Contacts of the helix formed by residues 58 - 79 (chain M) 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 HIS 58 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M ASN* 3.4 17.7 - - - +
29M LEU* 3.4 33.6 - - + +
40M SER* 4.8 10.2 - - - -
41M PRO 4.8 11.1 + - - -
42M LYS* 5.5 11.7 - - + -
44M TYR* 4.7 10.1 + + - -
54M CYS 5.8 0.4 - - - -
57M PHE* 1.3 73.7 - - - +
59M GLY* 1.3 57.3 + - - +
61M CYS* 3.4 15.0 - - + +
62M LEU* 2.9 56.4 + - + +
130N VAL* 4.1 14.8 - - + +
131N ALA 3.1 27.3 + - - -
132N TYR* 4.7 4.5 - - + -
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Residues in contact with GLY 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M PHE* 3.3 6.0 - - - -
58M HIS* 1.3 77.8 - - - +
60M ASP* 1.3 61.2 + - - +
62M LEU* 3.9 5.8 + - - +
63M THR* 3.1 24.4 + - - -
93N THR* 5.6 0.2 - - - +
97N TYR* 3.5 8.7 - - - -
128N LEU 4.9 2.9 - - - -
129N GLY 3.9 9.0 - - - +
130N VAL* 3.6 32.7 - - - +
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Residues in contact with ASP 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M PHE* 3.2 25.7 + - + +
58M HIS 3.2 0.2 - - - -
59M GLY* 1.3 75.3 - - - +
61M CYS* 1.3 57.6 + - - +
62M LEU 3.2 0.4 - - - -
63M THR* 3.2 1.7 + - - -
64M LEU* 2.8 31.7 + - - +
99M ARG* 4.2 2.1 + - - -
103M PRO 4.2 1.7 - - - +
104M TYR* 3.5 19.5 - - + -
105M TYR* 3.1 24.6 + - - +
106M VAL* 3.4 20.4 - - + -
97N TYR* 3.2 12.5 + - - -
100N ARG* 3.1 28.1 + - - -
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Residues in contact with CYS 61 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M TYR* 6.1 3.1 - - + -
54M CYS* 2.0 65.1 - - + -
55M SER* 3.8 5.2 - - - -
57M PHE 2.8 25.9 + - - -
58M HIS* 2.9 21.3 + - + +
60M ASP* 1.3 74.8 - - - +
62M LEU* 1.3 61.9 + - - +
64M LEU* 4.5 0.9 - - - -
65M THR* 3.0 30.9 + - - +
106M VAL* 3.8 5.2 - - - -
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Residues in contact with LEU 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M TYR* 3.8 24.0 - - + +
58M HIS* 2.9 40.0 + - + +
59M GLY* 3.9 8.5 - - - +
61M CYS* 1.3 76.4 - - - +
63M THR* 1.3 63.2 + - - +
65M THR* 3.1 4.7 + - - -
66M LYS* 3.0 55.8 + - - +
93N THR* 4.8 6.1 - - + -
94N ARG* 5.9 0.2 - - - +
129N GLY 4.4 3.1 - - - +
131N ALA* 3.6 46.4 - - + +
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Residues in contact with THR 63 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F PHE* 4.6 9.8 - - + -
59M GLY 3.1 13.4 + - - -
60M ASP 3.2 6.1 + - - -
62M LEU* 1.3 79.4 - - - +
64M LEU* 1.3 60.9 + - - +
66M LYS* 3.5 9.2 + - - +
67M ILE* 3.1 40.1 + - + +
104M TYR* 4.9 3.1 - - + +
93N THR* 5.2 5.4 - - - +
94N ARG* 5.5 2.8 + - - +
97N TYR* 3.4 49.6 - - + +
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Residues in contact with LEU 64 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M ASP 2.8 19.3 + - - +
61M CYS* 3.9 4.5 - - - +
63M THR* 1.3 77.4 - - - +
65M THR* 1.3 59.0 + - + +
67M ILE* 3.1 12.0 + - + +
68M ILE* 2.8 47.5 + - + +
92M LEU* 4.9 4.5 - - + -
95M ILE* 3.6 31.0 - - + -
96M LEU* 4.2 16.4 - - + -
104M TYR* 5.2 18.6 - - + -
106M VAL* 3.6 14.8 - - + -
108M ASN* 3.4 31.0 - - - +
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Residues in contact with THR 65 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M TYR* 4.4 20.5 - - + -
46M LEU* 5.2 2.9 - - - +
52M ILE* 4.2 37.7 - - + +
54M CYS* 4.8 11.9 - - + -
61M CYS 3.0 19.4 + - - +
62M LEU* 3.1 10.7 + - - -
64M LEU* 1.3 75.3 - - + +
66M LYS* 1.3 62.6 + - - +
68M ILE* 3.3 6.4 + - + +
69M GLU* 2.9 43.9 + - - +
108M ASN* 5.4 0.4 - - - +
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Residues in contact with LYS 66 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F PHE* 3.5 27.7 - - + +
100F ASP* 4.2 13.7 - - - +
44M TYR* 5.4 4.0 + - - -
62M LEU* 3.0 58.3 + - - +
63M THR* 3.8 5.2 - - - +
65M THR* 1.3 78.8 + - - +
67M ILE* 1.3 57.7 + - - +
69M GLU* 3.7 13.5 + - - +
70M ALA* 3.0 29.3 + - - +
93N THR* 5.9 0.4 - - - -
94N ARG* 3.3 43.5 - - - +
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Residues in contact with ILE 67 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F PHE* 4.0 17.9 - - + -
63M THR* 3.1 31.9 + - + +
64M LEU* 3.1 13.7 + - + +
66M LYS* 1.3 72.2 - - - +
68M ILE* 1.3 58.7 + - - +
70M ALA* 3.5 5.4 + - - +
71M ARG* 3.0 36.1 + - + +
95M ILE* 4.2 30.3 - - + -
104M TYR* 4.5 15.3 - - + +
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Residues in contact with ILE 68 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M LEU* 3.6 24.2 - - + -
52M ILE* 3.5 20.4 - - + -
64M LEU* 2.8 41.5 + - + +
65M THR* 3.3 8.0 + - - +
67M ILE* 1.3 75.7 - - - +
69M GLU* 1.3 55.9 + - - +
71M ARG* 3.4 5.6 + - - +
72M LEU* 2.9 32.6 + - + +
88M ILE* 5.2 9.4 - - + -
91M MET* 4.8 10.8 - - + +
92M LEU* 3.4 31.0 - - + -
95M ILE* 4.7 12.1 - - + -
110M ILE* 6.0 0.2 - - + -
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Residues in contact with GLU 69 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M TYR* 5.5 5.2 - - - +
45M LYS 5.3 4.1 - - - +
46M LEU* 3.7 32.5 - - + +
65M THR* 2.9 34.5 + - - +
66M LYS* 3.7 12.7 + - - +
68M ILE* 1.3 71.5 - - - +
70M ALA* 1.3 64.4 + - - +
72M LEU* 3.5 10.3 + - + +
73M LYS* 3.1 35.4 + - + +
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Residues in contact with ALA 70 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F LEU* 3.4 32.5 - - + +
97F PHE* 4.8 13.5 - - + -
66M LYS 3.0 17.7 + - - +
67M ILE* 3.8 6.3 - - - +
68M ILE 3.3 0.2 - - - -
69M GLU* 1.3 75.9 - - - +
71M ARG* 1.3 58.9 + - + +
73M LYS* 3.4 1.3 + - - +
74M MET* 3.0 35.6 + - + +
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Residues in contact with ARG 71 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E THR* 3.4 20.8 - - - +
103E TYR* 3.6 16.9 + - - -
67M ILE* 3.0 28.9 + - + +
68M ILE* 3.7 4.7 - - - +
70M ALA* 1.3 77.2 - - + +
72M LEU* 1.3 56.9 + - - +
74M MET* 3.3 29.6 + - + +
75M TYR* 3.0 25.3 + - - +
83M MET* 4.5 2.0 - - - +
91M MET* 3.3 37.7 - - - +
94M THR* 5.0 1.2 + - - -
95M ILE* 3.5 30.1 - - + +
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Residues in contact with LEU 72 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M LEU* 3.3 38.8 - - + +
47M THR* 4.4 20.0 - - + -
50M THR* 5.1 4.0 - - + -
68M ILE* 2.9 25.9 + - + +
69M GLU* 3.5 12.8 - - + +
71M ARG* 1.3 73.5 - - - +
73M LYS* 1.4 82.2 + - + +
75M TYR* 3.4 5.4 + - - +
76M LYS* 3.0 26.5 + - + +
83M MET* 3.8 41.5 - - + +
88M ILE* 5.2 3.4 - - + -
91M MET* 5.5 0.2 - - - -
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Residues in contact with LYS 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F ASN* 4.6 22.1 - - + +
93F LEU* 4.0 20.2 - - + -
96F ARG* 6.1 2.2 - - - +
46M LEU 4.6 12.5 + - - -
47M THR* 5.5 2.2 - - - +
69M GLU* 3.1 22.6 + - + +
70M ALA 3.6 4.0 - - - +
72M LEU* 1.4 88.2 - - + +
74M MET* 1.3 63.6 + - - +
75M TYR 3.2 0.2 - - - -
76M LYS* 3.1 13.6 + - + +
77M HIS* 3.1 35.5 + - + +
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Residues in contact with MET 74 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F ARG* 6.3 1.3 - - + -
90F GLN* 3.6 29.2 - - - +
93F LEU* 3.4 27.5 - - + +
70M ALA* 3.0 22.2 + - + +
71M ARG* 3.3 33.0 + - + +
73M LYS* 1.3 75.5 - - - +
75M TYR* 1.3 59.1 + - - +
77M HIS* 3.3 10.3 + - - +
78M SER* 2.9 29.7 + - - -
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Residues in contact with TYR 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E HIS* 3.9 16.2 - + - -
103E TYR* 4.3 26.7 - + - +
105E GLU* 2.6 35.6 + - - -
71M ARG 3.0 10.2 + - - +
72M LEU 3.5 7.9 - - - +
73M LYS 3.2 0.2 - - - -
74M MET* 1.3 75.9 - - - +
76M LYS* 1.3 53.7 + - - +
77M HIS 3.0 5.2 - - - -
78M SER* 4.1 5.2 - - - -
79M ASN* 2.7 67.3 + - + +
81M LYS* 3.3 32.9 + - - +
82M ALA 4.0 3.6 - - - -
83M MET* 4.0 39.9 - - + -
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Residues in contact with LYS 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F HIS* 5.7 0.3 - - - +
72M LEU* 3.0 17.7 + - + +
73M LYS* 3.1 18.1 + - + +
75M TYR* 1.3 76.2 - - + +
77M HIS* 1.3 62.8 + - + +
80M ASN* 2.9 25.7 - - - +
81M LYS* 3.4 26.0 - - - +
82M ALA* 3.8 27.5 - - - +
83M MET 4.9 1.3 - - - +
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Residues in contact with HIS 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E GLN* 5.5 1.0 + - - -
65F HIS* 3.4 24.9 + - + +
66F VAL 3.6 14.6 + - - -
67F ASP* 4.0 21.6 + - - -
68F ASN* 4.6 3.4 - - + -
89F ARG* 3.3 55.4 + - + +
92F CYS* 5.6 0.2 - - - +
93F LEU* 5.1 8.7 - - + +
73M LYS* 3.1 27.9 + - + +
74M MET* 3.6 9.0 - - - +
75M TYR 3.0 0.2 - - - -
76M LYS* 1.3 85.5 + - + +
78M SER* 1.3 63.6 + - - +
79M ASN 3.3 0.4 - - - -
80M ASN* 3.1 23.5 + - - +
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Residues in contact with SER 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E MET* 5.6 4.2 - - - +
110E GLU* 4.2 1.2 - - - +
111E SER* 3.1 18.7 + - - -
114E GLN* 3.8 25.1 + - - +
89F ARG* 4.7 3.6 - - - +
74M MET 2.9 18.8 + - - -
75M TYR* 3.7 7.0 - - - -
77M HIS* 1.3 77.4 - - - +
79M ASN* 1.3 67.4 + - - +
80M ASN* 4.9 0.7 + - - -
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Residues in contact with ASN 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E HIS* 4.3 12.6 + - - -
105E GLU* 4.4 2.2 + - - -
107E MET* 5.2 2.5 - - - +
108E THR* 3.9 21.7 + - - +
110E GLU* 4.0 9.5 - - - +
111E SER* 3.9 15.9 + - - -
75M TYR* 2.7 54.0 + - + +
78M SER* 1.3 86.1 + - - +
80M ASN* 1.4 73.0 + - - +
81M LYS* 3.4 23.1 + - + +
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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