Contacts of the helix formed by residues 49 - 70 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I ALA* 5.2 2.9 - - + -
31I CYS* 5.4 5.2 - - - -
47I GLY 3.4 2.8 + - - -
48I THR* 1.3 72.9 - - - +
50I ALA* 1.4 55.8 + - - +
52I THR* 2.8 15.6 - - - +
53I ASP* 2.9 19.3 + - - +
300I KNM 3.0 59.7 + - + +
124J ASP* 5.6 1.3 - - - +
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Residues in contact with ALA 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I THR* 3.3 12.7 - - + +
49I ALA* 1.4 75.2 - - - +
51I ASP* 1.3 64.3 + - - +
53I ASP* 3.4 2.9 + - - +
54I MET* 3.1 32.1 + - + +
300I KNM 4.8 0.6 + - - -
95J TYR* 4.1 15.0 - - + -
98J ARG* 5.5 4.5 - - - +
124J ASP* 4.9 16.4 + - + +
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Residues in contact with ASP 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I THR* 3.5 7.3 + - - +
49I ALA 3.4 0.2 - - - -
50I ALA* 1.3 76.4 - - - +
52I THR* 1.3 62.0 + - - +
55I THR* 2.9 35.9 + - - -
93I TYR 3.4 2.4 - - - +
94I ILE* 3.8 19.5 - - + +
95I GLY* 3.2 24.6 + - - -
96I ALA* 3.4 20.4 + - + +
95J TYR* 3.6 17.4 + - - -
98J ARG* 2.9 41.9 + - - +
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Residues in contact with THR 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I HIS* 4.6 10.0 + - + +
45I GLY* 3.0 29.0 - - - -
46I ALA 4.2 0.9 - - - -
48I THR 3.2 5.7 + - - +
49I ALA* 2.8 26.0 - - + +
51I ASP* 1.3 81.1 - - - +
53I ASP* 1.3 57.4 + - - +
55I THR* 4.3 2.1 - - - -
56I THR* 2.7 32.9 + - - -
96I ALA* 3.8 12.8 - - - -
97I ALA 4.1 0.3 + - - -
98I LEU* 3.3 13.2 - - - +
300I KNM 3.2 31.6 - - + -
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Residues in contact with ASP 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I HIS* 3.1 34.4 + - + -
49I ALA 2.9 18.5 + - - +
50I ALA* 3.9 4.9 - - - +
52I THR* 1.3 77.4 - - - +
54I MET* 1.3 63.0 + - + +
56I THR* 3.3 2.4 + - - -
57I GLN* 3.0 49.2 + - - +
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Residues in contact with MET 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I ALA* 3.1 17.6 + - - +
53I ASP* 1.3 79.0 - - + +
55I THR* 1.3 63.5 + - - +
57I GLN* 3.2 33.1 + - - +
58I LEU* 3.1 21.3 + - - +
91J ALA* 3.5 46.4 - - + +
92J ASN* 4.0 13.0 - - + +
95J TYR* 3.4 46.4 - - + -
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Residues in contact with THR 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I ASP 2.9 21.3 + - - -
52I THR* 4.3 3.1 - - - -
54I MET* 1.3 74.6 - - - +
56I THR* 1.3 61.9 + - - +
58I LEU* 3.2 9.5 + - + +
59I ILE* 3.0 22.1 + - + +
83I LEU* 4.3 8.3 - - + -
86I MET* 4.0 26.5 - - + +
87I LEU* 4.3 7.9 - - + -
90I TYR* 5.8 0.5 - - - -
94I ILE* 3.9 18.2 - - + +
98I LEU* 4.2 20.4 - - + -
95J TYR* 3.9 9.5 + - - -
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Residues in contact with THR 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I HIS* 3.6 32.4 - - + -
36I PHE 5.1 0.9 - - - -
37I ILE* 3.5 29.5 - - + +
43I CYS* 4.5 3.7 - - + -
52I THR* 2.7 24.1 + - - -
53I ASP* 3.6 4.9 - - - -
55I THR* 1.3 76.4 - - - +
57I GLN* 1.3 55.1 + - - +
59I ILE* 3.8 4.9 - - - +
60I SER* 2.8 27.5 + - - -
83I LEU* 6.3 0.2 - - - -
98I LEU* 3.4 24.6 - - - +
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Residues in contact with GLN 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 3.9 18.5 - - + +
101B GLN* 3.3 35.1 + - - +
53I ASP* 3.0 42.1 + - - +
54I MET* 3.2 36.8 + - - +
56I THR* 1.3 75.5 - - - +
58I LEU* 1.4 56.3 + - - +
60I SER* 3.5 7.0 - - - -
61I SER* 3.0 28.6 + - - -
87J MET* 6.2 1.8 - - - +
91J ALA* 6.1 0.4 - - - +
92J ASN* 5.5 0.2 - - - +
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Residues in contact with LEU 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 5.2 10.5 - - + -
54I MET 3.1 11.9 + - - +
55I THR* 3.2 12.5 + - - +
57I GLN* 1.4 73.3 - - - +
59I ILE* 1.3 61.2 + - + +
61I SER* 2.9 22.4 + - - +
62I ASN* 3.0 39.2 + - - +
86I MET* 3.6 38.4 - - + -
89I ARG* 5.9 0.4 - - - +
90I TYR* 4.8 5.6 - - - +
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Residues in contact with ILE 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I ILE* 4.0 20.4 - - + -
55I THR* 3.0 16.9 + - + +
56I THR* 4.1 3.6 - - - +
58I LEU* 1.3 73.7 - - + +
60I SER* 1.3 60.2 + - - +
62I ASN* 4.0 15.7 - - - +
63I LEU* 2.8 69.2 + - + +
79I ALA* 4.6 1.8 - - - +
82I MET* 3.8 30.5 - - + +
83I LEU* 3.7 24.5 - - + -
86I MET* 4.1 25.8 - - + -
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Residues in contact with SER 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TYR* 5.0 8.7 - - - -
36I PHE* 3.8 8.8 + - - -
37I ILE* 3.0 24.3 + - - +
56I THR* 2.8 20.2 + - - -
57I GLN* 3.5 9.0 - - - -
58I LEU 3.2 0.4 - - - -
59I ILE* 1.3 73.8 - - - +
61I SER* 1.3 61.3 + - - +
63I LEU* 4.1 0.2 - - - +
64I GLU* 2.2 66.6 + - - +
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Residues in contact with SER 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLN* 2.8 46.0 - - - +
97B TYR* 5.6 5.8 - - - -
98B LEU* 3.4 33.2 - - - +
57I GLN 3.0 11.2 + - - -
58I LEU* 2.9 18.2 + - - +
60I SER* 1.3 77.5 + - - +
62I ASN* 1.4 59.2 + - - +
64I GLU* 4.8 0.9 - - - -
65I LEU* 3.1 16.3 + - - +
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Residues in contact with ASN 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I LEU* 3.0 43.0 + - - +
59I ILE* 3.5 21.9 - - - +
60I SER 3.1 0.2 - - - -
61I SER* 1.4 77.1 + - - +
63I LEU* 1.3 65.6 + - - +
65I LEU* 3.4 9.3 + - - +
66I HIS* 3.3 21.7 + - - +
82I MET* 4.0 18.6 - - + +
86I MET* 4.7 6.5 - - - +
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Residues in contact with LEU 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I ILE* 3.4 27.6 - - + +
38I SER* 5.1 2.9 - - - -
41I ILE* 4.6 9.2 - - + -
59I ILE* 2.8 42.0 + - + +
60I SER 4.1 1.6 - - - +
62I ASN* 1.3 73.7 - - - +
64I GLU* 1.3 58.5 + - - +
66I HIS* 3.2 7.8 + - - +
67I SER* 3.1 30.6 + - - -
74I PRO* 4.5 21.6 - - + +
78I THR* 5.6 0.9 - - + -
79I ALA* 3.4 31.2 - - + +
82I MET* 2.8 45.3 - - + -
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Residues in contact with GLU 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LYS* 4.9 12.1 - - - -
94B GLN* 3.2 22.6 + - - +
97B TYR* 5.1 8.5 - - - -
36I PHE* 3.8 23.1 - - + -
37I ILE 2.9 14.7 - - - +
38I SER* 4.6 11.2 - - - +
39I PRO* 5.4 2.8 - - + +
60I SER* 2.2 43.1 + - - +
61I SER* 4.9 0.6 - - - -
63I LEU* 1.3 77.2 - - - +
65I LEU* 1.3 55.9 + - - +
67I SER* 3.6 8.0 + - - +
68I LEU* 2.9 28.9 + - - +
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Residues in contact with LEU 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B HIS 5.5 0.7 - - - +
90B ARG* 3.7 38.6 - - + +
91B LYS* 4.8 9.6 - - + +
94B GLN* 3.1 20.4 + - + +
61I SER 3.1 20.1 + - - +
62I ASN* 3.6 9.2 - - - +
63I LEU 3.2 0.2 - - - -
64I GLU* 1.3 77.4 - - - +
66I HIS* 1.3 57.5 + - - +
68I LEU* 3.5 3.9 + - + +
69I SER* 2.9 36.3 + - - +
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Residues in contact with HIS 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TRP* 3.4 20.8 - + - -
105A TYR* 3.7 43.4 - + + +
107A TYR* 2.9 29.6 + + - -
113A MET* 4.7 7.3 - - + +
62I ASN 3.3 9.2 + - - +
63I LEU* 3.2 10.7 + - - +
65I LEU* 1.3 75.7 - - - +
67I SER* 1.4 57.2 + - - +
69I SER* 3.3 7.3 + - - -
70I THR* 3.0 32.3 + - + +
72I ARG* 5.2 2.1 + - - -
74I PRO* 5.1 10.1 - - + +
78I THR* 3.8 17.9 - - + +
82I MET* 5.0 2.7 - - + +
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Residues in contact with SER 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I SER* 5.1 2.6 + - - -
63I LEU 3.1 15.8 + - - -
64I GLU* 3.6 11.8 + - - +
66I HIS* 1.4 73.6 - - - +
68I LEU* 1.3 60.6 + - - +
70I THR* 4.0 0.2 - - - -
71I GLY* 2.9 29.9 + - - -
72I ARG 3.6 23.1 + - - -
73I LEU* 4.2 7.0 - - - +
74I PRO* 3.7 26.7 - - - +
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Residues in contact with LEU 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B PRO* 3.7 37.1 - - + +
67B ILE 3.4 24.2 - - - +
68B THR* 4.6 6.1 - - - +
90B ARG* 3.3 39.2 + - + +
94B GLN* 4.8 10.1 - - + -
64I GLU 2.9 23.2 + - - +
65I LEU* 3.5 11.9 - - + +
67I SER* 1.3 77.3 + - - +
69I SER* 1.3 59.2 + - - +
71I GLY* 4.2 4.9 + - - -
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Residues in contact with SER 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A MET* 4.4 16.6 - - - +
116A LYS* 5.1 11.0 - - - +
65B GLU* 5.7 1.0 - - - +
87B HIS* 5.5 2.9 - - - -
90B ARG* 3.4 31.6 + - - +
65I LEU* 2.9 22.2 + - - +
66I HIS* 3.3 11.6 - - - -
67I SER 3.2 0.2 - - - -
68I LEU* 1.3 75.5 - - - +
70I THR* 1.3 62.4 + - - +
71I GLY 3.4 0.4 - - - -
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Residues in contact with THR 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PRO* 5.2 4.0 - - - +
112A ASP* 4.7 6.9 + - - +
113A MET* 3.7 32.6 - - - +
66I HIS* 3.0 28.9 + - + +
67I SER* 3.9 1.1 - - - +
69I SER* 1.3 73.1 - - - +
71I GLY* 1.3 60.3 + - - +
72I ARG* 2.8 54.8 + - + +
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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
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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