Contacts of the helix formed by residues 47 - 67 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ASP* 3.0 22.1 + - - +
45G THR* 3.3 17.9 - - - +
46G GLY* 1.3 76.3 - - - +
48G ASN* 1.3 63.0 + - - +
49G TYR* 3.7 8.3 + - - +
50G ASN* 3.1 24.5 + - - +
51G ASN* 3.0 20.4 + - - +
78G MET* 4.6 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G GLY 3.7 0.4 + - - -
47G THR* 1.3 69.6 - - - +
49G TYR* 1.3 62.9 + - - +
52G GLY* 2.8 31.7 + - - +
78G MET* 4.1 9.1 - - - +
81G ALA* 3.4 19.6 - - - +
82G ASN* 3.0 22.5 - - - +
85G TYR* 3.6 39.8 - - + -
108G LEU 4.1 10.1 + - - -
109G THR* 3.0 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G THR* 3.3 8.0 - - - +
48G ASN* 1.3 79.1 - - - +
50G ASN* 1.3 83.5 + - - +
53G PRO* 3.3 22.4 - - + +
85G TYR* 4.6 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G TRP* 3.4 38.6 + - + -
43G ASP* 3.0 31.4 + - + +
47G THR* 3.1 16.7 + - - +
49G TYR* 1.3 101.6 - - - +
51G ASN* 1.3 63.4 + - - +
53G PRO* 3.7 7.4 - - - +
54G VAL* 3.4 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 51 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G HIS* 5.4 0.6 - - - -
11G GLY 6.2 1.0 - - - -
41G PHE* 3.2 46.1 - - + +
42G TRP* 5.0 0.9 + - - -
43G ASP* 3.4 22.4 + - - +
46G GLY* 3.3 21.3 - - - -
47G THR 3.0 15.5 + - - +
50G ASN* 1.3 77.2 - - - +
52G GLY* 1.3 67.4 + - - +
54G VAL* 3.2 2.1 + - - +
55G LEU* 2.9 22.5 + - - +
82G ASN* 3.0 34.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ASN* 2.8 20.7 + - - +
51G ASN* 1.3 73.0 - - - +
53G PRO* 1.3 61.0 - - - +
55G LEU* 3.2 5.7 + - - +
56G SER 2.9 24.1 + - - -
82G ASN* 4.8 9.6 - - - +
85G TYR* 4.0 10.5 - - - -
86G TYR* 4.6 2.3 - - - -
90G LEU* 3.3 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ASN 3.9 1.6 - - - +
49G TYR* 3.3 25.8 - - + +
50G ASN 3.7 4.7 - - - +
51G ASN 3.7 1.8 - - - -
52G GLY* 1.3 89.8 - - - +
54G VAL* 1.3 55.8 + - - +
56G SER* 3.3 7.8 + - - -
57G ARG* 3.0 56.2 + - - +
85G TYR* 4.9 3.1 - - + -
90G LEU* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G VAL* 4.2 12.1 - - + -
40G ASP 4.2 9.0 - - - +
41G PHE* 3.8 22.0 - - + -
42G TRP* 3.8 25.1 - - + +
50G ASN 3.4 18.4 - - - +
51G ASN* 3.2 9.1 + - - +
53G PRO* 1.3 77.1 - - - +
55G LEU* 1.3 59.0 + - - +
57G ARG* 3.6 25.5 - - - +
58G PHE* 3.0 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 3.9 9.9 - - + -
9G VAL* 3.7 29.2 - - + -
39G VAL* 4.6 8.5 - - + -
41G PHE* 4.0 10.9 - - + -
51G ASN 2.9 16.3 + - - +
52G GLY 3.6 4.0 - - - +
54G VAL* 1.3 73.8 - - - +
56G SER* 1.3 66.4 + - - +
58G PHE* 3.3 5.3 + - + +
59G VAL* 2.9 43.3 + - + +
73G ILE* 5.0 2.9 - - + -
82G ASN* 4.0 6.1 - - + +
83G THR* 4.0 26.0 - - - +
86G TYR* 3.9 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G GLY 2.9 14.1 + - - -
53G PRO* 3.4 11.0 - - - -
54G VAL 3.3 0.2 - - - -
55G LEU* 1.3 78.0 - - - +
57G ARG* 1.3 64.6 + - - +
59G VAL* 3.4 2.4 + - - +
60G GLN* 3.1 24.5 + - - +
86G TYR* 3.5 19.5 + - - -
90G LEU* 4.1 7.6 - - - -
91G ASP* 2.6 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G TRP* 5.6 1.0 - - - +
53G PRO* 3.0 38.5 + - - +
54G VAL* 3.6 33.7 - - - +
56G SER* 1.3 77.3 - - - +
58G PHE* 1.3 58.6 + - - +
60G GLN* 3.4 7.5 + - - +
61G LYS* 3.0 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 3.9 24.9 - - + -
37G TYR* 3.6 40.4 - + + -
38G ALA 3.8 16.4 - - - -
39G VAL* 3.9 35.9 - - + -
40G ASP 5.5 0.2 - - - -
54G VAL* 3.0 17.9 + - + +
55G LEU* 3.6 5.8 - - - +
57G ARG* 1.3 77.6 - - - +
59G VAL* 1.3 61.2 + - - +
61G LYS* 3.2 20.2 + - + +
62G VAL* 3.0 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 4.1 17.0 - - + -
55G LEU* 2.9 36.7 + - + +
56G SER 3.9 0.4 - - - +
58G PHE* 1.3 75.1 - - - +
60G GLN* 1.3 63.6 + - - +
62G VAL* 3.1 9.2 + - - +
63G LEU* 2.9 34.1 + - + +
71G VAL* 3.7 29.2 - - + -
73G ILE* 4.9 2.2 - - + -
86G TYR* 3.2 35.7 - - + +
95G LYS* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G SER* 3.1 17.5 + - - +
57G ARG* 3.7 8.1 - - - +
59G VAL* 1.3 77.5 - - - +
61G LYS* 1.3 57.9 + - - +
63G LEU* 3.4 15.4 + - - +
64G ASP* 3.0 57.2 + - - +
86G TYR* 5.1 0.2 + - - -
91G ASP* 4.4 5.6 + - - +
95G LYS* 3.5 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G TYR* 6.1 0.2 - - - -
57G ARG 3.0 14.5 + - - +
58G PHE* 3.3 23.1 - - + +
59G VAL 3.1 0.2 - - - -
60G GLN* 1.3 76.2 - - - +
62G VAL* 1.3 61.1 + - + +
64G ASP* 3.4 5.9 + - - +
65G GLU* 2.6 71.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G PRO* 3.5 32.8 - - + -
7G VAL* 4.2 7.2 - - + -
37G TYR* 3.7 42.4 - - + -
58G PHE* 3.0 30.7 + - + +
59G VAL* 3.1 8.9 + - - +
61G LYS* 1.3 77.0 - - + +
63G LEU* 1.3 57.4 + - - +
65G GLU* 3.5 5.7 + - - -
66G THR* 2.6 35.9 + - - +
71G VAL* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G VAL* 2.9 23.3 + - + +
60G GLN* 3.7 17.5 - - - +
62G VAL* 1.3 76.6 - - - +
64G ASP* 1.3 57.9 + - - +
66G THR* 3.6 2.9 + - - -
67G GLY* 2.8 31.5 + - - -
68G ALA* 3.4 26.0 + - + +
69G LYS 3.7 6.5 - - - +
70G LYS* 3.6 18.6 - - - +
71G VAL* 3.5 25.8 - - + -
95G LYS* 3.8 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G GLN* 3.0 45.7 + - - +
61G LYS* 3.8 7.2 - - - +
63G LEU* 1.3 79.2 - - - +
65G GLU* 1.3 61.9 + - + +
66G THR 3.4 0.7 + - - -
67G GLY* 3.8 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G TYR* 3.9 27.6 + - - +
61G LYS* 2.6 66.7 + - + +
62G VAL* 4.1 2.6 - - - +
63G LEU 3.4 0.2 - - - -
64G ASP* 1.3 77.9 - - + +
66G THR* 1.3 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G PRO* 3.6 21.3 - - + +
35G LYS* 4.1 19.4 - - + -
37G TYR* 3.4 26.7 - - + +
62G VAL 2.6 21.9 + - - +
63G LEU 3.6 0.7 + - - -
65G GLU* 1.3 79.0 - - - +
67G GLY* 1.3 63.1 + - - +
68G ALA* 3.1 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G LEU 2.8 11.2 + - - -
64G ASP 3.8 5.3 + - - -
65G GLU 3.7 1.2 - - - -
66G THR* 1.3 78.3 - - - +
68G ALA* 1.3 65.3 + - - +
69G LYS* 3.8 4.9 + - - +
----------------------------------------------------------
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