Contacts of the helix formed by residues 116 - 129 (chain C) in PDB entry 1RX0
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 ASN 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C GLY* 1.3 75.6 - - - -
117C GLU* 1.3 65.4 + - - +
118C GLU* 3.0 21.9 + - - +
119C GLN* 2.8 51.6 + - - +
120C ARG* 2.9 20.1 + - - +
234C ALA 5.1 0.8 + - - -
236C ARG 5.5 0.2 + - - -
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Residues in contact with GLU 117 (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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72C ASP* 4.7 0.9 - - - +
115C GLY 5.2 0.9 - - - +
116C ASN* 1.3 72.9 - - - +
118C GLU* 1.3 74.9 + - - +
120C ARG* 2.9 38.9 + - - -
121C HIS* 3.1 44.6 + - + +
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Residues in contact with GLU 118 (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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116C ASN* 3.0 20.0 + - - +
117C GLU* 1.3 85.8 + - - +
119C GLN* 1.3 64.5 + - + +
121C HIS* 3.6 3.1 + - - +
122C LYS* 3.1 25.9 + - - +
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Residues in contact with GLN 119 (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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111C ILE* 3.9 3.0 - - + +
115C GLY* 3.2 10.8 - - - -
116C ASN* 2.8 52.7 + - - +
118C GLU* 1.3 76.1 - - + +
120C ARG* 1.3 65.5 + - - +
122C LYS* 3.2 3.5 + - - -
123C PHE* 3.0 47.4 + - + +
234C ALA 2.9 27.5 + - - +
235C ASN* 3.8 4.0 - - - +
236C ARG 2.8 31.3 + - - +
237C ILE* 3.7 14.3 - - + +
238C GLY 4.9 0.9 + - - -
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Residues in contact with ARG 120 (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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70C GLN* 3.6 10.1 - - - +
72C ASP* 2.9 40.0 + - - -
73C VAL* 3.7 16.3 - - + +
111C ILE* 3.7 18.6 - - - +
112C ASP* 2.6 41.3 + - - +
115C GLY 3.8 13.2 - - - +
116C ASN 2.9 17.0 + - - +
117C GLU* 2.9 39.2 + - - +
118C GLU 3.4 0.2 - - - -
119C GLN* 1.3 76.3 - - - +
121C HIS* 1.3 59.5 + - + +
124C CYS* 3.0 43.1 + - - +
125C PRO* 3.2 1.7 - - - +
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Residues in contact with HIS 121 (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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72C ASP* 3.6 29.8 + - + -
73C VAL* 3.7 16.1 - - + +
117C GLU* 3.1 46.8 + - + +
118C GLU* 3.9 3.1 - - - +
120C ARG* 1.3 80.2 + - - +
122C LYS* 1.3 57.6 + - - +
125C PRO* 3.4 23.0 - - - +
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Residues in contact with LYS 122 (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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118C GLU 3.1 18.1 + - - +
119C GLN* 3.2 5.1 + - - +
121C HIS* 1.3 79.2 - - - +
123C PHE* 1.3 96.8 + - + +
125C PRO* 4.2 0.2 - - - -
126C PRO* 3.5 20.4 - - - +
132C LYS* 6.2 0.2 - - - +
199C GLU* 4.2 17.0 + - - -
235C ASN* 5.1 5.4 - - - +
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Residues in contact with PHE 123 (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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111C ILE* 3.8 33.2 - - + -
119C GLN* 3.0 35.3 + - + +
122C LYS* 1.3 115.5 - - + +
124C CYS* 1.3 64.7 + - - +
125C PRO 3.5 0.2 - - - -
126C PRO* 3.1 11.4 - - - +
127C LEU* 3.2 22.3 + - + +
132C LYS* 6.3 0.2 - - - -
178C ILE* 3.7 19.9 - - + +
197C VAL* 3.7 32.1 - - + -
199C GLU* 3.7 17.7 - - - -
234C ALA 5.6 0.4 - - - -
235C ASN* 4.1 22.4 - - - -
237C ILE* 5.2 1.3 - - + -
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Residues in contact with CYS 124 (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 ILE* 4.8 4.9 - - + -
73C VAL* 3.8 19.7 - - + +
108C ALA* 3.7 13.0 - - + -
111C ILE* 3.9 13.0 - - - -
112C ASP* 3.7 39.0 - - - -
120C ARG* 3.0 21.9 + - - +
123C PHE* 1.3 76.8 - - - +
125C PRO* 1.3 69.5 - - + +
127C LEU* 3.1 8.6 + - - +
128C CYS* 2.9 25.8 + - - -
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Residues in contact with PRO 125 (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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73C VAL* 3.4 24.2 - - + +
74C GLY* 5.2 1.6 - - - -
120C ARG 3.2 13.2 - - - +
121C HIS* 3.4 28.5 - - + +
124C CYS* 1.3 90.3 - - + +
126C PRO* 1.3 71.6 - - + +
128C CYS* 3.2 10.9 + - + +
129C THR* 3.4 18.1 + - - +
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Residues in contact with PRO 126 (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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122C LYS 3.5 15.7 - - - +
123C PHE* 3.1 14.1 - - - +
125C PRO* 1.3 98.8 - - + +
127C LEU* 1.3 55.6 + - + +
129C THR* 3.3 6.6 + - - +
130C MET 3.0 4.3 + - - -
131C GLU* 2.8 47.2 + - + +
132C LYS* 3.2 38.1 + - + +
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Residues in contact with LEU 127 (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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65C GLY 3.7 2.3 - - - +
104C HIS* 2.7 36.8 + - + +
108C ALA* 4.0 31.6 - - + -
111C ILE* 4.3 15.5 - - + -
123C PHE* 3.2 23.1 - - + +
124C CYS* 3.1 8.4 + - - +
126C PRO* 1.3 77.6 - - + +
128C CYS* 1.3 64.2 + - - +
130C MET* 3.1 9.9 + - - +
132C LYS* 3.4 25.1 - - + +
133C PHE 4.0 2.2 - - - -
134C ALA* 3.8 23.1 - - + -
178C ILE* 4.2 16.2 - - + -
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Residues in contact with CYS 128 (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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60C ALA* 3.6 19.8 - - - +
63C GLY* 5.7 0.5 - - - -
65C GLY* 3.6 15.7 + - - -
66C GLY* 3.9 15.1 + - - +
69C ILE* 4.0 14.1 - - - -
73C VAL 3.9 4.7 - - - -
74C GLY* 3.4 22.3 - - - +
75C GLY* 3.6 28.7 - - - -
108C ALA* 5.4 1.1 - - - -
124C CYS* 2.9 20.4 + - - +
125C PRO 3.2 5.6 + - - +
127C LEU* 1.3 79.2 - - - +
129C THR* 1.3 61.1 + - + +
130C MET 3.3 0.9 - - - -
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Residues in contact with THR 129 (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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57C ARG* 4.1 9.5 - - - +
60C ALA* 3.4 15.1 - - - +
61C GLN* 6.0 0.7 - - - +
74C GLY* 6.5 0.4 - - - -
125C PRO 3.4 12.3 + - - +
126C PRO* 3.3 12.0 + - - +
128C CYS* 1.3 80.2 - - + +
130C MET* 1.3 67.5 + - - +
131C GLU* 3.3 17.9 + - - +
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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
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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