Contacts of the helix formed by residues 47 - 67 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F ASP* 2.7 19.3 + - - +
45F THR* 3.4 20.6 - - - +
46F GLY* 1.3 75.8 - - - +
48F ASN* 1.3 58.7 + - - +
49F TYR* 3.9 9.1 + - - +
50F ASN* 3.1 19.4 + - - +
51F ASN* 2.9 27.4 + - - +
78F MET* 5.7 2.0 - - - -
82F ASN* 3.9 0.2 - - - -
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Residues in contact with ASN 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F GLY 3.5 0.8 + - - -
47F THR* 1.3 73.7 - - - +
49F TYR* 1.3 63.5 + - - +
52F GLY 2.9 21.7 + - - +
78F MET* 6.0 1.5 - - - -
81F ALA* 3.2 7.1 - - - +
82F ASN* 2.8 44.6 + - - +
85F TYR* 3.4 44.1 - - + -
108F LEU* 4.6 6.3 + - - +
109F THR* 2.9 26.1 + - - +
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Residues in contact with TYR 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F THR* 3.1 9.3 - - - +
48F ASN* 1.3 78.6 - - - +
50F ASN* 1.3 75.8 + - - +
53F PRO* 3.3 20.8 - - - +
85F TYR* 4.4 15.6 + - - -
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Residues in contact with ASN 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F TRP* 3.3 36.3 + - + -
43F ASP* 2.8 41.7 + - + +
47F THR* 3.1 9.5 + - - +
48F ASN 3.2 0.2 - - - -
49F TYR* 1.3 98.9 - - - +
51F ASN* 1.3 62.6 + - - +
52F GLY 3.5 0.2 - - - -
53F PRO* 3.5 8.4 - - - +
54F VAL* 3.1 22.5 + - - +
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Residues in contact with ASN 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F HIS* 5.3 0.6 + - - -
11F GLY 5.8 1.4 + - - -
41F PHE* 3.2 44.0 - - + +
42F TRP* 5.1 0.7 + - - -
43F ASP* 3.5 23.2 + - - +
46F GLY* 3.3 17.8 - - - -
47F THR 2.9 21.8 + - - +
50F ASN* 1.3 73.3 - - - +
52F GLY* 1.3 65.5 + - - +
54F VAL* 3.1 2.9 + - - +
55F LEU* 2.8 26.8 + - - +
82F ASN* 2.9 35.2 - - - +
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Residues in contact with GLY 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F ASN* 2.9 21.9 + - - +
51F ASN* 1.3 73.7 - - - +
53F PRO* 1.3 59.8 - - - +
55F LEU* 3.2 6.3 + - - +
56F SER 2.9 24.1 + - - -
82F ASN* 4.7 8.9 - - - +
85F TYR* 3.9 10.8 - - - -
86F TYR* 4.4 2.9 - - - -
90F LEU* 3.3 21.0 - - - +
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Residues in contact with PRO 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F ASN 3.9 1.8 - - - +
49F TYR 3.3 24.5 - - - +
50F ASN* 3.5 8.7 - - - +
52F GLY* 1.3 89.4 - - - +
54F VAL* 1.3 60.7 + - - +
56F SER* 3.2 6.0 + - - -
57F ARG* 3.0 47.5 + - - +
85F TYR* 4.8 2.9 - - + +
90F LEU* 4.0 16.8 - - + -
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Residues in contact with VAL 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F VAL* 4.3 5.2 - - + -
40F ASP 3.6 16.6 - - - +
41F PHE* 3.6 24.2 - - + -
42F TRP* 3.5 29.8 - - + +
50F ASN 3.1 20.4 - - - +
51F ASN* 3.1 8.4 + - - +
53F PRO* 1.3 75.3 - - - +
55F LEU* 1.3 63.5 + - - +
57F ARG* 3.3 23.3 + - - +
58F PHE* 3.0 22.9 + - + +
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 4.2 10.5 - - + -
9F VAL* 3.9 24.7 - - + -
39F VAL* 4.5 11.9 - - + -
41F PHE* 4.0 8.7 - - + -
51F ASN 2.8 20.3 + - - +
52F GLY 3.5 4.5 - - - +
54F VAL* 1.3 74.5 - - - +
56F SER* 1.3 57.8 + - - +
58F PHE* 4.3 3.8 - - + -
59F VAL* 2.9 47.5 + - + +
73F ILE* 5.2 2.9 - - + -
82F ASN* 3.9 8.5 - - + +
83F THR* 3.7 27.6 - - + +
86F TYR* 3.7 34.1 - - + -
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Residues in contact with SER 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F GLY 2.9 12.9 + - - -
53F PRO* 3.4 13.9 - - - -
54F VAL 3.2 0.4 - - - -
55F LEU* 1.3 78.5 - - - +
57F ARG* 1.3 62.5 + - - +
59F VAL* 3.9 1.9 - - - +
60F GLN* 3.1 23.7 + - - +
86F TYR* 3.5 18.2 + - - -
90F LEU* 4.3 4.7 - - - -
91F ASP* 2.5 33.7 + - - +
95F LYS* 6.0 0.2 - - - +
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Residues in contact with ARG 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F TRP* 4.7 5.9 - - - +
53F PRO* 3.0 36.6 + - - +
54F VAL* 3.5 34.8 - - - +
56F SER* 1.3 78.1 - - - +
58F PHE* 1.3 57.9 + - - +
60F GLN* 3.4 6.4 + - - +
61F LYS* 3.0 27.9 + - - +
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Residues in contact with PHE 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 3.7 24.7 - - + -
37F TYR* 3.7 32.3 - + + -
38F ALA 3.4 25.4 - - - -
39F VAL* 3.7 34.8 - - + -
40F ASP* 4.9 2.7 - - - -
54F VAL* 3.0 17.3 + - + +
55F LEU* 3.7 4.3 - - + +
56F SER 3.3 0.2 - - - -
57F ARG* 1.3 74.2 - - - +
59F VAL* 1.3 65.5 + - - +
61F LYS* 3.2 20.1 + - + +
62F VAL* 3.0 34.8 + - + +
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Residues in contact with VAL 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 4.5 9.0 - - + -
55F LEU* 2.9 35.8 + - + +
56F SER 3.9 1.3 - - - +
58F PHE* 1.3 76.8 - - - +
60F GLN* 1.3 64.4 + - - +
62F VAL* 3.0 11.1 + - - +
63F LEU* 3.0 31.8 + - + +
71F VAL* 3.8 33.7 - - + -
73F ILE* 4.7 2.2 - - + -
86F TYR* 3.2 38.1 - - + +
95F LYS* 4.4 4.7 - - + -
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Residues in contact with GLN 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F SER 3.1 18.1 + - - +
57F ARG* 3.6 7.6 - - - +
59F VAL* 1.3 77.5 - - - +
61F LYS* 1.3 57.7 + - - +
63F LEU* 3.3 16.5 + - - +
64F ASP* 2.8 62.7 + - - +
86F TYR* 5.2 0.2 + - - -
91F ASP* 4.4 4.3 + - - +
95F LYS* 3.3 33.7 - - + +
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Residues in contact with LYS 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F TYR* 6.1 0.4 - - - -
57F ARG 3.0 13.6 + - - +
58F PHE* 3.3 25.4 - - + +
59F VAL 3.1 0.2 - - - -
60F GLN* 1.3 77.1 - - - +
62F VAL* 1.3 63.6 + - + +
64F ASP* 3.2 11.5 + - + +
65F GLU* 2.5 58.2 + - + +
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Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F PRO* 3.6 31.4 - - + -
7F VAL* 3.9 9.9 - - + -
37F TYR* 3.8 40.2 - - + -
58F PHE* 3.0 31.4 + - + +
59F VAL 3.4 7.0 - - - +
61F LYS* 1.3 78.6 - - + +
63F LEU* 1.3 61.7 + - - +
65F GLU* 3.2 4.6 + - - -
66F THR* 2.8 27.7 + - - +
71F VAL* 3.9 13.7 - - + -
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Residues in contact with LEU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F VAL* 3.0 19.7 + - + +
60F GLN* 3.6 20.9 - - - +
62F VAL* 1.3 75.7 - - - +
64F ASP* 1.3 60.1 + - - +
66F THR* 3.8 3.8 - - - +
67F GLY* 2.9 31.5 + - - -
68F ALA* 3.3 26.1 - - + +
69F LYS 3.9 6.7 - - - +
70F LYS* 3.8 17.5 - - - +
71F VAL* 3.6 24.9 - - + -
95F LYS* 3.8 37.0 - - + +
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Residues in contact with ASP 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F GLN* 2.8 52.3 + - - +
61F LYS* 3.4 10.8 - - + +
63F LEU* 1.3 76.7 - - - +
65F GLU* 1.3 59.9 + - + +
67F GLY* 4.7 1.6 + - - -
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Residues in contact with GLU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F TYR* 3.6 30.8 + - - +
61F LYS* 2.5 56.1 + - + +
62F VAL 3.9 3.6 - - - +
63F LEU 3.1 0.2 - - - -
64F ASP* 1.3 81.6 - - + +
66F THR* 1.3 59.0 + - - +
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Residues in contact with THR 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F PRO* 3.3 33.2 - - + +
35F LYS* 5.0 12.3 - - + -
37F TYR* 3.4 29.2 - - + +
62F VAL 2.8 21.8 + - - +
63F LEU* 3.8 1.7 + - - -
65F GLU* 1.3 81.6 - - - +
67F GLY* 1.3 61.4 + - - +
68F ALA* 3.1 12.3 + - - +
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Residues in contact with GLY 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F LEU 2.9 13.0 + - - -
64F ASP 4.7 1.2 + - - -
65F GLU 3.8 0.8 - - - -
66F THR* 1.3 77.0 - - - +
68F ALA* 1.3 64.6 + - - +
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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