Contacts of the helix formed by residues 126 - 134 (chain C) in PDB entry 1R1S
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 SER 126 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C TYR* 3.5 13.1 - - - +
124C PHE* 3.2 9.9 - - - +
125C PRO* 1.3 82.7 - - - +
127C LEU* 1.3 58.5 + - - +
128C ASN 3.5 1.7 + - - -
129C LYS* 3.2 17.8 + - - +
130C LEU* 3.1 24.3 + - - +
3487C SO4 2.3 39.7 + - - -
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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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60C TRP* 5.6 3.1 - - + -
61C PHE* 4.1 26.5 - - + -
84C ILE* 4.2 30.1 - - + -
94C PHE* 5.6 2.0 - - + -
109C VAL* 4.4 23.1 - - + -
117C TYR* 3.6 26.8 - - + -
126C SER* 1.3 73.1 - - - +
128C ASN* 1.3 58.7 + - - +
130C LEU* 3.3 16.8 + - + +
131C VAL* 2.9 32.9 + - - +
91G PRO* 3.8 34.3 + - + +
92G GLY* 4.4 4.0 - - - +
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Residues in contact with ASN 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PRO* 3.8 23.6 - - - +
60C TRP* 4.3 11.8 - - - -
126C SER* 3.3 2.2 + - - -
127C LEU* 1.3 77.8 - - - +
129C LYS* 1.3 60.0 + - - +
131C VAL* 3.4 7.5 + - - +
132C ASP* 3.1 44.7 + - - +
3487C SO4 3.4 35.3 + - - +
91G PRO* 5.9 2.8 - - - +
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Residues in contact with LYS 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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124C PHE* 3.8 15.8 - - + -
125C PRO* 3.4 34.3 - - + -
126C SER* 3.2 12.6 + - - +
128C ASN* 1.3 78.9 - - - +
130C LEU* 1.3 60.1 + - - +
132C ASP* 3.6 8.4 + - - +
133C TYR* 3.0 28.4 + - - +
3487C SO4 2.6 38.2 + - - +
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Residues in contact with LEU 130 (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 ILE* 3.8 27.8 - - + -
109C VAL* 5.1 2.9 - - + -
117C TYR* 3.7 34.1 - - + +
118C PHE* 4.0 17.3 - - - +
119C LEU* 4.1 9.2 - - + -
124C PHE* 3.6 21.6 - - + -
126C SER 3.1 14.7 + - - +
127C LEU* 3.4 18.2 - - + +
129C LYS* 1.3 72.9 - - - +
131C VAL* 1.3 68.6 + - + +
133C TYR* 3.3 9.7 + - - +
134C TYR* 3.3 37.0 + - + -
139C ILE* 5.7 0.7 - - + -
147C LEU* 6.0 0.7 - - + -
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Residues in contact with VAL 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TRP* 3.5 33.4 - - + -
82C PHE* 3.6 28.5 - - + -
84C ILE* 4.0 16.2 - - + -
96C ILE* 5.6 0.9 - - + -
127C LEU 2.9 22.2 + - - +
128C ASN* 3.4 8.5 + - - +
130C LEU* 1.3 76.7 - - + +
132C ASP* 1.3 64.0 + - - +
134C TYR* 3.2 4.5 + - - -
135C ARG* 3.2 40.7 + - - +
147C LEU* 3.8 14.5 - - + +
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Residues in contact with ASP 132 (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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128C ASN* 3.1 30.3 + - - +
129C LYS* 3.9 8.2 - - - +
130C LEU 3.3 0.2 - - - -
131C VAL* 1.3 76.8 - - - +
133C TYR* 1.3 64.4 + - - +
135C ARG* 2.8 56.9 + - - +
136C THR* 4.2 4.5 + - - -
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Residues in contact with TYR 133 (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 GLU* 3.9 22.6 + - + +
124C PHE* 3.5 27.8 - + + -
129C LYS 3.0 17.5 + - - +
130C LEU 3.7 2.0 - - - +
131C VAL 3.2 0.6 - - - -
132C ASP* 1.3 77.4 - - - +
134C TYR* 1.3 84.3 + + - +
135C ARG 3.2 0.2 - - - -
136C THR* 3.2 9.3 + - - -
137C THR* 3.2 51.1 + - + +
3485C SO4 2.4 32.1 + - - -
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Residues in contact with TYR 134 (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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119C LEU* 3.9 29.4 + - + +
120C TRP* 3.7 19.4 + + - +
122C GLU 4.8 4.2 + - - -
124C PHE* 4.4 5.2 - + - -
130C LEU* 3.3 30.8 + - + +
131C VAL 3.2 5.3 + - - -
133C TYR* 1.3 94.1 - + - +
135C ARG* 1.3 56.0 + - - +
137C THR* 3.2 24.3 - - + +
138C SER 3.6 16.6 - - - -
139C ILE* 3.6 16.8 + - + -
145C VAL 4.8 0.5 - - - +
146C PHE* 3.6 2.3 - - - -
147C LEU* 2.7 49.0 + - + +
3485C SO4 2.8 35.8 + - - -
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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
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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