Contacts of the helix formed by residues 36 - 61 (chain D) in PDB entry 2J3W
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 ASN 36 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 3.3 1.2 - - - +
35D GLU* 1.3 86.5 - - - +
37D ASP* 1.3 66.7 + - - +
38D GLU* 3.0 23.5 + - - +
39D ASP* 2.4 65.8 + - - +
40D VAL* 3.3 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D CYS* 5.2 0.6 - - - -
36D ASN* 1.3 71.7 - - - +
38D GLU* 1.3 62.7 + - - +
40D VAL* 3.0 10.6 + - - +
41D ASN* 2.8 34.6 + - - +
121D ASN 4.6 4.8 - - - +
122D HIS* 2.9 48.5 + - - -
124D ALA* 3.9 13.6 + - + -
125D LEU* 3.1 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ASN* 3.0 25.0 + - - +
37D ASP* 1.3 77.3 + - - +
39D ASP* 1.3 61.0 + - - +
41D ASN* 3.4 12.6 + - - +
42D LYS* 3.1 23.2 + - - +
124D ALA* 2.9 32.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 3.5 31.5 - - + -
35D GLU* 4.6 4.3 + - - +
36D ASN* 2.4 50.7 + - - +
38D GLU* 1.3 73.8 - - - +
40D VAL* 1.3 57.4 + - - +
42D LYS* 3.5 10.8 + - - +
43D GLN* 3.1 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D VAL* 4.7 3.1 - - + +
30D LEU* 3.8 41.5 - - + +
31D CYS* 3.9 20.0 - - - -
34D TYR* 4.1 8.1 - - + +
36D ASN 3.6 13.5 - - - +
37D ASP* 3.0 13.1 + - - +
39D ASP* 1.3 74.9 - - - +
41D ASN* 1.3 59.4 + - - +
43D GLN* 3.2 6.0 + - - +
44D LEU* 2.8 42.5 + - + +
125D LEU* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ASP 2.8 20.6 + - - +
38D GLU* 3.6 14.1 + - - +
40D VAL* 1.3 76.7 - - - +
42D LYS* 1.3 62.3 + - - +
44D LEU* 3.4 4.9 + - - +
45D ASP* 3.0 10.7 + - - +
124D ALA 3.0 24.9 + - - -
125D LEU* 3.6 7.1 - - - +
126D ILE* 2.6 46.7 + - + +
129D ASN* 2.8 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLU 3.1 14.0 + - - +
39D ASP* 3.7 11.9 - - - +
41D ASN* 1.3 79.5 - - - +
43D GLN* 1.3 57.7 + - - +
45D ASP* 3.0 8.9 + - + +
46D ARG* 2.9 74.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LEU* 4.0 25.6 - - + -
34D TYR* 3.6 32.9 + - + +
39D ASP 3.1 18.7 + - - +
40D VAL* 3.7 4.9 - - - +
42D LYS* 1.3 77.9 - - - +
44D LEU* 1.3 61.5 + - - +
46D ARG* 3.3 33.0 + - - +
47D MET* 3.1 37.9 + - - +
39F TYR* 3.4 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D TYR* 3.8 15.3 - - + +
26D LEU* 4.2 15.3 - - + -
27D VAL* 4.2 17.7 - - + -
30D LEU* 3.5 24.0 - - + -
40D VAL* 2.8 37.3 + - + +
41D ASN* 3.7 6.1 - - - +
43D GLN* 1.3 73.2 - - - +
45D ASP* 1.3 58.8 + - - +
47D MET* 3.6 3.1 + - - -
48D GLY 3.0 21.8 + - - -
125D LEU* 4.9 1.3 - - + -
126D ILE 3.9 12.6 - - - +
127D TYR* 3.6 23.8 - - - +
129D ASN* 4.1 2.9 - - + -
130D LEU* 3.4 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ASN 3.0 13.1 + - - +
42D LYS* 3.0 13.1 + - + +
44D LEU* 1.3 75.6 - - - +
46D ARG* 1.3 60.8 + - + +
48D GLY 3.3 0.3 + - - -
49D TYR* 2.9 25.1 + - - +
129D ASN* 3.7 16.7 + - - +
132D CYS* 3.9 13.3 - - - +
133D GLY* 3.5 18.7 + - - -
136D ARG* 2.9 31.6 + - - -
148D ALA 5.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 5.6 0.2 + - - -
42D LYS* 2.9 52.8 + - + +
43D GLN* 3.3 33.6 - - - +
45D ASP* 1.3 77.5 - - + +
47D MET* 1.3 62.1 + - + +
49D TYR* 3.0 10.4 + - - +
50D ASN* 2.9 33.5 + - - +
136D ARG* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 3.7 41.5 - - + -
30D LEU* 4.5 4.7 - - - -
43D GLN* 3.1 40.9 + - - +
44D LEU* 3.9 1.6 - - - +
46D ARG* 1.3 77.9 - - + +
48D GLY* 1.3 62.7 + - - +
50D ASN* 3.4 8.4 + - - +
51D ILE* 3.0 26.7 + - - +
130D LEU* 3.8 14.1 - - + -
32F LEU* 5.4 0.9 - - + -
35F GLU* 3.5 50.1 - - + +
36F MET* 4.1 2.7 - - + +
39F TYR* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LEU 3.0 11.7 + - - -
45D ASP 3.7 2.2 - - - -
46D ARG 3.2 0.2 - - - -
47D MET* 1.3 75.7 - - - +
49D TYR* 1.3 57.5 + - - +
51D ILE* 3.1 4.6 + - - +
52D GLY 2.8 24.6 + - - -
130D LEU* 3.3 34.2 - - - +
133D GLY 3.4 6.5 - - - -
134D VAL* 3.2 12.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ASP 2.9 14.0 + - - +
46D ARG* 3.1 12.3 - - - +
48D GLY* 1.3 76.1 - - - +
50D ASN* 1.3 77.4 + - - +
52D GLY* 2.9 12.3 + - - -
53D VAL* 2.9 37.3 + - + +
133D GLY 3.2 12.6 - - - +
136D ARG* 3.5 38.8 - - - +
137D GLY* 3.6 26.5 - - - -
140D GLU* 2.6 37.1 + - - -
141D MET* 4.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ARG* 2.9 34.0 + - - +
47D MET* 3.7 1.9 - - - +
49D TYR* 1.3 88.4 - - - +
51D ILE* 1.3 57.7 + - - +
53D VAL* 3.6 6.1 + - - +
54D ARG* 3.0 31.8 + - - +
35F GLU* 3.2 36.7 + - - +
38F GLN* 4.5 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D MET 3.0 17.5 + - - +
48D GLY* 3.3 8.7 - - - +
49D TYR 3.0 0.4 - - - -
50D ASN* 1.3 76.4 - - - +
52D GLY* 1.3 60.5 + - - +
54D ARG* 3.3 5.9 + - - +
55D LEU* 2.8 28.4 + - + +
130D LEU* 4.2 26.7 - - + -
134D VAL* 4.2 15.5 - - + -
1068D PLM 4.5 11.7 - - + -
31F LEU* 3.9 39.2 - - + +
32F LEU* 4.0 15.7 - - + +
35F GLU* 3.3 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D GLY 2.8 12.0 + - - -
49D TYR 2.9 3.3 + - - -
51D ILE* 1.3 72.1 - - - +
53D VAL* 1.3 61.6 + - - +
54D ARG 3.0 6.1 + - - -
55D LEU* 4.4 2.5 - - - -
56D ILE* 3.1 26.5 + - - +
134D VAL* 3.5 32.3 - - - -
137D GLY 4.1 0.2 - - - -
138D ALA* 3.5 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D TYR* 2.9 54.9 + - + +
50D ASN* 3.9 7.2 - - - +
51D ILE 3.3 0.2 - - - -
52D GLY* 1.3 75.7 - - - +
54D ARG* 1.3 59.5 + - + +
56D ILE* 3.5 13.0 - - - +
57D GLU* 5.5 1.7 - - - +
137D GLY 4.0 10.8 - - - +
141D MET* 3.9 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ASN* 3.0 22.2 - - - +
51D ILE* 3.3 5.3 + - - +
52D GLY 3.0 0.6 - - - -
53D VAL* 1.3 82.8 - - + +
55D LEU* 1.3 64.9 + - - +
56D ILE 3.1 2.7 + - - -
57D GLU* 3.6 13.1 + - - +
58D ASP* 3.9 8.5 + - - +
31F LEU* 4.3 18.9 - - + +
34F SER* 3.4 28.3 + - - -
35F GLU* 5.4 6.9 + - - -
38F GLN* 5.0 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ILE* 2.8 18.6 + - + +
52D GLY 4.3 0.4 - - - +
54D ARG* 1.3 77.2 - - - +
56D ILE* 1.3 67.4 + - - +
58D ASP* 3.4 8.7 + - - +
59D PHE* 3.0 23.4 + - + +
86D TYR* 3.8 40.6 - - + -
134D VAL* 4.3 10.5 - - + -
138D ALA* 4.6 7.0 - - + -
1068D PLM 3.9 51.1 - - + -
31F LEU* 3.7 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D GLY 3.1 13.7 + - - +
53D VAL 3.5 16.2 - - - +
55D LEU* 1.3 80.5 - - + +
57D GLU* 1.3 76.6 + - + +
59D PHE* 3.2 6.6 + - + +
60D LEU* 3.1 47.1 + - + +
138D ALA* 3.6 32.5 - - + +
141D MET* 3.4 34.3 - - + -
142D VAL* 4.3 10.1 - - + -
1068D PLM 4.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D VAL 5.5 1.6 - - - +
54D ARG 3.6 8.0 + - - +
55D LEU 3.5 0.2 - - - -
56D ILE* 1.3 86.6 - - + +
58D ASP* 1.3 61.5 + - - +
60D LEU* 3.7 10.7 + - - +
61D ALA* 3.3 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ARG 3.9 6.5 + - - +
55D LEU* 3.4 13.7 + - - +
56D ILE 3.1 0.2 - - - -
57D GLU* 1.3 77.4 - - - +
59D PHE* 1.3 64.3 + - - +
61D ALA* 3.2 14.7 + - - +
62D ARG* 3.3 53.4 + - - +
86D TYR* 2.7 29.5 + - - -
27F SER* 4.2 6.8 + - - -
31F LEU* 5.8 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D LEU* 3.0 15.9 + - + +
56D ILE* 3.2 9.8 + - + +
58D ASP* 1.3 75.9 - - - +
60D LEU* 1.3 69.3 - - + +
62D ARG* 3.3 13.1 + - - +
63D SER* 3.4 20.8 + - - +
77D VAL* 3.7 18.2 - - + -
81D VAL* 3.6 33.0 - - + -
82D ALA* 3.7 19.3 - - + -
85D MET* 3.6 25.6 - - + -
86D TYR* 3.5 20.1 + + + +
1068D PLM 3.7 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ILE* 3.1 39.1 + - + +
57D GLU* 3.9 8.7 - - - +
58D ASP 3.3 0.2 - - - -
59D PHE* 1.3 81.6 - - + +
61D ALA* 1.3 59.0 + - - +
62D ARG 3.2 1.8 + - - -
63D SER 3.4 19.1 + - - +
64D ASN* 5.5 2.4 - - - -
142D VAL* 4.5 13.5 - - + -
1068D PLM 4.5 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D GLU* 3.3 14.5 + - + +
58D ASP* 3.2 8.7 + - - +
60D LEU* 1.3 78.0 - - - +
62D ARG* 1.3 62.8 + - + +
63D SER 3.7 0.4 - - - -
----------------------------------------------------------
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