Contacts of the helix formed by residues 127 - 137 (chain C) in PDB entry 5Y1Z
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 CYS 127 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C CYS* 3.3 14.6 - - + +
106C CYS* 3.8 6.3 - - - -
108C ARG* 4.3 0.9 - - - -
110C TYR* 3.4 25.8 - - + -
125C TRP* 3.6 14.6 - - + -
126C PHE* 1.3 76.1 - - - +
128C PRO* 1.3 76.0 - - + +
129C GLU* 3.4 19.5 - - - -
130C CYS 3.2 4.7 + - - -
131C GLU* 2.9 20.9 + - - +
503C ZN 2.4 33.8 - - - -
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Residues in contact with PRO 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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110C TYR* 3.8 17.3 - - + +
115C LEU* 3.4 35.7 - - + -
125C TRP* 4.1 2.2 - - + -
127C CYS* 1.3 86.7 - - + +
129C GLU* 1.3 57.8 + - + +
131C GLU* 4.0 6.9 - - + +
132C LYS* 2.9 34.7 + - + +
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Residues in contact with GLU 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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92C TRP* 2.8 29.6 + - - +
108C ARG* 3.8 24.0 - - - +
110C TYR* 3.3 18.4 - - - +
127C CYS* 3.2 9.0 - - - -
128C PRO* 1.3 77.5 - - + +
130C CYS* 1.3 58.5 + - - +
132C LYS* 3.8 11.4 - - - +
133C ILE* 3.0 37.6 + - + +
215C ALA* 3.9 22.2 - - + +
218C LYS* 4.4 14.8 + - - +
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Residues in contact with CYS 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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103C CYS* 3.6 6.1 - - - -
105C LEU* 3.9 23.8 - - + -
106C CYS* 3.7 14.1 - - - -
108C ARG* 4.9 2.5 - - - -
126C PHE* 4.5 9.0 - - + -
127C CYS* 3.2 11.0 + - - +
129C GLU* 1.3 79.1 - - - +
131C GLU* 1.3 59.4 + - - +
133C ILE* 3.5 7.2 + - - +
134C THR* 2.9 33.6 + - - +
503C ZN 2.2 35.7 - - - -
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Residues in contact with GLU 131 (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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126C PHE* 5.0 13.2 - - + +
127C CYS 2.9 15.7 + - - +
128C PRO* 4.0 7.1 - - + +
130C CYS* 1.3 75.4 - - - +
132C LYS* 1.3 65.8 + - - +
134C THR* 3.1 9.5 + - + -
135C VAL* 3.0 40.1 + - + +
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Residues in contact with LYS 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 PRO 2.9 19.0 + - - +
129C GLU* 3.8 13.2 - - - +
131C GLU* 1.3 76.9 - - - +
133C ILE* 1.3 64.5 + - + +
135C VAL* 3.1 8.0 + - - +
136C ALA* 2.9 25.4 + - - +
211C GLU* 4.8 18.8 - - + -
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Residues in contact with ILE 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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108C ARG* 5.8 3.1 - - - +
129C GLU* 3.0 26.4 + - + +
130C CYS* 3.8 7.4 - - - +
132C LYS* 1.3 74.2 - - + +
134C THR* 1.3 64.8 + - - +
136C ALA* 3.1 6.5 + - - +
137C GLU* 2.9 53.7 + - + +
209C CYS* 4.2 2.5 - - - -
211C GLU* 4.2 6.7 - - + +
212C ALA* 3.5 35.9 - - + +
215C ALA* 4.4 13.9 - - + -
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Residues in contact with THR 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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130C CYS* 2.9 24.6 + - - +
131C GLU* 3.1 10.0 + - + -
133C ILE* 1.3 76.3 - - - +
135C VAL* 1.3 66.3 + - + +
137C GLU* 3.6 3.8 + - - +
138C CYS* 3.2 22.4 + - + +
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Residues in contact with VAL 135 (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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131C GLU* 3.0 28.2 + - + +
132C LYS* 3.6 8.1 - - - +
134C THR* 1.3 80.0 - - + +
136C ALA* 1.3 64.0 + - - +
138C CYS* 3.1 8.1 + - - -
141C THR* 2.9 48.8 + - + +
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Residues in contact with ALA 136 (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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132C LYS 2.9 16.3 + - - +
133C ILE 3.1 3.6 + - - +
135C VAL* 1.3 77.1 - - - +
137C GLU* 1.3 58.6 + - - +
138C CYS 3.5 0.2 - - - -
141C THR 4.5 5.6 - - - -
142C GLN* 3.4 23.5 - - - +
143C SER* 4.4 4.3 + - - +
146C MET* 4.5 5.7 - - + +
209C CYS* 4.0 14.3 - - + +
211C GLU* 3.3 36.8 - - - +
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Residues in contact with GLU 137 (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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133C ILE* 2.9 37.2 + - - +
134C THR* 3.9 5.4 - - - +
136C ALA* 1.3 77.0 - - - +
138C CYS* 1.3 60.1 + - - +
139C ILE* 3.6 6.4 + - - +
142C GLN* 5.0 4.6 - - - +
208C GLY* 3.3 35.9 + - - +
209C CYS* 3.6 22.9 - - + -
212C ALA* 4.0 4.0 - - - +
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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