Contacts of the helix formed by residues 47 - 67 (chain A) in PDB entry 2QXU
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 47 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASP* 2.6 20.2 + - - +
45A THR* 3.4 22.2 - - - +
46A GLY* 1.3 75.6 - - - +
48A ASN* 1.3 60.6 + - - +
49A TYR* 4.1 9.7 - - - +
50A ASN* 3.3 19.1 + - - +
51A ASN* 3.0 27.7 + - - +
78A MET* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY 3.6 1.2 + - - +
47A THR* 1.3 73.1 - - - +
49A TYR* 1.3 59.4 + - - +
52A GLY* 2.8 30.7 + - - +
78A MET* 5.6 0.8 - - - +
81A ALA* 3.4 8.1 - - - +
82A ASN* 2.8 40.4 + - - +
85A TYR* 3.5 40.7 - - + -
108A LEU* 4.1 11.3 + - - +
109A THR* 3.1 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 3.2 9.3 - - - +
48A ASN* 1.3 79.5 - - - +
50A ASN* 1.3 74.2 + - - +
53A PRO* 3.3 22.0 - - - +
85A TYR* 4.6 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TRP* 3.3 41.2 + - + -
43A ASP* 2.8 35.1 + - + +
47A THR* 3.3 8.7 + - - +
48A ASN 3.2 0.4 - - - -
49A TYR* 1.3 94.7 - - - +
51A ASN* 1.3 65.5 + - - +
52A GLY 3.5 0.2 - - - -
53A PRO* 3.6 8.3 - - - +
54A VAL* 3.4 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS* 5.3 0.4 - - - -
11A GLY 6.3 0.8 - - - -
41A PHE* 3.0 55.8 - - + +
42A TRP* 5.1 0.7 + - - -
43A ASP* 3.4 24.6 + - - +
46A GLY* 3.4 18.2 - - - -
47A THR 3.0 15.9 + - - +
50A ASN* 1.3 75.4 - - - +
52A GLY* 1.3 67.3 + - - +
54A VAL* 3.2 1.7 + - - +
55A LEU* 2.9 22.0 + - - +
82A ASN* 3.0 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 2.8 21.5 + - - +
51A ASN* 1.3 75.0 - - - +
53A PRO* 1.3 65.4 - - - +
55A LEU* 3.1 5.7 + - - +
56A SER 2.9 19.4 + - - -
82A ASN* 4.8 7.8 + - - -
85A TYR* 3.9 10.3 - - - -
86A TYR* 4.6 1.8 - - - -
90A LEU* 3.3 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN 3.8 1.8 - - - +
49A TYR 3.3 23.6 - - - +
50A ASN 3.6 6.7 - - - +
52A GLY* 1.3 90.2 - - - +
54A VAL* 1.3 59.6 + - - +
56A SER* 3.4 5.3 + - - -
57A ARG* 3.1 49.2 + - - +
85A TYR* 4.7 3.6 - - + +
90A LEU* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 4.2 12.6 - - + -
40A ASP 4.6 7.4 - - - +
41A PHE* 3.7 22.4 - - + -
42A TRP* 3.9 26.9 - - + +
50A ASN 3.4 16.4 + - - +
51A ASN* 3.2 7.8 + - - +
52A GLY 3.2 1.0 - - - -
53A PRO* 1.3 76.0 - - - +
55A LEU* 1.3 63.6 + - - +
57A ARG* 3.4 26.0 + - - +
58A PHE* 3.0 21.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
7A VAL* 4.0 9.4 - - + -
9A VAL* 4.0 29.6 - - + -
39A VAL* 4.9 7.0 - - + -
41A PHE* 4.0 7.6 - - + -
51A ASN 2.9 17.5 + - - +
52A GLY 3.5 3.8 - - - +
54A VAL* 1.3 76.2 - - - +
56A SER* 1.3 65.1 + - - +
58A PHE* 3.1 5.6 + - + +
59A VAL* 2.9 43.5 + - + +
73A ILE* 5.0 3.8 - - + -
82A ASN* 4.0 7.6 - - + +
83A THR* 3.9 35.2 - - - +
86A TYR* 3.9 24.0 - - + -
----------------------------------------------------------
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 GLY 2.9 13.3 + - - -
53A PRO* 3.5 12.6 - - - -
55A LEU* 1.3 76.6 - - - +
57A ARG* 1.3 58.1 + - - +
59A VAL* 3.4 2.1 + - - +
60A GLN* 3.0 28.9 + - - +
86A TYR* 3.4 21.3 + - - -
90A LEU* 4.3 5.2 - - - -
91A ASP* 2.5 33.7 + - - +
95A LYS* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TRP* 5.6 1.0 - - - +
53A PRO* 3.1 36.0 + - - +
54A VAL* 3.5 34.1 - - - +
56A SER* 1.3 79.4 - - - +
58A PHE* 1.3 65.8 + - - +
60A GLN* 3.4 7.1 + - - +
61A LYS* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.9 24.5 - - + -
37A TYR* 3.6 35.9 - + + -
38A ALA 3.7 18.2 - - - -
39A VAL* 3.9 37.9 - - + -
40A ASP 5.3 0.4 - - - -
54A VAL* 3.0 14.3 + - + +
55A LEU* 3.1 8.9 + - - +
57A ARG* 1.3 77.0 - - - +
59A VAL* 1.3 62.1 + - - +
61A LYS* 3.1 25.7 + - + +
62A VAL* 3.0 31.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
7A VAL* 4.3 15.0 - - + -
55A LEU* 2.9 37.6 + - + +
56A SER 3.7 0.7 - - - +
58A PHE* 1.3 75.1 - - - +
60A GLN* 1.3 64.3 + - - +
62A VAL* 3.1 9.9 + - - +
63A LEU* 2.9 37.2 + - + +
71A VAL* 3.9 26.0 - - + -
73A ILE* 5.0 2.2 - - + -
86A TYR* 3.2 36.3 - - + +
95A LYS* 4.4 3.4 - - + -
----------------------------------------------------------
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 SER* 3.0 18.0 + - - +
57A ARG* 3.7 7.6 - - - +
59A VAL* 1.3 76.9 - - - +
61A LYS* 1.3 62.4 + - - +
63A LEU* 3.3 10.2 + - - +
64A ASP* 2.8 63.2 + - - +
91A ASP* 4.2 6.1 + - - +
95A LYS* 3.6 34.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
37A TYR* 4.5 17.6 - - - -
57A ARG 3.0 13.2 + - - +
58A PHE* 3.1 27.8 + - + +
60A GLN* 1.3 78.2 - - - +
62A VAL* 1.3 57.4 + - + +
64A ASP* 3.3 7.1 + - - +
65A GLU* 2.8 76.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
5A PRO* 3.7 30.5 - - + -
7A VAL* 4.0 15.7 - - + -
37A TYR* 3.9 40.2 - - + -
58A PHE* 3.0 21.8 + - + +
59A VAL* 3.4 8.3 - - - +
61A LYS* 1.3 80.3 - - + +
63A LEU* 1.3 60.4 + - - +
65A GLU* 4.8 4.9 - - - -
66A THR* 2.8 33.6 + - + +
71A VAL* 4.0 11.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
59A VAL* 2.9 23.9 + - + +
60A GLN* 3.7 15.9 - - - +
62A VAL* 1.3 74.4 - - - +
64A ASP* 1.3 55.9 + - - +
66A THR* 3.8 2.7 - - - -
67A GLY* 2.7 35.2 + - - -
68A ALA* 3.4 25.4 + - + +
69A LYS 4.0 5.8 - - - +
70A LYS 3.7 18.8 - - - +
71A VAL* 3.5 25.1 - - + -
95A LYS* 3.8 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 2.8 46.4 + - - +
61A LYS* 3.7 5.9 - - - +
63A LEU* 1.3 79.7 - - - +
65A GLU* 1.3 63.5 + - + +
66A THR 3.4 0.5 + - - -
67A GLY* 3.8 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 4.6 11.0 + - - +
61A LYS* 2.8 62.9 + - + +
62A VAL* 4.2 2.6 - - - +
64A ASP* 1.3 78.9 - - + +
66A THR* 1.3 62.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 3.6 22.6 - - + +
35A LYS* 5.1 19.4 + - + -
37A TYR* 3.4 26.0 - - + +
62A VAL* 2.8 24.7 + - + +
63A LEU 3.5 0.3 + - - -
65A GLU* 1.3 79.9 - - - +
67A GLY* 1.3 64.4 + - - +
68A ALA* 3.1 22.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
63A LEU 2.7 11.5 + - - -
64A ASP* 3.8 6.2 + - - -
65A GLU 3.7 1.0 - - - -
66A THR* 1.3 77.9 - - - +
68A ALA* 1.3 63.6 + - - +
69A LYS* 5.0 8.8 + - - +
----------------------------------------------------------
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