Contacts of the helix formed by residues 134 - 145 (chain C) in PDB entry 6QPA
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 ASP 134 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C MET* 3.8 16.1 - - + +
131C SER* 2.9 40.3 + - - +
133C THR* 1.3 83.5 + - - +
135C VAL* 1.3 63.1 + - - +
136C PRO 3.5 0.9 - - - -
137C GLN* 3.3 9.9 + - - +
138C VAL* 3.0 28.7 + - + +
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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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130C MET* 4.1 14.8 - - - -
131C SER 3.5 10.8 - - - +
132C MET* 3.1 23.3 + - - +
134C ASP* 1.3 75.9 - - - +
136C PRO* 1.3 73.0 - - + +
138C VAL* 3.1 8.1 + - + +
139C LEU* 2.8 28.5 + - + +
149C VAL* 6.5 1.1 - - + -
152C VAL* 4.1 27.1 - - + -
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Residues in contact with PRO 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 MET 3.7 9.0 - - - +
133C THR* 4.1 7.6 - - - +
134C ASP 3.8 2.2 - - - -
135C VAL* 1.3 94.7 - - + +
137C GLN* 1.3 56.8 + - - +
139C LEU* 3.3 10.2 + - + +
140C GLY* 2.9 24.3 + - - -
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Residues in contact with GLN 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 THR 5.3 1.5 + - - +
134C ASP* 3.3 10.8 + - - +
135C VAL 3.2 0.8 - - - -
136C PRO* 1.3 76.2 - - - +
138C VAL* 1.3 63.5 + - + +
140C GLY* 3.7 1.3 - - - +
141C ASP* 2.8 51.8 + - - +
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Residues in contact with VAL 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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128C GLN* 3.8 22.2 - - - +
130C MET* 3.9 32.5 - - + -
134C ASP* 3.0 27.6 + - + +
135C VAL* 3.6 4.7 - - + +
137C GLN* 1.3 76.6 - - + +
139C LEU* 1.3 63.1 + - - +
141C ASP* 3.9 5.4 - - - +
142C SER* 3.0 31.4 + - - +
149C VAL* 5.0 3.4 - - + -
150C PRO* 4.0 22.4 - - + -
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Residues in contact with LEU 139 (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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135C VAL* 2.8 18.6 + - + +
136C PRO* 3.4 12.6 - - + +
138C VAL* 1.3 76.7 - - - +
140C GLY* 1.3 62.6 + - - +
142C SER* 3.3 6.1 + - - -
143C PHE* 3.1 46.2 + - + -
149C VAL* 3.5 36.3 - - + +
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Residues in contact with GLY 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 PRO 2.9 15.0 + - - -
137C GLN* 3.2 2.4 + - - -
139C LEU* 1.3 74.6 - - - +
141C ASP* 1.3 59.3 + - - +
143C PHE* 3.1 12.1 + - - +
144C ALA* 2.9 29.1 + - - +
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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 GLN* 2.8 45.9 + - - +
138C VAL* 4.0 5.6 - - - +
140C GLY* 1.3 72.8 - - - +
142C SER* 1.3 57.9 + - - +
144C ALA* 3.3 6.5 + - - +
145C LYS* 2.9 57.8 + - + +
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Residues in contact with SER 142 (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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138C VAL* 3.0 25.4 + - - +
139C LEU 3.5 4.7 - - - -
140C GLY 3.2 0.2 - - - -
141C ASP* 1.3 77.0 - - - +
143C PHE* 1.3 60.7 + - - +
145C LYS* 3.5 3.4 + - - +
146C GLN 3.1 2.8 + - - -
147C GLU* 2.8 48.1 + - - +
148C ARG 3.7 11.8 + - - -
149C VAL* 3.7 26.2 - - - -
150C PRO* 4.1 5.7 - - - +
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Residues in contact with PHE 143 (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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139C LEU* 3.1 43.2 + - + -
140C GLY* 3.1 10.5 + - - +
142C SER* 1.3 77.7 - - - +
144C ALA* 1.3 64.8 + - - +
146C GLN* 3.2 21.3 + - - +
147C GLU 5.0 3.8 - - - -
149C VAL* 4.1 17.9 - - + -
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Residues in contact with ALA 144 (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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140C GLY 2.9 15.9 + - - +
141C ASP* 3.6 9.0 - - - +
143C PHE* 1.3 78.7 - - - +
145C LYS* 1.3 62.9 + - + +
146C GLN* 3.2 12.8 + - - +
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Residues in contact with LYS 145 (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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141C ASP* 2.9 45.4 + - + +
142C SER* 4.2 3.4 + - - +
144C ALA* 1.3 76.5 - - + +
146C GLN* 1.3 69.8 + - - +
147C GLU* 3.0 42.9 + - + +
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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