Contacts of the helix formed by residues 51 - 82 (chain A) in PDB entry 4U7Y
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 51 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLN* 1.3 77.6 - - - +
52A ASP* 1.3 65.5 + - - -
53A LYS* 3.2 3.6 - - - -
54A ALA* 3.1 8.7 + - - +
55A LYS* 3.0 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLY* 1.3 70.4 - - - -
53A LYS* 1.3 58.1 + - - +
55A LYS* 3.1 16.1 + - - +
56A GLN* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLY 3.2 0.8 - - - -
52A ASP* 1.3 78.8 - - - +
54A ALA* 1.3 62.4 + - - +
56A GLN* 3.4 7.2 + - - +
57A SER* 3.1 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLN* 3.5 24.7 - - + -
51A GLY* 3.1 14.3 + - - +
53A LYS* 1.3 79.8 - - - +
55A LYS* 1.3 63.4 + - - +
57A SER* 3.3 6.8 + - - -
58A ILE* 3.0 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.9 22.9 - - + -
50A GLN* 3.3 49.6 - - + +
51A GLY 3.0 12.9 + - - +
52A ASP* 3.6 16.2 - - - +
54A ALA* 1.3 75.0 - - - +
56A GLN* 1.3 58.1 + - - +
58A ILE* 3.3 2.1 + - - +
59A ARG* 2.9 31.6 + - - +
321B PHE* 3.8 14.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP 2.8 16.8 + - - +
53A LYS* 3.7 8.3 - - - +
55A LYS* 1.3 78.0 - - - +
57A SER* 1.3 60.9 + - - +
59A ARG* 3.6 8.9 + - - +
60A ALA* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS 3.1 17.6 + - - -
54A ALA* 3.8 5.3 - - - -
56A GLN* 1.3 74.3 - - - +
58A ILE* 1.3 66.5 + - - +
60A ALA* 3.3 7.8 + - - +
61A LYS* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.5 16.4 - - + -
41A PHE* 3.5 48.0 - - + +
44A VAL* 3.9 26.7 - - + -
45A VAL* 3.9 21.3 - - + -
50A GLN* 4.4 7.9 - - + +
54A ALA* 3.0 26.9 + - + +
55A LYS 3.3 3.8 + - - +
57A SER* 1.3 74.4 - - - +
59A ARG* 1.3 60.8 + - - +
61A LYS* 3.2 5.9 + - - +
62A CYS* 2.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS 2.9 17.8 + - - +
56A GLN* 3.7 9.6 - - - +
58A ILE* 1.3 76.4 - - - +
60A ALA* 1.3 61.5 + - - +
62A CYS* 3.2 6.6 + - - +
63A THR* 2.8 33.0 + - - +
320B ASP 3.8 13.1 + - - -
321B PHE* 3.4 40.5 - - + -
324B LEU* 3.9 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN 3.1 14.5 + - - +
57A SER* 3.4 12.1 - - - +
59A ARG* 1.3 75.6 - - - +
61A LYS* 1.3 63.2 + - + +
63A THR* 3.3 9.5 + - - -
64A GLU* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 6.4 0.4 - - - +
41A PHE* 4.6 17.3 - - + -
57A SER* 3.0 22.8 + - - +
58A ILE* 3.8 4.7 - - - +
60A ALA* 1.3 74.7 - - + +
62A CYS* 1.3 65.3 + - - +
64A GLU* 3.2 12.4 + - - +
65A TYR* 3.0 67.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 4.1 15.6 - - + +
41A PHE* 3.5 32.9 - - - -
42A LEU* 3.9 28.7 - - - -
58A ILE* 2.8 19.2 + - - +
59A ARG* 3.4 6.5 - - - +
61A LYS* 1.3 77.3 - - - +
63A THR* 1.3 61.5 + - - +
65A TYR* 4.0 1.5 - - - -
66A LEU* 3.0 29.9 + - + +
321B PHE* 5.6 0.9 - - - -
324B LEU* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 2.8 19.2 + - - +
60A ALA* 3.4 9.9 - - - -
62A CYS* 1.3 76.7 - - - +
64A GLU* 1.3 62.3 + - - +
66A LEU* 4.0 2.3 - - - +
67A ASP* 3.0 44.3 + - - +
324B LEU* 3.8 18.8 - - + +
327B ARG* 4.6 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA 3.1 10.5 + - - +
61A LYS* 3.2 14.5 + - - +
63A THR* 1.3 80.1 - - - +
65A TYR* 1.3 79.6 + - + +
67A ASP* 3.3 9.2 + - + +
68A ARG* 3.0 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 3.6 31.2 - - + +
19A ALA* 6.2 2.2 - - + -
34A TYR* 3.8 38.5 - + + +
37A ALA* 4.9 2.9 - - + -
38A VAL* 3.6 19.1 - - + -
41A PHE* 3.6 20.8 - + - -
61A LYS* 3.0 52.9 + - + +
64A GLU* 1.3 96.1 + - - +
66A LEU* 1.3 60.1 + - - +
68A ARG* 4.1 1.9 - - + +
69A ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 3.7 27.6 - - + -
62A CYS* 3.0 20.9 + - + +
63A THR* 4.2 1.1 - - - +
65A TYR* 1.3 74.3 - - - +
67A ASP* 1.3 59.7 + - - +
69A ALA* 4.2 1.8 - - + -
70A GLU* 2.9 37.4 + - - +
324B LEU* 3.6 39.7 - - + +
327B ARG* 3.7 28.9 - - + +
328B PHE* 3.9 22.9 - - - +
331B LEU* 4.1 23.6 - - + -
----------------------------------------------------------
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 THR* 3.0 30.8 + - - +
64A GLU* 3.3 12.4 - - + +
66A LEU* 1.3 76.4 - - - +
68A ARG* 1.3 64.5 + - + +
70A GLU* 3.8 3.9 - - - +
71A LYS* 3.1 27.5 + - + +
327B ARG* 2.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP* 2.6 43.8 + - - +
27A TYR* 3.9 13.7 + - - -
34A TYR* 3.8 20.9 - - + +
64A GLU* 3.0 13.9 + - + +
65A TYR* 4.1 4.3 - - + +
67A ASP* 1.3 80.7 - - - +
69A ALA* 1.3 58.3 + - - +
71A LYS* 3.1 31.8 + - - +
72A LEU* 2.9 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.2 26.1 - - + +
34A TYR* 3.9 19.1 - - + -
35A GLN 4.9 0.2 - - - +
38A VAL* 6.0 0.2 - - + -
65A TYR 2.9 21.2 + - - +
66A LEU* 3.8 6.1 - - + +
67A ASP 3.2 0.2 - - - -
68A ARG* 1.3 78.3 - - - +
70A GLU* 1.3 58.4 + - - +
72A LEU* 3.1 4.6 + - - +
73A LYS* 2.9 24.6 + - - +
331B LEU* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 2.9 14.6 + - - +
67A ASP* 3.8 4.6 - - - +
69A ALA* 1.3 73.5 - - - +
71A LYS* 1.3 66.2 + - - +
73A LYS* 3.0 8.5 + - - +
74A GLU* 3.0 23.3 + - - +
327B ARG* 2.8 62.1 + - - +
330B GLU* 5.9 0.7 - - - +
331B LEU* 3.6 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 3.1 16.7 + - + +
68A ARG* 3.4 33.8 - - - +
70A GLU* 1.3 77.2 - - - +
72A LEU* 1.3 56.3 - - - +
74A GLU* 3.5 7.0 + - - +
75A TYR* 3.1 25.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
22A ASP* 4.6 2.2 - - - +
27A TYR* 3.5 50.9 - - + +
30A ALA* 3.7 19.3 - - + -
31A LEU* 3.9 16.2 - - + +
34A TYR* 4.3 12.1 - - + -
68A ARG* 2.9 49.2 + - - +
69A ALA 3.5 8.5 - - - +
71A LYS* 1.3 75.6 - - - +
73A LYS* 1.3 61.0 + - - +
75A TYR* 3.3 5.8 + - + +
76A LEU* 2.9 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.4 18.3 - - + +
69A ALA 2.9 13.2 + - - +
70A GLU* 3.4 13.0 - - - +
72A LEU* 1.3 75.9 - - - +
74A GLU* 1.3 57.1 + - - +
76A LEU* 3.2 5.5 + - - +
77A LYS* 2.9 29.7 + - - +
331B LEU* 5.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU 3.0 12.3 + - - +
71A LYS* 3.8 9.9 - - - +
73A LYS* 1.3 75.5 - - - +
75A TYR* 1.3 62.2 + - - +
77A LYS* 3.3 15.9 + - - +
78A ASN* 3.1 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.4 40.0 - + + -
71A LYS 3.1 15.0 + - - +
72A LEU* 3.5 13.7 - - + +
74A GLU* 1.3 76.5 - - - +
76A LEU* 1.3 72.3 + - + +
78A ASN* 3.1 7.7 + - - +
79A LYS* 2.9 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 4.0 11.4 - - + +
28A GLU* 3.8 37.5 - - + +
31A LEU* 3.7 26.7 - - + -
72A LEU 2.9 21.4 + - - +
73A LYS* 3.7 4.5 - - - +
75A TYR* 1.3 89.3 - - + +
77A LYS* 1.3 65.2 + - - +
79A LYS* 3.9 9.5 - - + +
80A GLU* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS 2.9 13.6 + - - +
74A GLU* 3.5 18.6 - - - +
75A TYR 3.2 0.2 - - - -
76A LEU* 1.3 76.0 - - - +
78A ASN* 1.3 68.8 + - - +
80A GLU* 3.4 6.7 + - - +
81A LYS* 3.0 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 3.1 22.8 + - - +
75A TYR* 3.1 7.7 + - + +
77A LYS* 1.3 86.0 - - - +
79A LYS* 1.3 65.1 + - - +
80A GLU 3.1 1.1 - - - -
81A LYS* 3.2 20.4 + - - +
82A LYS* 3.4 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 2.9 35.1 + - + +
76A LEU* 3.9 13.0 - - + +
78A ASN* 1.3 76.7 - - - +
80A GLU* 1.3 60.8 + - - +
82A LYS* 3.2 35.7 - - + +
83A ALA 4.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU 3.1 19.1 + - - +
77A LYS* 3.7 6.5 - - - +
78A ASN 3.1 0.2 - - - -
79A LYS* 1.3 74.7 - - - +
81A LYS* 1.3 63.7 + - - +
82A LYS 3.1 2.6 + - - -
83A ALA* 3.6 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 3.0 31.0 + - + +
78A ASN* 3.2 18.1 + - - +
80A GLU* 1.3 75.9 - - - +
82A LYS* 1.3 67.1 + - - +
83A ALA 3.3 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASN 3.4 10.1 + - - +
79A LYS* 3.2 30.1 - - + +
81A LYS* 1.3 80.3 - - - +
83A ALA* 1.3 60.7 + - - +
----------------------------------------------------------
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