Contacts of the helix formed by residues 49 - 70 (chain Z) in PDB entry 5A0Q
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 ALA 49 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Z VAL* 6.5 0.2 - - + -
45Z MET* 3.5 23.7 - - + +
47Z GLY 3.5 1.4 + - - -
48Z GLY* 1.3 73.6 - - - +
50Z ALA* 1.4 62.3 + - - +
51Z ASP 3.4 0.2 + - - -
52Z CYS 3.6 0.3 + - - -
53Z SER* 3.6 6.6 + - - -
300Z KNM 3.2 71.1 + - + +
125a ASP* 5.9 0.7 - - - +
129a SER* 5.3 7.4 - - - -
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Residues in contact with ALA 50 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Z GLY 3.4 0.2 - - - -
49Z ALA* 1.4 75.4 - - - +
51Z ASP* 1.3 62.2 + - - +
53Z SER* 2.9 17.6 + - - -
54Z PHE 3.1 4.3 + - - -
300Z KNM 5.5 0.6 + - - -
97a TYR* 1.8 51.9 + - + +
100a ARG* 3.2 18.8 - - - +
125a ASP* 5.1 1.5 + - - +
127a VAL* 3.6 13.9 - - + +
128a GLY 3.4 20.2 - - - +
129a SER* 5.7 1.3 - - - -
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Residues in contact with ASP 51 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Z GLY* 3.6 19.4 - - - +
49Z ALA 3.3 0.6 - - - -
50Z ALA* 1.3 77.8 - - - +
52Z CYS* 1.3 57.1 + - - +
54Z PHE* 3.7 0.7 - - - +
55Z TRP* 2.7 51.9 + - + +
94Z GLY 4.8 1.6 - - - +
95Z LEU* 3.4 29.7 - - - +
96Z SER 3.3 21.1 + - - +
97Z MET* 3.7 8.5 - - + -
97a TYR* 3.8 5.0 - - - -
100a ARG* 3.1 26.1 + - - -
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Residues in contact with CYS 52 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Z THR 4.2 0.7 - - - +
45Z MET* 3.6 36.8 - - + -
46Z ALA 3.0 32.1 - - - -
48Z GLY 3.1 14.8 - - - -
49Z ALA 3.6 0.2 + - - -
50Z ALA 3.3 0.2 - - - -
51Z ASP* 1.3 73.3 - - - +
53Z SER* 1.4 65.4 + - - +
55Z TRP* 4.6 0.7 - - - -
56Z GLU* 2.8 40.5 + - - +
97Z MET* 3.6 20.6 - - - -
99Z THR* 5.7 2.0 - - - -
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Residues in contact with SER 53 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Z ILE* 4.7 12.1 - - - +
45Z MET* 4.0 12.0 - - - +
49Z ALA 3.6 7.9 + - - -
50Z ALA* 2.9 24.0 + - - -
52Z CYS* 1.4 77.3 - - - +
54Z PHE* 1.3 55.0 + - - +
56Z GLU* 3.6 3.2 - - - +
57Z ARG* 2.8 45.0 + - - +
93a SER* 6.0 0.9 - - - -
97a TYR* 3.8 5.0 + - - -
128a GLY 4.4 5.9 + - - -
130a TYR* 5.3 14.2 - - - -
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Residues in contact with PHE 54 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101S PHE* 3.6 31.4 - + - -
50Z ALA 3.1 13.6 + - - +
51Z ASP* 3.7 3.4 - - - +
53Z SER* 1.3 78.3 + - - +
55Z TRP* 1.3 88.6 + + + +
57Z ARG* 3.2 10.5 + - - +
58Z LEU* 3.0 51.3 + - + +
93a SER 5.6 0.2 - - - -
94a THR* 4.1 16.8 - - + -
97a TYR* 3.7 52.9 - + + -
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Residues in contact with TRP 55 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Z ASP* 2.7 34.6 + - - +
52Z CYS* 4.3 1.3 - - - +
54Z PHE* 1.3 103.5 - + + +
56Z GLU* 1.3 61.1 + - + +
58Z LEU* 3.2 20.0 + - + +
59Z LEU* 2.8 27.2 + - - +
83Z LEU* 4.8 13.8 - - + +
86Z MET* 5.2 12.1 - - + +
87Z VAL* 4.7 7.4 - - + -
90Z TYR* 3.9 31.9 - + - -
95Z LEU* 2.4 39.9 - - + +
97Z MET* 2.8 47.5 - - + +
97a TYR* 6.1 3.1 - + - -
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Residues in contact with GLU 56 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Z ILE* 3.3 35.1 - - + +
36Z GLU 4.7 1.7 - - - +
37Z ILE* 3.8 9.9 - - + +
43Z GLY* 3.2 8.5 - - - -
44Z THR 2.6 44.2 + - - +
52Z CYS* 2.8 29.1 + - - +
53Z SER 3.6 2.0 - - - +
55Z TRP* 1.3 76.7 - - + +
57Z ARG* 1.4 58.6 + - - +
59Z LEU* 3.6 16.4 - - + +
60Z ALA* 3.0 25.8 + - - +
83Z LEU* 5.4 2.9 - - + -
97Z MET* 6.5 0.2 - - - -
99Z THR* 3.0 19.1 + - - +
101Z ILE* 5.5 0.2 - - - +
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Residues in contact with ARG 57 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100S TRP* 3.1 47.4 + - + -
101S PHE* 3.0 53.0 + - + -
104S ASN* 4.0 8.1 - - - +
35Z ILE* 6.1 3.6 - - + -
53Z SER* 2.8 28.2 + - - +
54Z PHE* 3.2 11.0 + - - +
56Z GLU* 1.4 73.2 - - - +
58Z LEU* 1.4 60.9 + - - +
59Z LEU 3.2 0.2 - - - -
60Z ALA* 3.4 5.3 + - - +
61Z ARG* 3.0 28.6 + - - +
90a ALA* 3.8 27.9 + - - +
93a SER* 5.3 5.2 - - - -
94a THR* 4.7 6.5 - - - +
130a TYR* 3.3 27.3 + - - +
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Residues in contact with LEU 58 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101S PHE* 3.6 19.5 - - + -
54Z PHE* 3.0 59.0 + - + +
55Z TRP* 3.5 20.9 - - + +
57Z ARG* 1.4 73.3 - - - +
59Z LEU* 1.3 58.7 + - - +
61Z ARG* 3.4 19.7 + - - +
62Z GLN* 2.9 37.4 + - - +
86Z MET* 4.5 27.1 - - + -
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Residues in contact with LEU 59 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Z ILE* 4.5 18.2 - - + -
55Z TRP 2.8 16.7 + - - +
56Z GLU* 3.8 14.1 - - + +
58Z LEU* 1.3 77.9 - - - +
60Z ALA* 1.4 55.8 + - - +
62Z GLN* 3.3 5.5 + - + +
63Z CYS* 2.9 45.1 + - - -
79Z ALA 3.8 11.0 - - - +
82Z LEU* 4.4 9.2 - - + +
83Z LEU* 3.7 59.5 - - + +
86Z MET* 5.3 7.6 - - - -
101Z ILE* 4.0 16.2 - - + -
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Residues in contact with ALA 60 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100S TRP* 5.0 14.4 - - + -
36Z GLU 4.4 4.3 - - - +
37Z ILE* 4.2 33.2 - - + +
56Z GLU 3.0 19.3 + - - +
57Z ARG* 3.4 8.5 + - - +
59Z LEU* 1.4 75.1 - - - +
61Z ARG* 1.4 57.2 + - - +
63Z CYS* 3.6 3.5 + - - +
64Z ARG* 3.0 28.6 + - - +
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Residues in contact with ARG 61 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94S VAL 5.4 0.4 - - - -
97S GLN* 3.7 32.9 - - + +
98S ASN* 3.6 26.8 + - - +
100S TRP* 6.0 4.4 - - + -
101S PHE* 3.5 54.7 - - + +
57Z ARG 3.0 16.5 + - - +
58Z LEU* 3.5 22.3 - - - +
60Z ALA* 1.4 75.9 - - - +
62Z GLN* 1.3 70.0 + - - +
64Z ARG* 3.1 7.2 + - - +
65Z ILE* 2.9 46.0 + - + +
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Residues in contact with GLN 62 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Z LEU* 2.9 23.7 + - + +
59Z LEU* 4.0 6.3 - - + +
61Z ARG* 1.3 94.1 - - - +
63Z CYS* 1.3 63.6 + - - +
65Z ILE* 4.0 22.6 - - - +
66Z TYR* 3.1 23.9 + - - +
69Z ARG* 5.1 4.9 + - - -
82Z LEU* 4.5 21.6 - - + +
86Z MET* 4.0 28.7 - - + +
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Residues in contact with CYS 63 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Z ILE* 4.0 27.6 - - + +
38Z ASN* 5.4 2.7 - - - +
59Z LEU* 2.9 38.0 + - - +
60Z ALA* 3.9 6.3 - - - +
62Z GLN* 1.3 75.5 - - - +
64Z ARG* 1.3 56.9 + - - +
66Z TYR* 3.5 4.2 + - - +
67Z GLU* 2.9 34.1 + - - +
74Z ILE* 3.8 43.7 - - + +
79Z ALA* 4.6 4.0 - - - -
82Z LEU* 6.0 0.9 - - - -
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Residues in contact with ARG 64 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71S ASP* 3.4 17.9 + - - +
72S ALA* 3.0 40.8 - - - +
73S HIS* 5.3 0.2 + - - -
97S GLN* 3.2 37.0 + - - +
100S TRP* 4.5 19.2 - - - +
106S THR* 5.1 8.9 - - - +
60Z ALA 3.0 19.1 + - - +
61Z ARG 3.5 4.9 - - - +
63Z CYS* 1.3 74.6 - - - +
65Z ILE* 1.3 63.1 + - - +
67Z GLU* 3.3 21.6 + - - +
68Z LEU* 3.2 35.6 + - + +
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Residues in contact with ILE 65 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93S ARG* 4.7 7.6 - - + +
94S VAL* 4.3 27.4 - - + +
97S GLN* 3.6 22.7 - - + -
61Z ARG* 2.9 39.5 + - + +
62Z GLN* 4.0 21.5 - - - +
64Z ARG* 1.3 75.0 - - - +
66Z TYR* 1.3 62.7 + - - +
68Z LEU* 3.5 6.8 + - + +
69Z ARG* 3.1 63.8 + - + +
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Residues in contact with TYR 66 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94R HIS* 5.0 4.0 + - - -
98R VAL* 3.8 34.3 - - + +
106R TYR* 6.0 3.1 - + - -
62Z GLN 3.1 18.3 + - - +
63Z CYS* 3.5 5.8 - - - +
65Z ILE* 1.3 76.7 - - - +
67Z GLU* 1.3 64.7 + - - +
69Z ARG* 4.5 9.4 - - - +
70Z ASN* 2.9 64.9 + - + +
72Z GLU* 4.0 6.2 + - - -
73Z ARG 3.6 25.6 + - - -
74Z ILE* 3.6 34.1 - - + -
75Z SER 5.4 0.3 + - - -
78Z ALA* 5.3 1.8 - - + +
82Z LEU* 5.5 6.1 - - + -
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Residues in contact with GLU 67 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69S GLU* 4.0 4.7 - - - +
37Z ILE 5.5 2.8 - - - +
38Z ASN* 4.5 15.7 + - - +
39Z PRO* 6.1 0.7 - - - +
40Z TYR* 5.5 4.4 + - - +
63Z CYS* 2.9 15.7 + - - +
64Z ARG* 3.4 35.9 + - - +
66Z TYR* 1.3 78.6 - - + +
68Z LEU* 1.4 72.2 + - + +
71Z LYS* 3.4 18.5 - - - -
72Z GLU 3.4 21.4 + - - +
73Z ARG* 5.2 4.3 - - - -
74Z ILE* 5.3 2.2 - - + +
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Residues in contact with LEU 68 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69S GLU* 3.5 35.1 - - + +
70S ILE 3.3 26.9 - - - +
71S ASP* 4.9 4.5 - - - -
72S ALA* 5.4 0.7 - - - +
93S ARG* 3.0 45.8 + - + +
97S GLN* 4.3 8.3 - - + +
64Z ARG* 3.2 39.2 + - + +
65Z ILE* 3.7 7.0 - - - +
66Z TYR 3.2 0.4 - - - -
67Z GLU* 1.4 85.5 - - + +
69Z ARG* 1.3 61.9 + - - +
71Z LYS* 3.4 14.8 - - - +
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Residues in contact with ARG 69 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106R TYR* 5.6 5.4 + - + -
109R ARG* 3.2 21.0 + - - +
90S ASP* 3.5 36.1 - - - +
93S ARG* 4.1 16.9 + - - +
94S VAL* 4.8 10.9 - - - +
62Z GLN* 5.1 5.5 + - - -
65Z ILE* 3.1 44.7 + - + +
66Z TYR* 4.3 6.9 - - - +
68Z LEU* 1.3 75.5 - - - +
70Z ASN* 1.3 63.9 + - - +
71Z LYS* 3.1 11.2 + - - +
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Residues in contact with ASN 70 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94R HIS* 5.1 4.4 + - - -
103R THR* 5.0 7.8 - - - +
106R TYR* 3.8 18.4 - - + +
109R ARG* 3.6 31.7 + - - +
66Z TYR* 2.9 52.0 + - + +
69Z ARG* 1.3 77.2 - - - +
71Z LYS* 1.4 63.7 + - - +
72Z GLU* 3.1 33.6 - - - +
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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