Contacts of the helix formed by residues 47 - 67 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ASP* 2.6 20.2 + - - +
45C THR* 3.4 21.3 - - - +
46C GLY* 1.3 79.1 - - - +
48C ASN* 1.3 59.6 + - - +
49C TYR* 4.0 9.4 - - - +
50C ASN* 3.1 21.5 + - - +
51C ASN* 2.9 27.5 + - - +
78C MET* 6.1 0.4 - - - -
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Residues in contact with ASN 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLY 3.5 1.0 + - - +
47C THR* 1.3 72.5 - - - +
49C TYR* 1.3 61.1 + - - +
52C GLY* 2.8 31.0 + - - +
78C MET* 5.4 1.7 - - - +
81C ALA* 3.3 6.2 - - - +
82C ASN* 2.8 42.9 + - - +
85C TYR* 3.6 38.3 - - + -
108C LEU* 4.2 9.5 + - - +
109C THR* 2.9 25.1 + - - +
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Residues in contact with TYR 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 4.0 9.1 - - - +
48C ASN* 1.3 79.7 - - - +
50C ASN* 1.3 75.3 + - - +
53C PRO* 3.1 22.7 - - - +
85C TYR* 4.5 15.8 + - - -
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Residues in contact with ASN 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TRP* 3.3 41.4 + - + -
43C ASP* 2.9 30.5 + - + +
47C THR* 3.1 13.9 + - - +
48C ASN 3.2 0.2 - - - -
49C TYR* 1.3 98.2 - - - +
51C ASN* 1.3 64.6 + - - +
52C GLY 3.5 0.2 - - - -
53C PRO* 3.5 8.6 - - - +
54C VAL* 3.2 22.3 + - - +
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Residues in contact with ASN 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C HIS* 5.5 0.4 - - - -
11C GLY 5.6 1.0 + - - -
41C PHE* 3.2 45.2 - - + +
42C TRP* 5.1 0.7 + - - -
43C ASP* 3.5 22.7 + - - +
46C GLY* 3.3 18.0 - - - -
47C THR 2.9 18.0 + - - +
50C ASN* 1.3 75.8 - - - +
52C GLY* 1.3 66.3 + - - +
54C VAL* 3.2 1.4 + - - +
55C LEU* 2.8 26.7 + - - +
82C ASN* 2.9 36.2 - - - +
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Residues in contact with GLY 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ASN* 2.8 21.5 + - - +
51C ASN* 1.3 72.8 - - - +
53C PRO* 1.3 65.5 - - - +
55C LEU* 3.1 6.4 + - - +
56C SER 2.9 18.7 + - - -
82C ASN* 4.7 9.7 - - - +
85C TYR* 3.9 10.8 - - - -
86C TYR* 4.5 2.3 - - - -
90C LEU* 3.3 21.1 - - - +
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Residues in contact with PRO 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ASN 3.7 1.8 - - - +
49C TYR 3.1 26.5 - - - +
50C ASN* 3.5 9.0 - - - +
52C GLY* 1.3 88.9 - - - +
54C VAL* 1.3 61.6 + - - +
56C SER* 3.3 6.2 + - - -
57C ARG* 3.0 47.6 + - - +
85C TYR* 4.8 3.1 - - + -
90C LEU* 4.1 15.0 - - + -
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Residues in contact with VAL 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 4.1 5.8 - - + -
40C ASP 3.7 23.6 - - - +
41C PHE* 3.7 14.6 - - + -
42C TRP* 3.6 26.2 - - + +
50C ASN 3.2 17.7 + - - +
51C ASN* 3.2 8.0 + - - +
53C PRO* 1.3 76.0 - - - +
55C LEU* 1.3 58.3 + - - +
57C ARG* 3.3 26.9 + - - +
58C PHE* 3.0 27.0 + - + +
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 4.1 10.3 - - + -
9C VAL* 3.9 26.0 - - + -
39C VAL* 4.4 11.9 - - + -
41C PHE* 4.1 9.1 - - + -
51C ASN 2.8 20.9 + - - +
52C GLY* 3.5 4.5 - - - +
54C VAL* 1.3 70.6 - - - +
56C SER* 1.3 60.9 + - - +
58C PHE* 3.3 4.1 + - + +
59C VAL* 2.8 47.9 + - + +
73C ILE* 5.0 3.8 - - + -
82C ASN* 4.1 6.5 - - + +
83C THR* 3.9 35.9 - - - +
86C TYR* 3.9 24.9 - - + -
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Residues in contact with SER 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLY 2.9 12.1 + - - -
53C PRO* 3.5 10.5 - - - -
55C LEU* 1.3 78.3 - - - +
57C ARG* 1.3 63.6 + - - +
59C VAL* 3.4 1.6 + - - +
60C GLN* 3.0 24.9 + - - +
86C TYR* 3.4 22.2 + - - -
90C LEU* 4.3 6.7 - - - -
91C ASP* 2.6 34.0 + - - +
95C LYS* 6.0 0.2 - - - +
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Residues in contact with ARG 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TRP* 5.1 3.0 - - - +
53C PRO* 3.0 37.5 + - - +
54C VAL* 3.4 34.8 - - - +
55C LEU 3.3 0.2 - - - -
56C SER* 1.3 77.5 - - - +
58C PHE* 1.3 58.5 + - - +
60C GLN* 3.5 6.5 + - - +
61C LYS* 3.0 27.9 + - - +
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Residues in contact with PHE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 3.9 18.4 - - + -
37C TYR* 3.6 37.5 - + + -
38C ALA 3.5 19.1 - - - -
39C VAL* 3.6 41.7 - - + -
40C ASP* 5.0 1.8 - - - -
54C VAL* 3.0 17.3 + - + +
55C LEU* 3.6 4.9 - - - +
56C SER 3.2 0.2 - - - -
57C ARG* 1.3 75.5 - - - +
59C VAL* 1.3 65.2 + - - +
61C LYS* 3.1 35.7 + - + +
62C VAL* 2.9 30.2 + - + +
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 4.5 9.4 - - + -
55C LEU* 2.8 37.5 + - + +
56C SER 3.9 1.1 - - - +
58C PHE* 1.3 72.7 - - - +
60C GLN* 1.3 63.6 + - - +
62C VAL* 3.0 9.1 + - - +
63C LEU* 2.9 34.0 + - + +
71C VAL* 3.8 32.8 - - + -
73C ILE* 5.0 3.1 - - + -
86C TYR* 3.2 39.3 - - + +
95C LYS* 4.4 4.0 - - + -
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Residues in contact with GLN 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C SER 3.0 17.4 + - - +
57C ARG* 3.7 7.2 - - - +
59C VAL* 1.3 77.2 - - - +
61C LYS* 1.3 52.6 + - - +
63C LEU* 3.3 16.3 + - - +
64C ASP* 2.8 69.5 + - - +
86C TYR* 5.0 0.2 + - - -
91C ASP* 4.4 5.2 + - - +
95C LYS* 3.3 30.5 - - + +
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Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C TYR* 4.7 11.4 - - - -
57C ARG 3.0 14.6 + - - +
58C PHE* 3.2 44.4 - - + +
59C VAL 3.1 0.2 - - - -
60C GLN* 1.3 77.5 - - - +
62C VAL* 1.3 56.8 + - + +
64C ASP* 3.2 7.4 + - - +
65C GLU* 2.9 64.3 + - + +
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PRO* 3.5 31.6 - - + -
7C VAL* 4.0 8.5 - - + -
37C TYR* 3.5 47.1 - - + -
58C PHE* 2.9 31.1 + - + +
59C VAL 3.0 7.4 + - - +
61C LYS* 1.3 78.0 - - + +
63C LEU* 1.3 56.2 + - - +
65C GLU* 4.9 0.2 - - - -
66C THR* 2.7 37.9 + - - +
71C VAL* 3.7 14.8 - - + -
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Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL* 2.9 19.9 + - + +
60C GLN* 3.5 20.4 - - - +
62C VAL* 1.3 75.4 - - - +
64C ASP* 1.3 59.1 + - - +
66C THR* 3.8 3.1 - - - -
67C GLY* 2.8 32.1 + - - -
68C ALA* 3.5 24.7 + - + +
69C LYS 3.8 18.4 - - - +
70C LYS* 3.9 5.6 - - - +
71C VAL* 3.5 25.6 - - + +
95C LYS* 3.7 40.2 - - + +
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Residues in contact with ASP 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLN* 2.8 48.3 + - - +
61C LYS* 3.2 8.3 + - - +
63C LEU* 1.3 78.1 - - - +
65C GLU* 1.3 61.8 - - + +
66C THR 3.7 0.2 + - - -
67C GLY* 4.3 3.6 + - - -
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Residues in contact with GLU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C TYR* 3.4 30.5 + - - +
61C LYS* 2.9 47.7 + - + +
62C VAL 4.2 1.3 - - - +
64C ASP* 1.3 78.6 - - + +
66C THR* 1.3 60.8 + - - +
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Residues in contact with THR 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PRO* 3.5 13.7 - - + +
35C LYS* 3.6 32.5 - - + +
37C TYR* 3.7 22.0 - - + +
62C VAL 2.7 22.7 + - - +
63C LEU 3.6 0.7 + - - -
65C GLU* 1.3 78.4 - - - +
67C GLY* 1.3 63.7 + - - +
68C ALA* 3.1 22.0 + - - +
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Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU 2.8 11.8 + - - -
64C ASP 4.3 3.8 + - - -
65C GLU 3.8 1.0 - - - -
66C THR* 1.3 77.7 - - - +
68C ALA* 1.3 63.8 + - - +
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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) + - + + + + + -
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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