Contacts of the helix formed by residues 127 - 138 (chain C) in PDB entry 1YI8
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 127 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C HIS 3.6 6.3 + - - +
124C LEU* 3.5 10.0 + - + +
125C ARG 3.4 1.4 - - - -
126C GLN* 1.3 74.1 - - - +
128C PRO* 1.3 66.0 - - - +
129C THR* 2.7 35.5 + - - +
130C VAL* 2.9 32.5 + - + +
131C LYS* 3.0 28.6 + - - +
151C PRO* 3.9 18.0 - - + +
174C PRO* 4.0 21.3 + - - +
175C MET* 4.4 1.6 - - - +
178C GLN* 4.6 7.7 + - - +
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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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126C GLN 2.9 10.0 - - - +
127C ASN* 1.3 85.1 - - - +
129C THR* 1.3 62.0 + - - +
131C LYS* 3.9 10.2 - - + +
132C ALA* 3.3 22.7 + - - +
174C PRO* 3.9 26.0 - - + -
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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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127C ASN* 2.7 34.2 + - - +
128C PRO* 1.3 73.8 - - - +
130C VAL* 1.3 64.7 + - + +
132C ALA* 3.4 5.9 + - - +
133C GLU* 3.0 42.1 + - - +
150C TYR* 4.8 4.9 + - - +
171C ASP* 3.2 29.1 + - - +
172C GLN* 5.3 0.9 - - - -
174C PRO* 3.5 20.2 - - + -
175C MET* 4.8 6.5 - - + +
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Residues in contact with VAL 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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124C LEU 4.0 10.8 - - - +
125C ARG 5.1 2.2 - - - +
127C ASN* 2.9 45.7 + - + +
129C THR* 1.3 76.2 - - + +
131C LYS* 1.3 72.1 + - + +
133C GLU* 3.1 10.7 + - - +
134C ILE* 2.9 36.8 + - + +
147C PHE* 4.9 8.1 - - + +
148C PHE* 5.3 8.7 - - + +
150C TYR* 4.0 18.4 - - + -
151C PRO* 3.5 26.7 - - + -
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Residues in contact with LYS 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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125C ARG* 3.9 44.0 - - - +
126C GLN* 4.6 9.6 - - - +
127C ASN 3.2 13.5 - - - +
128C PRO* 3.9 9.0 - - + +
130C VAL* 1.3 83.1 - - + +
132C ALA* 1.3 57.0 + - - +
134C ILE* 3.6 10.1 + - - +
135C ALA* 3.1 26.3 + - - +
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Residues in contact with ALA 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 3.3 17.1 + - - +
129C THR* 3.6 7.0 - - - +
130C VAL 3.1 0.4 - - - -
131C LYS* 1.3 78.2 - - - +
133C GLU* 1.3 60.0 + - + +
135C ALA* 3.2 8.3 + - - +
136C GLN* 2.9 29.6 + - - +
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Residues in contact with GLU 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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129C THR* 3.0 28.0 + - - +
130C VAL* 3.1 15.2 + - - +
132C ALA* 1.3 73.0 - - + +
134C ILE* 1.3 56.9 - - - +
136C GLN* 2.9 22.8 + - + +
137C LYS* 2.7 41.6 + - + +
147C PHE* 3.8 22.9 - - + -
150C TYR* 2.8 31.7 + - - -
3000C TRP 5.7 0.2 - - - +
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Residues in contact with ILE 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 VAL* 2.9 28.5 + - + +
131C LYS* 3.8 8.7 - - - +
133C GLU* 1.3 72.9 - - - +
135C ALA* 1.3 66.9 + - - +
137C LYS* 3.7 7.4 - - - -
138C GLY* 3.0 18.2 + - - -
139C TYR* 3.4 21.0 + - + -
140C GLY 4.1 12.2 + - - +
143C VAL* 3.8 37.2 - - + -
147C PHE* 3.9 19.5 - - + -
148C PHE* 4.8 14.4 - - + -
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Residues in contact with ALA 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 LYS 3.1 15.1 + - - +
132C ALA* 3.2 14.4 - - - +
133C GLU 3.1 0.2 - - - -
134C ILE* 1.3 78.6 - - - +
136C GLN* 1.3 61.6 + - - +
138C GLY* 3.0 15.2 + - - -
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Residues in contact with GLN 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 ALA 2.9 16.9 + - - +
133C GLU* 2.9 23.1 + - + +
135C ALA* 1.3 76.5 - - - +
137C LYS* 1.3 95.5 + - - +
138C GLY 3.5 0.2 + - - -
215C LYS* 5.2 9.7 - - - +
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Residues in contact with LYS 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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68C ASP* 3.3 25.4 + - - +
69C HIS* 6.0 0.2 + - - -
133C GLU* 2.7 27.6 + - - +
134C ILE 3.7 4.7 - - - +
136C GLN* 1.3 109.3 + - - +
138C GLY* 1.3 63.5 + - - +
139C TYR* 3.3 44.2 + - + -
147C PHE* 4.4 15.5 - - - -
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Residues in contact with GLY 138 (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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134C ILE 3.0 6.6 + - - -
135C ALA 3.0 12.7 + - - -
136C GLN 3.2 0.8 - - - -
137C LYS* 1.3 79.1 - - - +
139C TYR* 1.3 65.0 + - - +
140C GLY* 3.3 3.7 + - - -
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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