Contacts of the helix formed by residues 25 - 55 (chain J) in PDB entry 2DYS
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 GLY 25 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J LEU* 5.8 1.1 - - - +
22J LEU 3.2 7.0 + - - +
23J LYS 3.3 2.4 + - - -
24J GLY* 1.3 82.0 - - - +
26J ALA* 1.3 55.3 + - - -
27J THR* 3.2 3.6 - - - -
28J ASP* 3.0 17.3 + - - +
29J ASN* 2.7 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J GLY* 1.3 67.8 - - - -
27J THR* 1.3 64.4 + - - +
28J ASP 3.3 0.2 - - - -
29J ASN* 3.3 14.7 + - - +
30J ILE* 3.1 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 27 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C CDL 3.7 30.0 + - + +
24J GLY 5.9 1.3 - - - -
25J GLY* 3.1 1.7 + - - -
26J ALA* 1.3 73.6 - - - +
28J ASP* 1.3 72.0 + - - +
30J ILE* 3.0 15.5 + - + +
31J LEU* 2.9 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 28 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLN* 4.6 1.7 - - - +
59C ARG* 3.7 13.4 + - - +
63C ARG* 2.7 43.4 + - - -
309C CDL 3.9 8.3 + - - -
21J HIS 3.3 17.5 - - - +
22J LEU* 3.3 12.4 - - - +
24J GLY* 2.8 21.5 + - - -
25J GLY 3.0 14.0 + - - +
27J THR* 1.3 78.3 - - - +
29J ASN* 1.3 63.3 + - - +
31J LEU* 3.5 3.8 + - - +
32J TYR* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 29 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J LEU* 6.1 0.3 - - - +
22J LEU* 3.8 35.1 + - - +
25J GLY 2.7 36.4 + - - -
26J ALA* 3.5 11.2 - - - +
27J THR 3.1 0.2 - - - -
28J ASP* 1.3 80.6 - - - +
30J ILE* 1.3 62.2 + - + +
32J TYR* 3.4 3.6 - - - +
33J ARG* 3.0 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J ALA* 3.1 19.5 + - + +
27J THR* 3.0 17.2 + - + +
29J ASN* 1.3 76.2 - - + +
31J LEU* 1.3 64.9 + - + +
33J ARG* 2.9 22.3 + - - +
34J VAL* 2.9 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 4.0 22.7 - - + -
55C TYR* 4.0 26.9 - - + -
56C GLN* 3.6 23.8 - - + +
59C ARG* 4.4 7.4 - - - +
309C CDL 4.0 31.0 - - + -
27J THR* 2.9 24.9 + - + +
28J ASP* 3.7 4.7 - - - +
30J ILE* 1.3 72.8 - - - +
32J TYR* 1.3 58.0 + - - +
34J VAL* 3.3 11.8 + - + +
35J THR* 2.8 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 32 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 3.7 20.9 - + - -
15C PRO* 3.7 16.6 - - + -
16C TRP* 3.7 26.7 - + + -
56C GLN* 3.8 7.4 + - - -
21J HIS* 4.5 7.4 - + - +
22J LEU* 4.5 13.5 - - + -
28J ASP 3.0 19.8 + - - +
29J ASN* 3.4 5.8 - - - +
31J LEU* 1.3 78.2 - - - +
33J ARG* 1.3 67.5 + - + +
35J THR* 3.3 2.1 + - - -
36J MET* 2.8 58.5 + - + +
101J CHD 3.5 43.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J ASN* 3.0 21.4 + - - +
30J ILE* 2.9 24.5 + - - +
32J TYR* 1.3 84.3 - - + +
34J VAL* 1.3 58.9 + - + +
36J MET* 4.2 0.8 - - - +
37J THR* 2.5 38.7 + - - -
101J CHD 3.2 62.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 4.2 15.9 - - + -
309C CDL 5.3 9.6 - - + -
30J ILE* 2.9 30.6 + - + +
31J LEU* 3.4 16.8 - - + +
33J ARG* 1.3 77.2 - - + +
35J THR* 1.3 64.2 + - - +
37J THR* 3.2 5.0 + - - -
38J LEU* 3.0 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 35 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 4.2 6.1 - - + -
19C THR* 4.0 27.6 - - + -
49C THR* 4.3 2.2 - - - +
52C LEU* 3.4 31.2 - - + +
53C THR* 4.2 6.5 - - - +
56C GLN* 2.9 27.0 + - - +
31J LEU 2.8 22.2 + - - -
32J TYR 3.6 4.9 - - - -
34J VAL* 1.3 77.3 - - - +
36J MET* 1.3 57.4 + - - +
38J LEU* 3.2 3.3 + - - +
39J CYS* 2.9 35.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 36 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 4.2 10.1 - - + -
15C PRO* 3.8 13.0 - - + +
18C LEU* 4.7 8.3 - - + -
19C THR* 3.5 27.8 - - + -
22C LEU* 5.5 0.4 - - - -
32J TYR* 2.8 50.2 + - + +
33J ARG* 4.2 1.8 - - - +
35J THR* 1.3 75.0 - - - +
37J THR* 1.3 57.1 + - - +
39J CYS* 3.7 4.4 - - - +
40J LEU* 2.9 48.2 + - + +
101J CHD 3.6 49.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 37 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ARG 2.5 24.7 + - - -
34J VAL* 3.6 4.9 - - - -
36J MET* 1.3 73.3 - - - +
38J LEU* 1.3 62.8 + - + +
40J LEU* 4.3 1.3 - - - +
41J GLY* 2.7 34.3 + - - -
101J CHD 3.8 48.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 3.9 19.2 - - + +
48C THR* 4.1 19.5 - - + -
49C THR* 3.4 18.2 - - + -
52C LEU* 4.0 23.3 - - + -
309C CDL 6.1 1.1 - - + -
34J VAL* 3.0 27.3 + - + +
35J THR 3.6 3.8 - - - +
37J THR* 1.3 78.6 - - + +
39J CYS* 1.3 55.2 + - - +
42J GLY* 2.7 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 39 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C THR* 3.6 39.9 - - + -
22C LEU* 4.0 18.6 - - + -
23C SER 4.7 0.9 - - - -
26C LEU* 4.2 6.8 - - - +
49C THR* 3.6 27.1 - - - -
35J THR* 2.9 21.0 + - - +
36J MET* 3.7 8.7 - - - +
38J LEU* 1.3 76.5 - - - +
40J LEU* 1.3 54.5 - - - +
42J GLY 3.9 0.2 - - - -
43J THR* 2.7 38.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LEU* 5.5 2.9 - - + -
22C LEU* 3.9 22.2 - - + -
36J MET* 2.9 26.6 + - + +
37J THR* 4.3 2.2 - - - +
39J CYS* 1.3 74.9 - - - +
41J GLY* 1.3 65.8 + - - +
43J THR* 3.5 6.3 + - + +
44J LEU* 3.1 31.8 + - + +
101J CHD 3.6 61.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 41 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J THR* 2.7 24.0 + - - -
38J LEU* 5.1 0.2 - - - -
40J LEU* 1.3 70.3 - - - +
42J GLY* 1.3 58.5 + - - +
44J LEU* 3.0 13.7 + - - +
45J TYR* 2.8 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 3.2 25.7 - - - +
42C LEU* 3.7 2.8 - - - +
45C ILE* 4.4 16.1 - - - +
38J LEU* 2.7 23.3 + - - +
41J GLY* 1.3 71.1 - - - +
43J THR* 1.3 55.6 + - - +
45J TYR* 3.3 9.2 + - - +
46J SER* 2.8 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 5.9 1.1 - - + -
22C LEU* 3.7 27.8 - - + +
25C LEU* 4.4 16.2 - - + +
26C LEU* 3.7 8.0 - - - +
39J CYS 2.7 24.9 + - - -
40J LEU* 3.6 9.4 - - + -
42J GLY* 1.3 73.5 - - - +
44J LEU* 1.3 68.0 + - + +
46J SER* 2.6 24.5 + - - +
47J LEU* 3.0 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J LEU* 3.1 20.2 + - + +
41J GLY* 3.0 11.1 + - - +
43J THR* 1.3 80.6 - - + +
45J TYR* 1.3 63.7 + - - +
47J LEU* 3.2 22.2 + - + +
48J TYR* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 45 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C MET* 5.9 1.5 - - + +
39C SER* 4.4 6.2 + - - -
41C THR* 3.3 41.4 + - + +
42C LEU* 3.9 29.8 - - + -
45C ILE* 4.5 8.3 - - + -
41J GLY 2.8 12.8 + - - +
42J GLY* 3.5 8.7 - - - +
43J THR 3.2 0.2 - - - -
44J LEU* 1.3 76.7 - - - +
46J SER* 1.3 56.4 + - - +
48J TYR* 3.1 23.6 + + + +
49J CYS* 3.0 43.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 46 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 4.9 2.1 - - - +
25C LEU* 4.1 13.7 - - - +
26C LEU* 4.3 4.3 - - - -
29C SER* 4.2 13.0 - - - -
42C LEU* 4.0 27.4 - - - -
42J GLY 2.8 15.4 + - - -
43J THR* 2.6 22.3 + - - -
45J TYR* 1.3 77.0 - - - +
47J LEU* 1.3 63.9 + - - +
49J CYS* 3.2 3.8 + - - +
50J LEU* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 3.8 37.7 - - + -
43J THR* 3.0 23.8 + - + +
44J LEU* 3.2 26.0 + - + +
46J SER* 1.3 80.8 + - - +
48J TYR* 1.3 62.9 + - - +
50J LEU* 3.3 14.4 + - + +
51J GLY* 3.0 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 48 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J LEU 3.1 11.9 + - - +
45J TYR* 3.1 32.5 + + - +
47J LEU* 1.3 77.6 - - - +
49J CYS* 1.3 65.1 + - - +
51J GLY* 3.1 3.6 + - - +
52J TRP* 2.9 49.8 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C MET* 3.7 37.0 - - + +
42C LEU* 4.4 10.1 - - + -
45J TYR* 3.0 50.2 + - - -
46J SER* 3.5 10.8 - - - +
48J TYR* 1.3 82.8 - - - +
50J LEU* 1.3 56.9 + - - +
52J TRP* 3.4 8.1 + - - +
53J ALA* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 5.2 15.0 - - + -
114A ALA* 3.6 39.9 - - + -
117A MET* 4.2 14.8 - - + -
118A VAL* 4.1 11.9 - - + -
145A LEU* 5.6 0.2 - - + -
46J SER 3.0 12.6 + - - +
47J LEU* 3.5 16.8 - - + +
49J CYS* 1.3 75.3 - - - +
51J GLY* 1.3 68.7 + - - +
53J ALA* 3.3 3.7 + - - +
54J SER* 2.7 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A MET* 6.2 0.4 - - - -
47J LEU 3.0 14.4 + - - -
48J TYR* 3.1 4.4 + - - -
50J LEU* 1.3 82.8 - - - +
52J TRP* 1.3 61.6 + - - +
54J SER* 3.4 6.9 + - - -
55J PHE* 3.3 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 52 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C MET* 3.8 20.2 - - + -
37C PHE* 3.1 43.7 - + + -
48J TYR* 2.9 38.6 + + + +
49J CYS* 3.4 9.4 - - - +
51J GLY* 1.3 78.8 - - - +
53J ALA* 1.3 70.9 + - - +
54J SER 3.2 1.4 + - - -
55J PHE* 3.4 6.4 + - - +
57J HIS* 3.1 58.2 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 3.6 28.6 - - + +
119A GLU* 4.3 5.5 + - - +
33C MET* 5.4 0.4 - - + -
37C PHE* 3.5 38.4 - - + -
49J CYS 3.0 17.0 + - - +
50J LEU* 3.3 2.9 + - - +
52J TRP* 1.3 80.0 - - + +
54J SER* 1.3 63.0 + - - +
55J PHE 3.2 6.2 + - - +
57J HIS* 4.8 2.0 - - - -
46L LYS* 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A MET* 3.4 36.9 - - - +
118A VAL* 4.2 1.6 - - - +
50J LEU* 2.7 27.0 + - - +
51J GLY* 3.5 11.5 - - - -
52J TRP 3.1 0.6 - - - -
53J ALA* 1.3 78.3 - - - +
55J PHE* 1.3 68.8 + - - +
42L HIS* 3.1 21.9 + - - -
46L LYS* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 55 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A MET* 5.8 2.0 - - + -
51J GLY* 3.3 20.9 - - - -
52J TRP 3.4 5.7 + - - +
53J ALA 4.0 5.3 - - - +
54J SER* 1.3 83.9 - - - +
56J PRO* 1.3 72.5 - - + +
57J HIS* 3.1 30.8 + - + +
42L HIS* 3.6 30.7 - + - -
46L LYS* 4.8 3.4 - - + -
----------------------------------------------------------
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