Contacts of the helix formed by residues 129 - 141 (chain C) in PDB entry 1YV0
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 THR 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C ARG* 4.6 4.5 - - - +
127C HIS* 5.5 2.0 - - - +
128C VAL* 1.3 77.6 - - - +
130C GLU* 1.3 68.0 + - - +
131C GLU* 2.5 29.8 + - + +
132C ASP* 2.5 67.7 + - - +
133C ILE* 2.9 17.8 + - - +
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Residues in contact with GLU 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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114C ILE* 5.0 15.2 - - - +
122C ARG* 3.3 32.5 + - - +
129C THR* 1.3 74.0 + - - +
131C GLU* 1.3 64.9 + - + +
133C ILE* 4.2 14.6 - - - +
134C GLU* 3.8 22.3 + - - +
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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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129C THR* 2.5 22.6 + - + +
130C GLU* 1.3 89.9 - - + +
132C ASP* 1.3 58.0 + - - +
133C ILE 3.1 5.1 + - - -
134C GLU* 4.3 18.4 - - - +
135C ASP* 3.6 19.9 + - - +
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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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121C LEU* 3.7 9.8 - - + +
128C VAL* 2.7 15.5 - - + -
129C THR* 2.5 57.0 + - - +
131C GLU* 1.3 75.2 - - - +
133C ILE* 1.3 58.5 + - - +
135C ASP* 4.2 7.4 - - - +
136C LEU* 3.9 14.9 + - - +
13I ARG* 2.6 35.9 + - - +
17I LEU* 5.0 6.4 - - + +
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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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114C ILE* 3.3 37.2 - - + +
117C LEU* 4.6 9.4 - - + +
118C GLY* 3.3 30.3 - - - +
121C LEU* 3.5 21.5 - - + -
122C ARG* 3.9 30.5 - - - +
128C VAL* 4.9 3.6 - - + -
129C THR 2.9 15.0 + - - +
130C GLU* 4.4 12.6 - - - +
132C ASP* 1.3 76.9 - - - +
134C GLU* 1.3 53.9 + - - +
135C ASP 2.7 16.2 + - - -
136C LEU* 3.0 14.0 + - - +
137C MET* 3.4 10.7 + - - +
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Residues in contact with GLU 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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114C ILE* 4.0 16.8 - - + +
130C GLU* 3.8 21.5 + - - +
131C GLU* 4.6 18.6 - - - +
133C ILE* 1.3 75.4 - - - +
135C ASP* 1.3 57.5 + - + +
137C MET* 4.5 6.9 - - - +
138C LYS* 4.4 17.0 + - - +
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Residues in contact with ASP 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 3.6 17.0 + - - +
132C ASP* 4.2 6.8 - - - +
133C ILE 2.7 6.1 + - - -
134C GLU* 1.3 77.3 - - + +
136C LEU* 1.3 66.3 + - - +
137C MET 3.4 0.4 - - - -
138C LYS* 3.3 32.1 + - - +
139C ASP* 4.2 1.7 + - - +
10I ALA* 5.5 2.8 - - - +
14I ARG* 3.2 42.0 + - - +
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Residues in contact with LEU 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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117C LEU* 4.3 22.7 - - + -
121C LEU* 4.5 24.9 - - + -
132C ASP 3.9 8.2 + - - +
133C ILE* 3.0 8.6 + - - +
135C ASP* 1.3 80.0 + - - +
137C MET* 1.3 58.3 + - - +
138C LYS 2.9 10.9 + - - -
139C ASP* 2.9 17.9 + - + +
140C SER* 3.9 6.0 + - - +
156C MET* 3.7 25.4 - - + -
14I ARG* 3.7 29.8 - - + +
17I LEU* 4.9 7.4 - - + -
18I LYS* 3.8 23.1 - - + +
21I MET* 4.7 5.2 - - - -
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Residues in contact with MET 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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112C ILE 4.7 0.4 - - - +
113C ASP* 3.4 4.9 - - - -
114C ILE* 2.9 54.3 - - + +
117C LEU* 4.4 13.4 - - + +
133C ILE 3.4 10.4 + - - +
134C GLU* 4.8 5.6 - - - +
135C ASP 3.4 0.6 - - - -
136C LEU* 1.3 76.2 - - - +
138C LYS* 1.3 55.6 + - - +
139C ASP 3.2 4.8 + - - -
140C SER 4.6 1.1 - - - +
141C ASP* 3.6 28.3 + - + +
146C GLY* 2.9 47.3 - - - +
147C ARG* 3.9 2.2 - - - +
148C ILE* 5.8 7.9 - - + -
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Residues in contact with LYS 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 GLU* 4.4 15.6 + - - +
135C ASP* 3.3 24.2 + - - +
136C LEU 2.9 1.4 + - - -
137C MET* 1.3 77.4 - - - +
139C ASP* 1.3 58.3 + - - +
141C ASP 5.2 3.8 - - - -
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Residues in contact with ASP 139 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C ASP 4.7 2.2 - - - +
136C LEU* 2.9 11.9 + - + +
137C MET 3.2 0.2 - - - -
138C LYS* 1.3 81.4 - - - +
140C SER* 1.3 63.3 + - - +
141C ASP 3.6 2.5 - - - -
142C LYS* 3.8 23.9 + - - +
155C LYS* 5.8 0.3 - - - +
156C MET* 5.3 1.6 - - - +
14I ARG* 4.5 23.7 + - - +
18I LYS* 3.9 20.1 + - - -
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Residues in contact with SER 140 (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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136C LEU 3.9 5.3 + - - -
137C MET 4.2 0.6 + - - -
139C ASP* 1.3 76.9 + - - +
141C ASP* 1.3 60.5 + - - +
142C LYS* 2.9 13.9 + - - +
148C ILE* 3.2 28.7 - - - -
152C GLU* 2.9 34.2 - - - +
155C LYS* 5.9 1.1 - - - -
156C MET* 2.6 49.1 - - - +
18I LYS* 4.8 0.5 + - - -
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Residues in contact with ASP 141 (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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137C MET* 3.6 22.7 + - + +
138C LYS* 5.6 3.0 - - - -
139C ASP 5.0 2.2 - - - -
140C SER* 1.3 74.5 - - - +
142C LYS* 1.3 62.7 + - - +
143C ASN* 2.9 2.8 - - - +
144C ASN* 2.7 17.7 + - - +
145C ASP* 2.2 47.7 + - - +
146C GLY* 3.2 9.9 + - - -
147C ARG 3.2 18.4 - - - +
148C ILE* 4.2 2.3 - - + +
152C GLU* 3.2 8.3 - - - -
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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