Contacts of the helix formed by residues 49 - 76 (chain A) in PDB entry 2W5J
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 ILE 49 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 4.8 1.8 - - + -
39A ILE* 3.0 39.9 - - + -
45A ALA 3.3 5.8 + - - +
47A GLY 2.8 3.1 - - - +
48A LYS* 1.3 72.9 - - - +
50A ARG* 1.3 69.0 + - + +
52A THR* 2.7 22.3 + - - -
53A LEU* 3.3 7.1 + - - -
36B VAL* 3.7 29.1 - - + +
39B ILE* 4.8 4.9 - - - +
40B ALA* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 6.0 2.0 - - + +
46A GLU* 3.4 23.9 + - + +
47A GLY* 2.9 22.2 + - - +
49A ILE* 1.3 78.1 - - + +
51A GLY* 1.3 64.2 + - - +
52A THR 2.8 0.7 + - - -
53A LEU* 2.9 8.7 + - - -
54A LEU* 2.7 41.0 + - + +
47V GLY 4.0 0.2 + - - -
48V LYS* 2.8 25.2 + - - +
51V GLY* 3.4 14.4 + - - -
52V THR* 2.5 58.6 + - + +
55V LEU* 4.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY 2.6 16.7 + - - -
50A ARG* 1.3 72.2 - - - +
52A THR* 1.3 55.5 + - - +
54A LEU* 4.4 6.6 - - - +
55A LEU* 3.2 21.7 + - - +
50B ARG* 3.3 22.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS 3.8 3.6 + - - -
49A ILE* 2.7 13.8 + - - -
51A GLY* 1.3 70.3 - - - -
53A LEU* 1.3 56.6 + - - -
54A LEU 3.2 1.6 - - - -
55A LEU* 2.8 16.6 + - + +
56A SER* 2.5 39.9 + - - +
32B ALA 5.7 0.9 - - - +
35B ALA* 5.3 3.6 - - + -
36B VAL* 5.5 9.1 - - - +
39B ILE* 5.3 6.6 - - + +
50B ARG* 2.5 36.8 + - + +
53B LEU* 3.0 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 5.6 4.0 - - - +
32A ALA* 3.8 20.4 - - - +
35A ALA* 3.9 19.3 - - + -
49A ILE 3.3 4.1 + - - +
50A ARG* 2.9 13.4 + - - +
52A THR* 1.3 78.7 - - - +
54A LEU* 1.3 68.3 + - + +
56A SER* 3.3 3.4 - - - -
57A LEU* 2.4 69.5 + - + +
32B ALA* 5.8 0.7 - - - -
36B VAL* 4.9 5.8 - - + +
52V THR* 3.1 25.8 - - + -
55V LEU* 3.3 27.4 - - + -
56V SER* 3.6 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 2.7 32.7 + - + +
51A GLY* 4.4 5.2 - - - +
53A LEU* 1.3 81.7 - - + +
55A LEU* 1.3 53.6 + - - +
57A LEU* 3.8 2.7 - - - -
58A ALA* 2.6 36.1 + - - +
55V LEU* 3.1 47.6 - - + -
59V PHE* 4.5 8.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLY 3.2 16.2 + - - +
52A THR* 2.8 19.4 + - + +
54A LEU* 1.3 77.5 - - - +
56A SER* 1.3 59.0 + - - +
58A ALA* 3.1 22.8 - - - +
59A PHE* 3.2 22.5 - - + -
50B ARG* 4.5 8.3 - - + -
53B LEU* 3.1 22.0 - - + -
54B LEU* 2.9 46.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A THR* 2.5 22.5 + - - +
53A LEU* 3.3 4.4 + - - -
55A LEU* 1.3 68.1 - - - +
57A LEU* 1.3 55.1 + - - +
58A ALA 2.7 15.3 + - - -
59A PHE* 2.7 20.1 + - - -
60A MET* 3.2 10.5 + - - +
32B ALA* 3.2 35.7 - - - +
53B LEU* 3.4 18.5 - - - +
57B LEU* 3.5 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLN* 3.9 31.6 - - + +
31A ALA* 4.0 13.2 - - + -
32A ALA* 4.3 1.8 - - + +
53A LEU* 2.4 67.1 + - + +
54A LEU* 3.6 4.3 - - - +
56A SER* 1.3 70.8 - - - +
58A ALA* 1.3 64.5 + - - +
60A MET* 4.1 8.9 - - - +
61A GLU* 3.7 10.4 + - - +
56V SER* 3.5 22.7 - - - +
59V PHE* 3.3 49.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU 2.6 16.4 + - - +
55A LEU* 3.1 17.9 - - - +
56A SER 2.7 2.6 + - - -
57A LEU* 1.3 77.1 - - - +
59A PHE* 1.3 65.8 + - + +
60A MET 3.2 0.2 - - - -
61A GLU* 2.9 22.7 + - - +
62A ALA* 3.2 4.2 + - - -
59V PHE* 5.1 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.2 31.4 - - + -
56A SER 2.7 11.0 + - - -
58A ALA* 1.3 77.9 - - + +
60A MET* 1.3 58.6 + - - +
62A ALA* 3.4 14.1 - - + -
63A LEU* 3.9 3.6 - - - +
28B GLN* 5.8 6.5 - - + +
54B LEU* 4.4 8.7 - - + -
57B LEU* 3.1 64.6 - - + -
58B ALA* 5.6 0.7 - - - -
61B GLU* 2.8 45.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PRO* 4.3 14.6 - - + -
28A GLN* 3.6 37.2 - - + +
56A SER 3.2 10.3 + - - +
57A LEU* 4.3 3.1 - - - +
58A ALA 3.0 1.6 + - - -
59A PHE* 1.3 75.4 - - - +
61A GLU* 1.3 58.7 + - + +
62A ALA 2.9 5.2 + - - -
63A LEU* 2.9 32.1 - - - +
64A THR* 3.7 3.8 + - - +
25B GLY* 5.5 3.8 - - - +
28B GLN* 6.4 1.8 - - + -
29B GLY* 5.9 4.0 - - - +
63V LEU* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PRO* 5.0 0.2 - - - +
57A LEU 3.7 3.5 + - - +
58A ALA* 2.9 12.4 + - - +
60A MET* 1.3 79.6 - - + +
62A ALA* 1.3 57.9 + - - +
64A THR* 2.9 30.2 + - - -
65A ILE* 3.2 13.0 - - - +
59V PHE* 2.9 48.6 - - + +
62V ALA* 3.1 21.3 - - - +
63V LEU* 3.3 18.2 + - + +
66V TYR* 2.8 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA 3.2 4.7 + - - +
59A PHE* 3.4 19.1 - - + -
60A MET 2.9 0.8 + - - -
61A GLU* 1.3 77.3 - - - +
63A LEU* 1.3 55.7 + - - +
64A THR 3.1 0.4 - - - -
65A ILE* 2.7 37.8 + - + +
66A TYR* 2.8 19.8 - - + +
61B GLU* 2.9 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 4.1 1.7 - - - +
24A PRO* 3.2 26.0 - - + -
59A PHE 3.9 3.6 - - - +
60A MET* 2.9 26.7 - - - +
62A ALA* 1.3 77.4 - - - +
64A THR* 1.3 59.0 + - - +
66A TYR* 3.6 20.6 - - + +
67A GLY 4.6 0.3 + - - -
20B ALA 4.4 1.1 - - - +
21B SER* 3.7 19.0 + - - -
24B PRO* 3.8 15.0 - - + -
25B GLY* 4.3 4.9 - - - +
28B GLN* 6.5 0.9 - - + -
60B MET* 6.0 0.4 - - + -
61B GLU* 3.3 26.0 - - + +
64B THR* 3.1 47.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 2.6 44.0 - - - +
24A PRO* 3.1 23.3 - - + -
60A MET 3.8 4.5 - - - +
61A GLU* 2.9 25.8 + - - -
62A ALA 3.0 0.4 + - - -
63A LEU* 1.3 75.4 - - - +
65A ILE* 1.3 68.2 + - - +
66A TYR 3.2 1.6 - - - -
67A GLY 3.1 4.2 + - - -
68A LEU* 3.1 16.5 + - - +
63V LEU* 3.2 25.6 - - + +
66V TYR* 3.6 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 3.2 13.2 - - + +
62A ALA* 2.7 31.1 + - + +
64A THR* 1.3 78.5 + - - +
66A TYR* 1.3 66.1 + - + +
67A GLY 2.9 1.8 - - - -
68A LEU* 2.7 13.3 + - + -
69A VAL* 2.5 45.9 + - + +
66V TYR* 3.3 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA* 2.8 34.2 - - + +
63A LEU* 3.6 17.9 - - + +
65A ILE* 1.3 82.9 - - + +
67A GLY* 1.3 61.3 + - - +
69A VAL* 3.4 6.4 - - - +
70A VAL* 3.2 28.5 + - - +
61B GLU* 2.5 33.0 + - - +
64B THR* 3.5 10.5 - - - -
65B ILE* 3.1 32.9 - - + +
68B LEU* 3.2 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.1 29.3 - - - +
20A ALA* 4.6 2.7 - - - +
63A LEU 4.6 1.4 + - - -
64A THR 3.1 7.0 + - - -
65A ILE 2.8 0.6 + - - -
66A TYR* 1.3 76.5 - - - +
68A LEU* 1.3 55.0 + - - +
69A VAL 2.9 1.6 - - - -
70A VAL* 2.7 7.2 + - - -
71A ALA 2.3 37.1 + - - -
17B VAL 5.9 2.7 - - - -
18B GLY* 6.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.0 3.9 + - - +
64A THR 3.1 7.7 + - - +
65A ILE* 2.7 22.9 + - + +
67A GLY* 1.3 70.7 - - - +
69A VAL* 1.3 59.3 + - - +
71A ALA* 3.5 6.3 - - + +
72A LEU* 3.1 45.1 + - + +
66V TYR* 3.3 56.8 - - + +
69V VAL* 4.9 3.4 - - + -
70V VAL* 3.4 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 2.5 35.4 + - + +
66A TYR* 3.4 10.5 - - - +
67A GLY 2.8 0.2 + - - -
68A LEU* 1.3 72.1 - - - +
70A VAL* 1.3 63.9 + - + +
72A LEU* 3.2 5.4 + - - +
73A ALA* 2.7 40.6 + - + +
68B LEU* 4.7 5.8 - - + -
72B LEU* 4.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY* 5.6 0.5 - - - -
17A VAL* 5.4 5.5 - - + +
66A TYR 3.2 6.0 + - - +
67A GLY* 2.7 7.8 + - - +
69A VAL* 1.3 76.0 - - + +
71A ALA* 1.3 62.8 + - - +
73A ALA* 3.7 7.6 - - - -
74A LEU* 3.2 22.5 + - + +
14B GLY 5.6 2.7 - - - -
15B LEU* 5.5 12.0 - - + +
68B LEU* 3.1 29.2 - - + -
71B ALA* 4.4 17.5 - - + +
72B LEU* 3.1 33.9 - - + -
75B LEU* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY* 4.4 21.1 - - - +
17A VAL* 4.3 17.2 - - + +
67A GLY 2.3 31.2 + - - +
68A LEU* 3.3 21.5 - - + +
70A VAL* 1.3 71.7 - - - +
72A LEU* 1.3 63.0 + - + +
74A LEU* 3.9 2.9 + - - +
75A LEU* 3.4 19.2 + - - +
70V VAL* 4.7 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.1 33.9 + - + +
69A VAL* 3.9 2.7 - - - +
71A ALA* 1.3 72.0 - - - +
73A ALA* 1.3 60.2 + - - +
74A LEU 3.2 2.0 - - - -
75A LEU* 3.0 22.2 + - + -
76A PHE* 2.7 44.5 + - + +
77A ALA 3.4 2.3 + - - -
69V VAL* 5.0 6.7 - - + -
70V VAL* 3.2 29.8 - - + -
73V ALA* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 2.7 27.8 + - + +
70A VAL* 3.8 10.5 - - - -
72A LEU* 1.3 75.1 - - - +
74A LEU* 1.3 56.3 + - - +
77A ALA* 3.0 38.4 - - + +
78A ASN* 3.8 0.2 - - - -
72B LEU* 4.9 2.9 - - + -
75B LEU* 4.3 3.4 - - + -
76B PHE* 3.3 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.7 20.9 - - - +
13A ALA* 6.0 0.7 - - + -
14A GLY* 5.1 4.7 - - - +
70A VAL* 3.2 20.5 + - + +
71A ALA 4.2 3.8 - - - +
73A ALA* 1.3 77.2 - - - +
75A LEU* 1.3 58.2 - - - +
78A ASN* 2.7 31.6 - - - +
11B ILE* 3.9 22.7 - - + -
15B LEU* 6.4 1.1 - - + -
75B LEU* 4.3 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 5.3 10.4 - - + +
11A ILE* 3.9 26.9 - - + -
14A GLY* 6.2 1.1 - - - -
71A ALA 3.4 12.7 + - - +
72A LEU* 3.0 20.1 + - + +
74A LEU* 1.3 82.8 - - - +
76A PHE* 1.3 93.7 + - + +
77A ALA 3.5 0.2 - - - -
78A ASN* 4.1 6.8 - - - +
70V VAL* 4.2 16.6 - - + -
73V ALA* 4.5 9.2 - - + +
74V LEU* 4.7 6.3 - - + +
79V PRO* 3.6 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 2.7 27.4 + - + +
75A LEU* 1.3 104.6 - - + +
77A ALA* 1.3 55.7 + - - +
78A ASN 3.6 1.1 - - - -
73V ALA* 3.5 31.9 - - + -
77V ALA* 3.4 20.4 - - + -
79V PRO* 3.4 30.5 - - + -
----------------------------------------------------------
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