Contacts of the helix formed by residues 79 - 102 (chain C) in PDB entry 4R3O
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 ILE 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B PHE* 3.7 30.5 - - + -
16B GLY 5.6 0.2 - - - +
18B LEU* 3.9 21.1 - - + -
21B ILE* 5.7 1.1 - - + -
151B SER* 5.1 11.2 - - - +
27C ALA* 4.2 12.8 - - + -
78C GLY* 1.3 73.6 - - - -
80C THR* 1.3 65.0 + - - +
81C SER* 3.4 23.1 - - - +
82C ASP* 3.5 15.4 + - - +
83C ALA* 3.3 4.8 + - - +
128C ARG* 5.4 0.4 - - - +
131C GLY* 2.9 26.3 + - - +
132C VAL* 3.2 21.1 - - - +
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Residues in contact with THR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ALA* 3.3 26.9 - - - +
155B PHE* 5.9 1.6 - - + -
63C GLU 6.2 0.4 - - - +
64C LYS* 6.3 2.7 - - + -
66C TYR* 5.3 3.6 - - - +
76C VAL* 5.6 8.3 - - + -
78C GLY 4.4 7.4 - - - +
79C ILE* 1.3 72.6 - - - +
81C SER* 1.3 61.7 + - - +
83C ALA* 3.0 11.0 + - - +
84C ASN* 2.9 35.9 + - - +
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Residues in contact with SER 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLN* 3.4 16.0 - - - +
121B THR* 5.3 0.2 + - - -
151B SER* 2.8 29.7 + - - -
152B GLY 3.7 19.1 - - - -
153B ALA* 4.2 0.9 - - - +
79C ILE* 3.4 14.8 - - - +
80C THR* 1.3 79.8 + - - +
82C ASP* 1.3 69.1 + - - +
84C ASN* 3.0 17.2 + - - +
85C VAL* 3.0 24.6 + - - +
128C ARG* 5.4 0.2 + - - -
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Residues in contact with ASP 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLN* 3.2 23.3 + - - +
79C ILE* 3.6 19.6 - - - +
80C THR 3.3 0.4 - - - -
81C SER* 1.3 82.3 + - - +
83C ALA* 1.3 57.5 - - - +
85C VAL* 3.3 5.7 + - - +
86C LEU* 2.9 34.7 + - - +
128C ARG* 2.7 37.1 + - - -
130C PHE* 3.7 16.2 - - + -
131C GLY* 3.3 14.7 + - - -
132C VAL* 3.7 13.7 - - + -
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C TYR* 4.1 7.6 - - + +
76C VAL* 3.5 42.0 - - + -
79C ILE 3.3 10.0 + - - +
80C THR* 3.0 15.4 + - - +
82C ASP* 1.3 76.2 - - - +
84C ASN* 1.3 52.5 + - - +
86C LEU* 3.9 4.8 - - - +
87C THR* 2.6 43.3 + - - +
132C VAL* 3.7 5.8 - - + +
134C LEU* 6.0 0.4 - - - -
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Residues in contact with ASN 84 (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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114B ALA* 5.7 0.8 - - - +
115B SER* 5.7 4.3 - - - +
152B GLY 4.4 5.1 + - - -
153B ALA* 5.3 1.2 - - - +
154B TYR* 3.6 34.8 + - - -
66C TYR* 2.9 27.9 + - - -
80C THR* 2.9 21.0 + - - +
81C SER* 3.0 15.4 + - - +
83C ALA* 1.3 73.7 - - - +
85C VAL* 1.3 65.3 + - + +
87C THR* 2.9 18.1 + - - -
88C ASN* 3.0 16.5 + - - +
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER* 5.9 6.5 - - - +
118B GLN* 3.4 32.8 - - + +
81C SER 3.0 17.2 + - - +
82C ASP* 3.4 8.1 - - - +
84C ASN* 1.3 78.8 - - + +
86C LEU* 1.3 66.0 + - + +
88C ASN* 3.3 5.6 + - - +
89C GLU* 3.0 24.0 + - + +
130C PHE* 4.1 23.3 - - + -
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Residues in contact with LEU 86 (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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82C ASP 2.9 18.6 + - - +
83C ALA* 4.0 4.0 - - - +
85C VAL* 1.3 79.9 - - + +
87C THR* 1.3 57.9 + - - +
89C GLU* 3.3 5.9 + - + +
90C LEU* 2.9 33.5 + - - +
114C LEU* 3.8 29.3 - - + +
117C ILE* 5.5 2.7 - - + -
118C LYS* 4.1 17.9 - - + -
130C PHE* 3.8 52.3 - - + -
132C VAL* 3.9 24.0 - - + -
134C LEU* 4.2 11.0 - - + -
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Residues in contact with THR 87 (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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66C TYR* 3.4 52.0 - - + -
68C LEU* 4.3 3.7 - - + +
74C CYS* 3.8 15.7 - - - -
76C VAL* 5.6 0.7 - - + -
83C ALA* 2.6 26.4 + - + +
84C ASN* 2.9 17.3 + - - -
86C LEU* 1.3 70.8 - - - +
88C ASN* 1.3 65.0 + - - +
90C LEU* 3.2 11.2 + - + +
91C ARG* 3.0 33.2 + - - +
134C LEU* 4.8 5.4 - - + -
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Residues in contact with ASN 88 (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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84C ASN 3.0 17.7 + - - +
85C VAL* 3.5 6.3 - - - +
87C THR* 1.3 75.8 + - - +
89C GLU* 1.3 62.8 + - - +
91C ARG* 3.2 20.6 + - - +
92C LEU* 3.0 36.5 + - - +
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Residues in contact with GLU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C VAL* 3.0 16.0 + - + +
86C LEU* 3.6 12.1 - - + +
88C ASN* 1.3 75.5 - - - +
90C LEU* 1.3 57.7 + - - +
92C LEU* 3.2 21.5 + - - +
93C ILE* 2.9 39.6 + - + +
96C ARG* 3.5 28.5 + - - -
114C LEU* 4.5 5.6 - - + -
117C ILE* 3.7 30.8 - - + +
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 4.0 21.3 - - + -
74C CYS* 4.7 0.2 - - - -
86C LEU 2.9 22.0 + - - +
87C THR* 3.4 15.7 - - + +
89C GLU* 1.3 75.9 - - - +
91C ARG* 1.3 63.3 + - - +
93C ILE* 3.2 4.3 + - + +
94C ALA* 3.0 22.1 + - - +
110C LEU* 3.4 42.5 - - + +
114C LEU* 3.7 40.2 - - + -
134C LEU* 4.1 11.0 - - + -
136C TYR* 3.9 22.7 - - + -
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Residues in contact with ARG 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C TYR* 4.3 20.7 - - - +
67C LYS* 2.9 34.7 + - - +
68C LEU* 3.7 29.9 - - + +
87C THR* 3.0 20.7 + - - +
88C ASN* 3.4 22.0 + - - +
90C LEU* 1.3 75.1 - - - +
92C LEU* 1.3 64.2 + - - +
94C ALA* 3.3 3.6 + - - +
95C GLN* 3.0 30.8 + - + +
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Residues in contact with LEU 92 (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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88C ASN* 3.0 30.7 + - - +
89C GLU* 3.3 28.7 - - - +
91C ARG* 1.3 76.7 - - - +
93C ILE* 1.3 56.8 + - - +
95C GLN* 3.3 7.9 + - + +
96C ARG* 2.9 58.0 + - + +
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Residues in contact with ILE 93 (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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89C GLU* 2.9 36.1 + - + +
90C LEU* 3.2 10.7 + - - +
92C LEU* 1.3 74.6 - - - +
94C ALA* 1.3 65.4 + - - +
96C ARG* 3.1 26.7 + - + +
97C TYR* 2.9 22.6 + - + +
105C ILE* 4.2 11.2 - - + -
110C LEU* 3.6 15.9 - - + +
113C ALA* 3.7 37.0 - - + +
114C LEU* 4.0 14.8 - - + +
117C ILE* 4.6 3.8 - - + -
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Residues in contact with ALA 94 (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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68C LEU 4.5 13.0 - - - +
69C ASN* 4.5 14.9 + - + +
90C LEU 3.0 13.1 + - - +
91C ARG 3.6 8.3 - - - +
93C ILE* 1.3 77.8 - - - +
95C GLN* 1.3 60.8 + - - +
97C TYR* 3.3 3.3 + - - +
98C LEU* 2.9 27.9 + - - +
105C ILE* 3.8 29.3 + - + +
110C LEU* 4.0 9.8 - - + +
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Residues in contact with GLN 95 (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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68C LEU 5.2 4.0 + - - -
69C ASN* 4.1 20.4 - - - +
91C ARG* 3.0 21.5 + - + +
92C LEU* 3.8 7.0 - - + +
94C ALA* 1.3 77.9 - - - +
96C ARG* 1.3 57.6 + - + +
98C LEU* 3.4 27.5 + - - +
99C LEU* 2.9 29.6 + - - +
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Residues in contact with ARG 96 (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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89C GLU* 3.5 26.4 + - - -
92C LEU* 2.9 44.7 + - + +
93C ILE* 3.1 24.9 + - - +
95C GLN* 1.3 72.3 - - - +
97C TYR* 1.3 67.1 + - - +
99C LEU* 3.2 10.2 + - + +
100C GLN* 3.0 27.4 + - - +
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Residues in contact with TYR 97 (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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93C ILE* 2.9 11.8 + - + +
94C ALA 3.6 8.3 - - - +
96C ARG* 1.3 75.8 - - - +
98C LEU* 1.3 57.1 + - - +
100C GLN* 3.1 3.5 + - - -
101C TYR* 2.9 69.6 + + + -
103C GLU* 3.3 34.8 + - + -
104C PRO 3.6 10.8 - - - -
105C ILE* 3.4 33.7 - - + -
106C PRO* 3.4 19.1 - - + +
109C GLN* 3.3 29.8 + - - -
142C HIS* 5.9 0.2 + - - -
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Residues in contact with LEU 98 (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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69C ASN* 5.5 5.2 - - - +
94C ALA 2.9 17.7 + - - +
95C GLN* 3.4 31.6 - - - +
96C ARG 3.2 0.2 - - - -
97C TYR* 1.3 78.9 - - - +
99C LEU* 1.3 57.4 + - - +
102C GLN* 2.8 45.9 + - - +
103C GLU* 3.7 35.0 - - - +
104C PRO* 4.2 7.6 - - + -
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Residues in contact with LEU 99 (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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95C GLN 2.9 17.2 + - - +
96C ARG* 3.2 9.2 + - + +
98C LEU* 1.3 75.9 - - - +
100C GLN* 1.3 61.0 - - - +
102C GLN* 3.5 18.1 - - - +
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Residues in contact with GLN 100 (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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96C ARG* 3.0 17.9 + - - +
97C TYR* 3.1 4.8 + - - +
99C LEU* 1.3 81.2 - - + +
101C TYR* 1.3 88.0 + - + +
102C GLN* 3.6 2.1 - - - +
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Residues in contact with TYR 101 (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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97C TYR* 2.9 64.0 + + + +
100C GLN* 1.3 107.8 + - + +
102C GLN* 1.3 71.5 + - - +
103C GLU* 3.2 16.5 + - + +
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Residues in contact with GLN 102 (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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98C LEU* 2.8 38.5 + - - +
99C LEU* 3.5 20.7 - - - +
100C GLN 5.3 1.3 - - - +
101C TYR* 1.3 80.7 - - - +
103C GLU* 1.3 60.2 + - - +
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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
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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