Contacts of the helix formed by residues 32 - 62 (chain A) in PDB entry 2DF9
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 GLN 32 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY* 3.1 1.5 - - - -
31A GLY* 1.3 76.5 - - - +
33A LYS* 1.3 57.4 + - - +
35A THR* 2.7 46.5 + - + +
36A VAL* 3.1 21.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.0 45.5 - - + +
28A GLN* 4.1 12.0 + - - -
29A ALA* 2.9 38.3 - - + +
30A GLY* 2.8 31.3 + - - +
32A GLN* 1.3 76.3 - - - +
34A CYS* 1.3 58.7 + - - +
36A VAL* 2.7 22.2 - - + +
37A SER* 2.7 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 5.9 0.2 - - - -
26A PRO* 5.7 10.5 - - - -
29A ALA* 4.9 2.9 - - - +
30A GLY 4.0 3.1 + - - -
31A GLY* 3.7 13.0 + - - +
32A GLN 3.0 1.2 + - - -
33A LYS* 1.3 75.3 - - - +
35A THR* 1.3 62.2 + - - +
37A SER* 2.6 24.4 + - - -
38A ILE* 3.1 13.6 - - + +
90A SER* 4.7 27.7 + - - +
93A THR* 4.8 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY 4.9 0.2 + - - -
32A GLN* 2.7 40.9 + - + +
34A CYS* 1.3 76.9 - - - +
36A VAL* 1.4 70.3 + - + +
38A ILE* 2.8 32.0 + - - +
39A ASN* 3.1 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 5.0 3.8 - - + -
32A GLN* 3.6 37.5 - - + +
33A LYS* 2.7 52.3 + - + +
35A THR* 1.4 85.5 - - + +
37A SER* 1.3 54.7 + - - +
39A ASN* 2.6 37.1 + - + +
40A VAL* 3.1 8.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 4.6 13.5 - - - -
25A LEU* 4.1 18.8 - - - -
33A LYS 2.7 17.1 + - - -
34A CYS* 2.6 25.8 + - - -
36A VAL* 1.3 70.2 - - - +
38A ILE* 1.3 66.9 + - - +
40A VAL* 2.8 24.9 + - - +
41A LEU* 2.8 20.9 + - - +
86A VAL* 6.3 3.6 - - - -
90A SER* 4.8 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A CYS 3.1 18.2 - - - +
35A THR* 2.8 23.8 + - - +
37A SER* 1.3 77.9 + - - +
39A ASN* 1.3 61.8 + - - +
41A LEU* 2.9 21.2 + - + +
42A LEU* 3.0 14.2 + - + +
87A LEU* 2.9 40.4 - - + -
90A SER* 4.5 4.9 - - - +
91A GLN* 5.2 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR 3.1 3.6 + - - +
36A VAL* 2.6 19.3 + - + +
38A ILE* 1.3 82.7 - - - +
40A VAL* 1.3 55.9 + - + +
42A LEU* 3.2 11.0 + - - +
43A ALA* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.1 31.0 - - + +
22A ALA* 4.4 5.4 - - + -
25A LEU* 4.9 12.8 - - + -
36A VAL* 3.1 14.5 + - + +
37A SER* 2.8 18.7 + - - +
39A ASN* 1.3 78.3 - - + +
41A LEU* 1.3 51.2 + - + +
43A ALA* 4.5 4.9 - - + +
44A GLN* 2.6 56.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 5.6 4.9 - - + -
37A SER* 2.8 20.9 + - - +
38A ILE* 2.9 13.9 + - + +
40A VAL* 1.3 78.0 - - + +
42A LEU* 1.3 51.7 + - - +
44A GLN* 2.9 15.1 - - + +
45A THR* 2.6 45.6 + - - +
83A CYS* 3.1 41.1 - - + +
84A VAL* 4.9 0.9 - - + +
86A VAL* 4.2 8.7 - - + -
87A LEU* 3.2 49.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 3.0 12.6 + - + +
39A ASN* 3.5 14.8 - - - +
41A LEU* 1.3 77.2 - - - +
43A ALA* 1.3 58.4 + - - +
45A THR* 3.1 7.9 + - + -
46A VAL* 2.8 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 6.3 1.3 - - + -
39A ASN* 2.9 20.3 + - - +
40A VAL* 3.8 6.3 - - + +
42A LEU* 1.3 81.1 - - - +
44A GLN* 1.3 58.9 + - - +
46A VAL* 2.7 18.8 - - - +
47A PHE* 2.7 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 4.2 19.7 - - + +
18A LEU* 4.7 10.0 - - + +
19A VAL* 3.8 26.7 - - - +
22A ALA* 4.9 0.3 - - - +
40A VAL* 2.6 51.4 + - + +
41A LEU* 2.9 30.2 - - - +
43A ALA* 1.3 72.4 - - - +
45A THR* 1.3 59.9 + - - +
47A PHE* 3.7 6.7 + - - +
48A LEU* 3.2 33.4 + - + +
79A ILE* 4.4 4.8 + - - +
83A CYS* 2.9 39.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 2.6 27.9 + - - +
42A LEU* 3.5 9.1 - - + -
44A GLN* 1.3 78.4 - - - +
46A VAL* 1.3 68.2 + - + +
48A LEU* 3.4 7.7 + - - +
49A PHE* 3.1 24.0 + - + +
80A VAL* 4.7 18.5 - - + +
83A CYS* 5.0 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 2.8 43.9 + - + +
43A ALA* 2.7 30.3 - - - +
45A THR* 1.3 74.0 - - + +
47A PHE* 1.3 86.8 + - + +
49A PHE* 3.2 6.4 + - - +
50A LEU* 3.1 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 6.4 1.6 - - + -
18A LEU* 5.9 4.7 - - + -
43A ALA* 2.7 42.0 + - + +
44A GLN* 4.2 6.3 - - - +
46A VAL* 1.3 94.8 - - + +
48A LEU* 1.3 61.4 + - + +
50A LEU* 3.4 16.1 + - + +
51A ILE* 2.7 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 4.7 14.6 - - + -
44A GLN* 3.2 21.4 + - + +
45A THR* 4.0 5.6 - - - +
46A VAL 3.3 0.6 - - - -
47A PHE* 1.3 78.1 - - + +
49A PHE* 1.3 64.3 + - - +
51A ILE* 3.0 24.6 + - + +
52A ALA* 2.9 22.1 + - - +
76A ALA* 4.2 19.3 - - + +
79A ILE* 3.0 41.3 - - + -
80A VAL* 4.9 12.1 - - + -
83A CYS* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 3.1 18.7 + - + +
46A VAL* 3.2 7.2 + - - +
48A LEU* 1.3 79.4 - - - +
50A LEU* 1.3 67.7 + - + +
52A ALA* 3.1 20.9 + - + +
53A GLN* 2.9 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 3.1 19.4 + - + +
47A PHE* 3.8 19.1 - - + +
49A PHE* 1.3 79.6 - - + +
51A ILE* 1.3 67.2 + - + +
53A GLN* 2.7 42.5 + - - +
54A LYS* 2.9 17.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.9 16.2 - - + -
11A PRO* 5.1 14.6 - - + -
47A PHE* 2.7 28.7 + - + +
48A LEU* 3.0 35.2 + - + +
50A LEU* 1.3 77.1 - - + +
52A ALA* 1.3 57.8 + - - +
54A LYS* 2.9 32.9 - - - +
55A ILE* 2.9 47.3 + - + +
72A VAL* 5.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU 2.9 10.7 + - - +
49A PHE* 3.2 23.1 - - + +
51A ILE* 1.3 78.9 - - - +
53A GLN* 1.4 49.3 + - + +
55A ILE* 3.1 18.0 - - + +
56A PRO* 2.7 28.9 - - - +
73A MET* 6.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 2.9 43.6 - - + +
50A LEU* 2.7 39.0 + - - +
52A ALA* 1.4 72.8 - - + +
54A LYS* 1.3 51.9 + - - +
56A PRO* 2.8 23.5 - - - +
57A GLU* 2.6 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 5.8 5.9 - - - +
50A LEU* 2.9 13.2 + - + +
51A ILE* 2.9 55.7 - - - +
53A GLN* 1.3 74.3 - - - +
55A ILE* 1.3 69.4 + - + +
57A GLU* 3.2 15.8 + - - +
58A THR* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.9 12.1 - - + -
51A ILE* 2.9 33.4 + - + +
52A ALA* 3.1 26.9 - - + +
54A LYS* 1.3 79.1 - - + +
56A PRO* 1.3 72.5 - - + +
58A THR* 3.0 9.6 + - - -
59A SER* 2.9 21.9 + - - -
69A LEU* 6.1 5.8 - - + -
72A VAL* 4.7 22.9 - - + -
73A MET* 5.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA 2.7 28.3 - - - +
53A GLN* 2.8 28.7 - - - +
55A ILE* 1.3 85.4 - - + +
57A GLU* 1.3 67.5 + - + +
59A SER* 2.6 26.1 + - - +
60A LEU* 3.0 17.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLN* 2.6 31.7 - - - +
54A LYS* 3.3 16.7 - - - +
56A PRO* 1.3 84.2 - - + +
58A THR* 1.3 64.2 + - - +
60A LEU* 3.4 7.1 + - - +
61A SER* 3.0 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 6.0 9.2 - - + -
54A LYS* 3.0 16.1 + - - +
55A ILE* 3.4 10.5 - - - -
57A GLU* 1.3 78.8 - - - +
59A SER* 1.3 56.7 + - - +
61A SER* 3.1 7.8 + - - -
62A VAL* 2.8 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE 2.9 12.6 + - - -
56A PRO* 2.6 26.9 + - - +
58A THR* 1.3 78.6 - - - +
60A LEU* 1.3 56.6 + - - +
62A VAL* 2.5 36.7 - - - +
63A PRO 4.6 0.7 - - - -
64A LEU* 3.1 36.0 - - - +
69A LEU* 4.7 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 3.0 17.9 + - + +
57A GLU* 3.9 6.5 - - - +
59A SER* 1.3 88.3 + - - +
61A SER* 1.3 63.5 + - - +
62A VAL 3.3 6.1 - - - +
64A LEU* 4.5 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 3.0 16.2 + - - +
58A THR* 3.1 11.2 + - - -
60A LEU* 1.3 78.3 - - - +
62A VAL* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 2.8 40.9 + - + +
59A SER* 2.5 27.5 - - - +
60A LEU 3.3 7.6 - - - +
61A SER* 1.3 83.1 - - - +
63A PRO* 1.3 84.7 - - + +
64A LEU* 3.6 3.6 - - - +
----------------------------------------------------------
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