL* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 3.8 24.5 - - + -
21D LYS* 5.5 4.0 - - - +
26D GLU* 2.9 33.8 + - + +
27D ALA* 4.1 2.5 - - - +
29D VAL* 1.3 77.6 - - + +
31D SER* 1.3 64.8 + - - +
33D ILE* 3.2 11.1 + - + +
34D ILE* 2.9 23.4 + - + +
46D THR* 4.1 8.1 - - + -
61D ASP* 4.1 25.4 - - + +
62D LEU* 4.0 28.5 - - + -
71D ILE* 6.3 1.1 - - + -
73D VAL* 5.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C SER* 4.2 17.6 - - - -
35C HIS* 2.9 29.4 + - - -
17D LEU* 5.0 10.5 - - - -
27D ALA 2.7 24.0 + - - -
28D TYR* 2.9 5.7 + - - -
30D VAL* 1.3 77.8 - - - +
32D ARG* 1.3 56.5 + - - +
34D ILE* 3.4 4.7 + - - +
35D HIS* 2.9 43.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C HIS* 3.5 45.2 + - + +
38C ASN* 2.6 33.3 + - - +
40C PHE* 4.8 6.5 - - - -
28D TYR* 2.9 45.6 + - - +
29D VAL* 3.7 4.3 - - - +
31D SER* 1.3 78.9 + - - +
33D ILE* 1.3 62.8 + - + +
36D LEU* 2.9 59.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D VAL* 3.0 35.2 + - + +
30D VAL* 3.5 7.6 - - + +
32D ARG* 1.3 77.1 - - + +
34D ILE* 1.3 62.2 + - + +
36D LEU* 4.2 1.7 - - - +
37D LEU* 2.9 40.0 + - + +
62D LEU* 3.8 21.3 - - + -
64D PHE* 4.6 5.2 - - + -
71D ILE* 3.8 42.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 4.3 20.2 - - + -
30D VAL* 2.9 24.6 + - + +
31D SER* 3.9 4.7 - - - +
33D ILE* 1.3 77.0 - - - +
35D HIS* 1.3 63.7 + - + +
37D LEU* 4.0 5.1 - - + +
38D ASN* 3.0 24.4 + - - -
39D ASP 4.7 0.9 + - - -
40D PHE* 4.0 19.4 - - + -
44D PHE* 3.9 51.1 - - + -
62D LEU* 3.9 20.2 - - + -
64D PHE* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 3.2 39.2 - + - -
31C SER* 3.2 26.9 + - - -
32C ARG* 3.2 56.5 + - + +
35C HIS* 4.0 8.4 - - + -
36C LEU* 3.7 15.0 - - + +
17D LEU* 4.4 5.8 - - + +
31D SER* 2.9 28.8 + - - +
32D ARG 4.3 1.3 - - - +
34D ILE* 1.3 81.5 - - + +
36D LEU* 1.3 72.4 + - + +
38D ASN* 3.5 15.9 - - - +
40D PHE* 5.0 0.4 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
35C HIS* 3.7 39.9 - - + +
36C LEU* 4.4 9.4 - - + -
38C ASN* 6.1 0.2 - - - -
32D ARG* 2.9 59.0 + - + +
33D ILE* 4.2 2.2 - - - +
35D HIS* 1.3 75.9 - - - +
37D LEU* 1.3 66.0 + - - +
38D ASN* 4.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ILE* 2.9 26.2 + - + +
34D ILE* 4.0 5.2 - - + +
36D LEU* 1.3 79.1 - - - +
38D ASN* 1.3 68.3 + - - +
39D ASP* 3.1 23.2 + - + +
42D LEU* 4.2 16.8 - - + -
64D PHE* 4.2 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ARG* 3.0 36.4 + - - +
36C LEU* 6.0 0.9 - - - +
140C HIS* 3.8 13.8 + - - -
34D ILE 3.0 16.5 + - - -
35D HIS 3.5 9.0 - - - +
36D LEU 3.3 4.0 - - - +
37D LEU* 1.3 77.7 - - - +
39D ASP* 1.3 58.5 + - - +
40D PHE* 3.9 11.9 + - - -
----------------------------------------------------------
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