Contacts of the helix formed by residues 79 - 98 (chain C) in PDB entry 5M73
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 ASP 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73C HIS 4.7 0.9 - - - +
74C GLY* 3.7 10.0 + - - +
75C LEU* 3.6 8.3 - - - +
77C HIS* 3.6 26.0 + - + +
78C GLY* 1.3 72.0 - - - +
80C PHE* 1.3 61.0 + - - +
81C GLN* 3.1 11.5 + - - +
82C ARG* 2.7 45.7 + - + +
83C TYR 3.1 9.7 + - - -
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Residues in contact with PHE 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 3.8 31.9 - - + -
78C GLY* 3.0 37.4 + - - -
79C ASP* 1.3 72.5 - - - +
81C GLN* 1.3 55.7 + - - +
84C ARG* 3.0 16.1 + - - +
135C TRP* 4.5 9.2 - + - -
136C SER* 2.8 35.4 + - - +
139C MET* 3.6 42.0 - - + -
140C GLN* 4.1 16.2 - - + +
143C GLN* 3.3 24.2 - - - -
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Residues in contact with GLN 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A U 5.3 1.8 - - - +
79C ASP* 3.1 7.4 + - - +
80C PHE* 1.3 79.7 - - - +
82C ARG* 1.3 62.9 + - - +
84C ARG* 3.0 27.0 + - - +
85C GLY* 3.0 16.8 + - - -
140C GLN* 2.8 33.3 + - + +
144C GLU* 4.8 2.8 - - - +
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Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A G 4.4 10.3 + - - -
72C GLN 4.0 6.1 + - - -
73C HIS* 3.1 52.0 + - + +
74C GLY* 4.1 5.2 - - - +
77C HIS* 5.0 7.8 - - - -
79C ASP* 2.7 35.6 + - - +
81C GLN* 1.3 70.3 - - - +
83C TYR* 1.3 54.7 + - - +
85C GLY* 2.5 25.0 + - - -
86C TYR* 2.8 11.9 + - + -
89C ARG* 4.2 20.2 + - - +
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Residues in contact with TYR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 4.7 5.0 + - - +
69C SER* 4.3 9.7 - - - -
70C GLN* 3.2 48.9 + - + +
73C HIS* 3.9 12.1 + - + +
75C LEU* 3.7 29.4 - - + -
79C ASP 3.1 6.6 + - - +
80C PHE 4.0 2.0 - - - +
82C ARG* 1.3 76.3 - - - +
84C ARG* 1.3 64.2 + - - +
86C TYR* 3.8 15.9 - + - +
87C CYS* 2.8 54.3 + - - -
129C MET* 4.7 3.7 - - + +
132C GLU* 2.4 40.6 + - + +
135C TRP* 4.6 2.9 - + - -
136C SER* 3.8 22.2 - - - -
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A G 5.1 0.4 + - - -
223A U 2.4 47.2 + - - -
224A G 4.7 9.5 + - - +
80C PHE 3.0 16.2 + - - +
81C GLN* 3.0 31.7 + - - +
83C TYR* 1.3 76.5 - - - +
85C GLY* 1.3 57.1 + - - +
87C CYS* 3.4 7.1 - - - +
88C SER* 2.9 32.3 + - - +
133C ARG* 4.4 20.6 - - + +
136C SER* 3.5 16.2 + - - +
137C TYR* 3.2 35.4 + - - -
140C GLN* 2.4 36.0 + - - +
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Residues in contact with GLY 85 (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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81C GLN 3.0 10.7 + - - -
82C ARG* 2.5 15.8 + - - -
84C ARG* 1.3 73.1 - - - +
86C TYR* 1.3 55.5 + - - -
88C SER* 3.1 7.7 + - - -
89C ARG* 2.8 41.6 + - - +
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Residues in contact with TYR 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A A 3.5 29.2 + - - -
120A G 3.5 14.1 - - - +
69C SER* 3.9 19.9 + - - -
73C HIS* 3.2 65.0 - + + -
82C ARG* 2.8 12.8 + - + +
83C TYR* 3.9 15.0 - + - +
85C GLY* 1.3 72.0 - - - +
87C CYS* 1.3 63.0 + - - +
89C ARG* 3.0 23.2 + - + +
90C ARG* 2.8 63.0 + - + +
93C ARG* 5.1 2.0 - - - -
129C MET* 5.9 1.3 - - - -
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Residues in contact with CYS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C TYR* 2.8 71.8 + - - +
84C ARG* 3.4 7.6 - - - +
86C TYR* 1.3 79.0 - - - +
88C SER* 1.3 62.7 + - - +
90C ARG* 3.6 3.0 + - - +
91C GLN* 3.1 21.7 + - - +
129C MET* 4.3 28.2 - - - +
132C GLU* 4.6 5.4 - - - -
133C ARG* 4.5 18.8 - - + +
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Residues in contact with SER 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A G 3.6 11.6 + - - -
84C ARG* 2.9 16.8 + - - +
85C GLY* 3.5 9.6 - - - -
87C CYS* 1.3 74.6 - - - +
89C ARG* 1.3 67.2 + - - +
91C GLN* 3.1 8.7 + - - +
92C ARG* 3.0 20.3 + - - +
95C ARG* 5.0 1.0 + - - -
133C ARG* 3.0 41.0 + - - +
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Residues in contact with ARG 89 (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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120A G 3.6 32.1 + - - +
121A U 4.3 18.0 + - - -
82C ARG* 4.2 24.4 + - - +
85C GLY* 2.8 24.2 + - - +
86C TYR* 3.6 28.5 - - + +
88C SER* 1.3 71.4 - - - +
90C ARG* 1.3 57.5 + - - +
92C ARG* 2.9 12.9 + - - +
93C ARG* 2.9 49.7 + - - +
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Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A A 5.1 7.5 + - - -
119A A 3.7 28.4 + - - +
65C ILE* 4.3 18.4 - - - +
69C SER* 3.6 16.4 + - - -
86C TYR* 2.8 43.7 + - + +
87C CYS* 3.8 5.6 - - - +
89C ARG* 1.3 73.3 - - - +
91C GLN* 1.3 68.0 + - - +
93C ARG* 3.0 10.6 + - + +
94C LEU* 2.8 33.7 + - + +
125C LEU* 3.3 31.8 - - - +
129C MET* 4.3 20.7 - - + +
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Residues in contact with GLN 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A C 3.9 0.4 + - - -
87C CYS 3.1 10.1 + - - +
88C SER 3.1 8.8 + - - +
90C ARG* 1.3 79.4 - - - +
92C ARG* 1.3 57.3 + - - +
94C LEU* 3.3 7.2 + - - +
95C ARG* 2.8 61.8 + - - +
102C MET* 3.3 14.2 - - - +
111C LYS* 4.2 3.1 + - - -
126C LEU* 3.6 27.6 - - + +
129C MET* 4.4 7.9 + - + +
130C ASP* 2.5 41.9 + - - +
133C ARG* 3.6 19.1 - - - +
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Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A U 4.0 30.1 + - - -
227A G 2.7 58.2 + - - -
228A A 4.9 1.0 + - - -
88C SER 3.0 10.4 + - - +
89C ARG* 2.9 14.8 + - - +
91C GLN* 1.3 75.6 - - - +
93C ARG* 1.3 59.6 + - + +
95C ARG* 3.3 21.3 + - - +
96C LYS* 2.8 79.3 + - + +
101C LYS* 5.2 1.4 - - - +
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Residues in contact with ARG 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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118A A 5.3 9.2 - - - +
119A A 2.6 77.8 + - - +
120A G 3.0 55.9 + - - -
86C TYR* 5.1 2.0 - - - -
89C ARG* 2.9 32.0 + - - +
90C ARG* 3.0 10.1 + - + +
92C ARG* 1.3 77.1 - - + +
94C LEU* 1.3 64.2 + - + +
96C LYS* 3.2 5.3 + - - +
97C THR* 2.9 31.5 + - - +
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Residues in contact with LEU 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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118A A 4.3 18.2 - - - +
90C ARG* 2.8 32.8 + - + +
91C GLN* 3.8 6.3 - - - +
93C ARG* 1.3 75.8 - - + +
95C ARG* 1.3 64.5 + - - +
97C THR* 4.7 0.4 - - - -
98C LEU* 2.9 46.8 + - + +
122C ARG* 4.7 17.9 - - + +
123C TYR* 6.5 0.2 - - + -
125C LEU* 3.6 39.3 - - + -
126C LEU* 4.0 25.6 - - + +
129C MET* 4.8 2.2 - - + -
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Residues in contact with ARG 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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225A C 3.2 28.5 + - - -
226A U 2.0 47.5 + - - +
88C SER 5.0 1.2 + - - -
91C GLN* 2.8 66.8 + - - +
92C ARG* 3.8 18.6 - - - +
94C LEU* 1.3 78.9 - - - +
96C LYS* 1.3 61.2 + - - +
99C ASN* 3.3 18.4 + - - -
100C PHE* 3.0 42.0 + - + +
101C LYS* 4.4 5.3 - - + -
102C MET* 3.7 18.6 - - - +
111C LYS* 6.2 0.2 - - - -
126C LEU* 4.0 15.2 - - + +
133C ARG* 5.1 0.2 - - - +
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Residues in contact with LYS 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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227A G 4.7 5.1 + - - -
228A A 4.0 48.1 + - - -
229A U 5.7 4.3 - - - +
92C ARG* 2.8 59.3 + - + +
93C ARG* 3.9 4.5 - - - +
95C ARG* 1.3 74.2 - - - +
97C THR* 1.3 64.6 + - - +
99C ASN* 3.6 15.1 - - - +
101C LYS* 4.4 14.4 + - - +
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Residues in contact with THR 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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117A U 3.1 37.6 + - - +
118A A 4.1 12.7 + - - +
93C ARG* 2.9 17.6 + - - +
94C LEU* 4.7 0.7 - - - -
96C LYS* 1.3 80.6 - - - +
98C LEU* 1.3 78.7 + - + +
99C ASN* 3.0 11.0 + - - +
122C ARG* 4.6 6.1 - - - +
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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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117A U 5.7 0.4 - - - +
94C LEU* 2.9 40.1 + - + +
97C THR* 1.3 93.4 - - + +
99C ASN* 1.3 69.1 + - - +
100C PHE* 3.2 9.8 + - + +
120C ASP* 5.3 3.1 - - - +
122C ARG* 3.9 25.6 - - - +
123C TYR* 3.1 50.9 + - + +
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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