Contacts of the helix formed by residues 55 - 81 (chain A) in PDB entry 3D0G
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 THR 55 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 4.8 2.1 - - - -
53A ASN* 2.8 34.8 + - - -
54A ILE* 1.3 75.2 + - - +
56A GLU* 1.3 64.1 + - + +
57A GLU* 3.1 31.1 + - + +
58A ASN* 2.9 18.7 + - - +
59A VAL* 3.1 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 1.3 77.7 - - + +
57A GLU* 1.3 61.3 + - - +
59A VAL* 3.3 23.7 - - - +
60A GLN* 3.2 48.2 + - - +
----------------------------------------------------------
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 ASN* 5.2 3.6 + - - -
55A THR* 3.1 24.2 + - + +
56A GLU* 1.3 78.1 - - - +
58A ASN* 1.3 72.6 + - - +
60A GLN* 3.6 8.0 - - - +
61A ASN* 3.4 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA 4.9 1.7 - - - +
49A ASN* 3.2 30.8 + - - +
50A TYR* 4.1 13.5 - - + +
53A ASN* 2.8 37.9 + - - +
55A THR* 2.9 16.0 + - - +
57A GLU* 1.3 91.8 - - - +
59A VAL* 1.3 59.7 + - - +
60A GLN 3.0 1.8 - - - -
61A ASN* 2.9 13.1 + - - +
62A MET* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 4.2 25.0 - - + +
55A THR 3.1 7.1 + - - +
56A GLU* 3.3 48.7 - - - +
58A ASN* 1.3 75.0 - - - +
60A GLN* 1.3 61.5 + - - +
62A MET* 4.5 6.7 - - + -
63A ASN* 3.0 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU* 3.2 41.7 + - - +
57A GLU* 3.6 10.3 - - - +
58A ASN 3.0 0.2 - - - -
59A VAL* 1.3 84.9 - - - +
61A ASN* 1.3 59.5 + - - +
63A ASN* 3.9 3.4 - - - +
64A ASN* 3.1 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA* 3.8 14.1 - - + +
57A GLU* 3.4 16.4 + - - +
58A ASN* 2.9 16.7 + - - +
60A GLN* 1.3 78.9 - - - +
62A MET* 1.3 58.7 + - - +
63A ASN 3.2 1.3 - - - -
64A ASN* 3.1 15.4 + - - +
65A ALA* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER 5.3 1.0 - - - +
46A ALA* 3.9 17.5 + - - +
47A SER* 3.4 37.0 - - - -
50A TYR* 4.2 28.3 - - + -
51A ASN* 5.2 0.7 - - - +
58A ASN 2.8 19.0 + - - +
59A VAL* 4.2 7.4 - - + +
61A ASN* 1.3 72.0 - - - +
63A ASN* 1.3 76.7 + - - +
65A ALA* 4.4 0.7 - - - +
66A GLY* 3.0 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.0 31.1 + - - +
60A GLN* 3.9 5.2 - - - +
61A ASN 3.2 0.4 - - - -
62A MET* 1.3 93.7 - - - +
64A ASN* 1.3 56.8 + - - +
66A GLY* 4.9 0.4 - - - -
67A ASP* 2.8 54.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 3.1 24.1 + - - +
61A ASN* 3.3 22.4 - - - +
63A ASN* 1.3 78.1 - - - +
65A ALA* 1.3 59.9 + - - +
67A ASP* 3.5 6.1 + - - +
68A LYS* 3.4 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.7 1.2 - - - +
42A GLN* 3.6 31.6 - - + +
43A SER* 3.7 14.2 + - - +
46A ALA* 4.0 7.0 - - + -
61A ASN 3.0 14.3 + - - +
62A MET 4.6 0.4 - - - +
64A ASN* 1.3 74.8 - - + +
66A GLY* 1.3 63.4 + - - +
68A LYS* 3.8 6.3 + - - +
69A TRP* 3.2 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 3.8 14.1 + - - +
62A MET 3.0 19.6 + - - -
63A ASN* 3.7 1.3 - - - -
65A ALA* 1.3 74.8 - - - +
67A ASP* 1.3 63.0 + - - +
69A TRP* 4.2 2.3 - - - +
70A SER* 2.8 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASN* 2.8 40.1 + - - +
64A ASN* 3.8 6.1 + - - +
66A GLY* 1.3 76.7 - - - +
68A LYS* 1.3 55.5 + - - +
70A SER* 2.7 20.0 + - - -
71A ALA* 2.8 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.6 34.7 - - + +
42A GLN* 5.3 3.5 + - - +
64A ASN 3.4 13.4 + - - +
65A ALA* 4.0 6.5 - - - +
67A ASP* 1.3 76.9 - - - +
69A TRP* 1.3 58.2 + - - +
71A ALA* 3.3 5.0 + - - +
72A PHE* 2.8 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 4.6 0.9 - + - -
36A ALA* 3.6 32.5 - - + -
39A LEU* 3.7 25.7 - - + +
40A SER* 3.7 22.5 + - - -
43A SER* 3.6 27.1 - - - +
65A ALA 3.2 17.9 + - - +
66A GLY* 4.2 3.4 - - - +
68A LYS* 1.3 78.9 - - - +
70A SER* 1.3 62.8 + - - +
72A PHE* 3.6 23.5 - + - +
73A LEU* 3.2 55.8 + - + +
390A PHE* 4.0 12.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLY 2.8 18.5 + - - -
67A ASP* 2.7 23.6 + - - -
69A TRP* 1.3 76.3 - - - +
71A ALA* 1.3 64.2 + - - +
73A LEU* 3.1 22.0 + - - +
74A LYS* 3.2 13.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
67A ASP 2.8 21.7 + - - +
68A LYS* 3.7 6.1 - - - +
70A SER* 1.3 75.0 + - - +
72A PHE* 1.3 62.9 + - - +
74A LYS* 3.3 8.0 + - - +
75A GLU* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 3.6 28.7 - + - -
35A GLU* 3.7 32.8 - - + -
36A ALA* 4.0 8.7 - - - -
39A LEU* 3.3 21.5 - - + -
68A LYS 2.8 18.0 + - - +
69A TRP* 3.6 28.5 - + - +
71A ALA* 1.3 74.2 - - - +
73A LEU* 1.3 57.5 + - - +
75A GLU* 3.1 15.2 + - - +
76A GLN* 2.8 67.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 4.2 17.0 - - + -
69A TRP* 3.2 60.3 + - + +
70A SER* 3.1 15.7 + - - +
72A PHE* 1.3 78.9 - - - +
74A LYS* 1.3 54.3 + - - +
76A GLN* 2.9 6.7 + - - +
77A SER* 2.7 37.9 + - - -
100A LEU* 4.3 6.6 - - + +
102A GLN* 6.0 6.1 - - - +
391A LEU* 6.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A SER 3.2 8.4 + - - +
71A ALA* 3.4 11.0 - - - +
73A LEU* 1.3 78.7 - - - +
75A GLU* 1.3 58.6 + - - +
77A SER* 3.1 9.2 + - - +
78A THR* 2.7 49.8 + - + +
103A ASN 5.3 2.5 - - - +
106A SER* 3.9 33.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA 3.0 13.4 + - - +
72A PHE* 3.1 17.8 + - - +
74A LYS* 1.3 78.8 - - - +
76A GLN* 1.3 76.0 + - - +
78A THR* 2.8 18.7 + - - +
79A LEU* 3.2 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 3.3 31.2 - - - -
32A PHE* 3.5 32.2 - - + +
72A PHE* 2.8 56.3 + - + +
73A LEU 3.4 6.3 - - - +
75A GLU* 1.3 81.8 + - - +
77A SER* 1.3 54.8 + - - +
79A LEU* 3.1 20.9 + - - +
80A ALA* 2.7 35.0 + - - +
100A LEU* 3.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU 2.7 17.3 + - - -
74A LYS* 3.1 14.2 + - - +
76A GLN* 1.3 71.9 - - - +
78A THR* 1.3 66.8 + - - +
80A ALA* 2.8 23.0 + - - +
81A GLN* 2.9 21.7 + - - -
100A LEU* 2.9 32.9 - - - +
102A GLN* 3.4 22.8 + - - -
103A ASN* 4.1 8.1 + - - -
106A SER* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS* 2.7 40.7 + - + +
75A GLU* 2.8 16.1 + - - +
77A SER* 1.3 80.3 + - - +
79A LEU* 1.3 60.1 + - - +
81A GLN* 3.6 25.7 + - - +
82A MET* 3.9 9.9 - - - +
103A ASN* 5.9 2.2 - - - +
106A SER* 5.3 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 4.0 15.5 - - + -
75A GLU* 3.2 30.4 + - + +
76A GLN* 3.1 29.3 + - - +
77A SER 3.1 0.8 - - - -
78A THR* 1.3 76.9 - - - +
80A ALA* 1.3 59.9 + - - +
81A GLN 3.2 0.4 - - - -
82A MET* 3.0 40.9 + - - +
83A TYR* 3.7 8.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 3.7 26.0 - - + -
76A GLN 2.7 16.4 + - - +
77A SER* 2.8 13.2 + - - +
79A LEU* 1.3 65.9 - - - +
81A GLN* 1.3 58.1 + - - +
82A MET 3.0 9.0 + - - -
83A TYR* 3.3 19.4 + - - +
97A LEU* 3.7 14.2 - - + +
100A LEU* 3.8 18.2 - - + -
101A GLN* 3.5 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A SER* 2.9 21.7 + - - +
78A THR* 3.8 24.7 - - - +
79A LEU 3.2 0.8 - - - -
80A ALA* 1.3 72.5 - - - +
82A MET* 1.3 57.2 - - + +
83A TYR 3.1 11.8 + - - +
84A PRO* 5.7 0.2 - - - +
101A GLN* 3.3 49.7 - - + +
103A ASN* 4.0 31.9 + - - +
----------------------------------------------------------
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