Contacts of the helix formed by residues 132 - 147 (chain C) in PDB entry 6GL7
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 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C LYS* 4.0 26.2 + - - +
130C PRO 4.3 1.2 + - - -
131C VAL* 1.3 81.0 - - + +
133C SER* 1.3 64.8 + - - +
134C ARG 3.3 0.7 + - - -
135C LEU* 3.8 13.9 + - - +
136C SER* 4.4 3.3 + - - -
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Residues in contact with SER 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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96C LYS* 5.8 1.6 - - - +
130C PRO* 2.7 39.8 + - - +
132C THR* 1.3 73.3 + - - +
134C ARG* 1.3 51.1 + - - +
135C LEU 3.2 1.6 - - - -
136C SER* 2.9 14.2 + - - -
137C ASP* 2.6 48.2 + - - -
140C ARG* 5.5 5.3 + - - -
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Residues in contact with ARG 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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126C SER* 4.6 3.8 + - - -
129C GLU* 3.0 42.3 + - + +
130C PRO 3.9 1.1 + - - +
131C VAL* 3.0 50.8 + - - +
133C SER* 1.3 76.6 - - - +
135C LEU* 1.3 62.5 + - - +
137C ASP* 3.3 14.3 + - - +
138C ILE* 3.2 26.9 + - - +
273C ALA* 5.8 1.4 - - - +
274C ASN* 4.8 6.2 + - - +
289C ASN* 3.8 5.2 + - - +
292C ALA* 6.0 5.2 - - + -
116F PHE* 4.7 21.0 - - - -
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Residues in contact with LEU 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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132C THR 3.8 9.7 + - - +
133C SER 3.2 0.4 - - - -
134C ARG* 1.3 76.0 - - - +
136C SER* 1.3 67.0 + - - +
138C ILE* 3.0 31.7 + - + +
139C PHE* 3.2 40.5 + - + -
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Residues in contact with SER 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 THR 4.7 2.4 + - - -
133C SER* 2.9 19.4 + - - +
135C LEU* 1.3 78.6 - - - +
137C ASP* 1.3 52.5 + - - +
139C PHE* 2.9 15.0 + - - +
140C ARG* 2.7 53.4 + - - +
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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
----------------------------------------------------------
130C PRO* 5.7 2.1 - - - +
133C SER* 2.6 34.3 + - - +
134C ARG* 3.4 14.9 + - - +
135C LEU 3.2 0.2 - - - -
136C SER* 1.3 70.8 - - - +
138C ILE* 1.3 64.6 + - - +
140C ARG* 3.2 29.2 + - - +
141C LEU 3.6 1.4 + - - -
289C ASN* 3.9 9.6 - - - +
291C GLN* 3.1 44.1 + - + +
292C ALA* 4.5 10.9 - - - +
295C GLY* 6.1 1.1 - - - -
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Residues in contact with ILE 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 ARG* 3.6 10.8 - - + +
135C LEU* 3.0 23.5 + - + +
137C ASP* 1.3 78.3 - - - +
139C PHE* 1.3 69.6 + - + +
141C LEU* 3.1 28.4 + - + +
142C ALA 4.1 1.0 + - - -
287C ALA* 5.5 9.6 - - + +
289C ASN* 3.4 33.2 - - + +
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Residues in contact with PHE 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 LEU* 3.2 51.1 + - + -
136C SER* 2.9 11.9 + - - +
138C ILE* 1.3 81.2 - - + +
140C ARG* 1.3 67.4 + - - +
142C ALA* 2.8 27.1 + - + +
143C SER* 3.5 6.0 + - - -
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Residues in contact with ARG 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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133C SER* 5.5 5.1 + - - -
136C SER* 2.7 32.8 + - - +
137C ASP* 3.2 33.3 + - - +
139C PHE* 1.3 71.8 - - - +
141C LEU* 1.3 57.5 + - - +
143C SER* 3.1 11.0 + - - -
144C ILE* 2.8 34.9 + - + +
213C SER* 4.6 16.8 + - - -
217C TYR* 6.2 0.7 - - - -
291C GLN* 4.1 20.6 - - - +
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Residues in contact with LEU 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 4.0 5.8 - - - +
138C ILE* 3.1 20.5 + - + +
139C PHE 3.0 1.0 + - - -
140C ARG* 1.3 78.3 - - - +
142C ALA* 1.3 56.5 + - - +
144C ILE* 3.3 1.5 + - - -
145C PHE* 2.9 29.0 + - - +
288C ASP 5.3 1.8 - - - +
289C ASN* 3.7 20.0 - - - +
290C TYR* 4.0 18.4 - - + +
291C GLN* 3.9 11.0 - - + +
355C PHE* 3.4 29.2 - - + -
359C THR* 3.4 31.0 - - + +
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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 ILE 4.1 1.0 + - - +
139C PHE* 2.8 17.9 + - + +
141C LEU* 1.3 79.0 - - - +
143C SER* 1.3 62.2 + - - +
145C PHE* 3.3 20.4 + - - +
146C SER* 3.4 7.8 + - - -
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Residues in contact with SER 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 PHE 3.5 5.9 + - - -
140C ARG* 3.1 14.5 + - - -
142C ALA* 1.3 78.8 - - - +
144C ILE* 1.3 59.0 + - - +
146C SER* 2.9 8.9 + - - -
147C GLY 2.8 33.0 + - - +
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Residues in contact with ILE 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 ARG* 2.8 22.3 + - + +
141C LEU* 3.3 0.9 + - - +
143C SER* 1.3 76.1 - - - +
145C PHE* 1.3 62.6 + - - +
146C SER 3.1 1.0 + - - -
147C GLY* 3.3 17.0 + - - -
213C SER* 6.5 0.9 - - - -
214C GLU* 6.5 1.1 - - - -
217C TYR* 4.7 12.3 - - + -
291C GLN* 3.1 28.3 - - - +
294C LEU* 4.5 6.1 - - + -
355C PHE* 3.7 24.9 - - + +
358C GLY* 4.2 8.8 - - - +
359C THR 3.4 28.3 - - - +
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Residues in contact with PHE 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 LEU 2.9 13.8 + - - +
142C ALA* 3.4 14.4 - - - +
143C SER 3.2 0.2 - - - -
144C ILE* 1.3 76.7 - - - +
146C SER* 1.3 63.0 + - - +
358C GLY* 3.2 30.8 - - - +
359C THR* 4.3 9.8 + - + +
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Residues in contact with SER 146 (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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142C ALA 3.4 6.2 + - - -
143C SER* 2.9 10.3 + - - -
144C ILE 3.8 0.2 - - - -
145C PHE* 1.3 84.7 - - - +
147C GLY* 1.3 58.1 + - - +
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Residues in contact with GLY 147 (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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143C SER* 2.8 25.1 + - - +
144C ILE* 3.3 12.6 + - - -
146C SER* 1.3 77.1 + - - +
214C GLU* 4.5 22.0 - - - +
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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