Contacts of the helix formed by residues 132 - 142 (chain C) in PDB entry 3Q29
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 GLU 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C PRO* 3.5 30.6 - - + +
128C LYS* 3.4 6.9 + - - +
129C THR* 2.7 46.1 + - - +
130C TRP 3.1 0.2 + - - -
131C GLU* 1.3 76.9 - - - +
133C ILE* 1.3 63.8 + - - +
134C PRO* 3.4 1.1 - - - -
135C ALA* 3.4 10.3 + - + +
136C LEU* 3.0 21.6 + - + +
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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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116C LEU* 6.1 0.7 - - + -
127C PRO* 4.1 17.5 - - + -
129C THR 3.8 9.4 - - - +
130C TRP* 3.0 43.0 + - + +
132C GLU* 1.3 75.8 - - - +
134C PRO* 1.3 71.1 - - + +
136C LEU* 3.0 6.6 + - - +
137C ASP* 2.8 23.5 + - + +
147C ALA* 4.0 18.6 - - + -
148C LEU* 4.3 18.2 - - + -
199C LEU* 4.7 12.8 - - + -
204C HIS* 5.9 1.6 - - + -
225C MET* 4.2 17.9 - - + -
249C PRO* 4.4 10.1 - - + -
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Residues in contact with PRO 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 TRP 3.6 7.2 - - - +
131C GLU 3.1 17.7 - - - +
132C GLU 3.4 1.1 - - - -
133C ILE* 1.3 92.2 - - + +
135C ALA* 1.3 62.4 + - - +
137C ASP 3.1 2.1 + - - -
138C LYS* 3.0 20.0 + - - +
195C PHE* 4.1 12.8 - - + -
199C LEU* 4.0 15.7 - - + -
204C HIS* 3.4 39.4 - - + +
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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 GLU 5.1 0.6 + - - +
132C GLU* 3.4 11.3 + - + +
133C ILE 3.3 0.2 - - - -
134C PRO* 1.3 79.2 - - - +
136C LEU* 1.3 63.5 + - - +
138C LYS* 3.4 10.8 + - - +
139C GLU* 3.3 31.2 + - - +
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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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123C LEU* 4.0 41.7 - - + -
127C PRO* 4.2 17.7 - - + -
132C GLU* 3.0 14.5 + - + +
133C ILE* 3.0 10.9 + - - +
135C ALA* 1.3 78.7 - - - +
137C ASP* 1.3 60.9 + - - +
139C GLU* 3.3 18.3 + - - +
140C LEU* 3.1 35.2 + - + +
147C ALA* 4.2 2.9 - - + -
225C MET* 4.1 18.6 - - + -
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Residues in contact with ASP 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* 2.8 12.7 + - + +
134C PRO 3.1 2.9 + - - +
136C LEU* 1.3 74.7 - - - +
138C LYS* 1.3 54.5 + - - +
140C LEU* 3.0 2.0 + - - +
141C LYS* 2.7 73.5 + - - +
146C SER* 3.3 7.6 - - - -
147C ALA* 2.9 37.9 + - + +
203C LYS 4.2 0.3 - - - +
204C HIS* 2.7 44.5 + - + +
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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 PRO 3.0 11.8 + - - +
135C ALA* 3.6 13.9 - - - +
136C LEU 3.3 0.2 - - - -
137C ASP* 1.3 77.8 + - - +
139C GLU* 1.3 62.7 + - + +
141C LYS* 3.4 14.8 + - - +
142C ALA* 3.5 11.8 + - - +
204C HIS* 4.6 6.7 - - + -
395C SO4 2.9 42.3 + - - +
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Residues in contact with GLU 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 ALA* 3.3 17.4 + - - +
136C LEU* 3.6 18.8 - - + +
137C ASP 3.2 0.6 - - - -
138C LYS* 1.3 76.9 - - + +
140C LEU* 1.3 65.0 + - + +
142C ALA* 3.3 19.5 + - - +
143C LYS* 3.9 21.8 + - - +
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Residues in contact with LEU 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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122C LEU* 4.2 25.4 - - + +
123C LEU* 5.4 1.3 - - + -
136C LEU* 3.1 34.4 + - + +
137C ASP 3.0 4.7 + - - +
139C GLU* 1.3 75.3 - - + +
141C LYS* 1.3 64.2 + - - +
143C LYS* 2.9 33.8 + - + +
145C LYS* 2.8 47.6 + - + -
146C SER 3.7 4.0 - - - +
147C ALA* 3.6 27.6 - - - -
224C ALA* 3.7 20.4 - - + -
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Residues in contact with LYS 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 ASP* 2.7 60.9 + - - +
138C LYS* 3.6 9.9 - - - +
139C GLU 3.2 0.2 - - - -
140C LEU* 1.3 71.4 - - - +
142C ALA* 1.3 57.8 + - - +
144C GLY* 2.8 20.7 + - - -
145C LYS 2.9 25.4 - - - +
146C SER* 4.2 10.6 - - - -
203C LYS 3.3 19.4 + - - -
204C HIS* 4.3 3.4 + - - +
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Residues in contact with ALA 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 LYS 3.5 7.4 + - - +
139C GLU* 3.3 13.2 + - - +
140C LEU 3.1 0.6 - - - -
141C LYS* 1.3 77.5 - - - +
143C LYS* 1.3 60.5 + - + +
144C GLY 3.3 1.2 + - - -
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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