Contacts of the helix formed by residues 124 - 134 (chain C) in PDB entry 7CE1
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 MET 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C LYS 3.9 4.5 + - - +
122C ASP 3.2 0.4 - - - -
123C SER* 1.3 84.0 + - - +
125C VAL* 1.3 65.3 + - + +
126C PRO* 3.6 1.3 - - - -
127C ILE* 3.4 8.7 + - + +
128C ARG* 3.3 63.3 + - + +
149C PRO* 3.9 17.3 - - + +
150C ARG* 3.8 30.7 - - - -
153C PHE* 3.4 47.1 - - + -
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C HIS* 5.5 0.4 - - + -
121C LYS 4.9 0.7 - - - +
122C ASP* 3.3 35.0 + - + +
124C MET* 1.3 80.0 - - + +
126C PRO* 1.3 71.7 - - + +
127C ILE 3.4 0.2 + - - -
128C ARG* 3.4 8.3 + - - +
129C TYR* 3.3 18.7 + - + +
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Residues in contact with PRO 126 (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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83C VAL* 4.3 14.8 - - + -
115C THR* 3.7 29.8 - - + +
116C PRO 5.4 1.3 - - - +
117C HIS* 4.2 20.2 - - + -
122C ASP 3.4 14.4 - - - +
123C SER 3.9 4.5 - - - +
124C MET 3.7 1.8 - - - -
125C VAL* 1.3 93.8 - - + +
127C ILE* 1.3 69.5 + - + +
129C TYR* 3.2 11.3 - - + +
130C ILE* 2.9 33.9 + - + +
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Residues in contact with ILE 127 (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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83C VAL* 4.5 16.6 - - + -
123C SER 3.4 26.0 - - - +
124C MET* 3.7 12.6 - - + +
125C VAL 3.2 0.6 - - - -
126C PRO* 1.3 84.9 - - + +
128C ARG* 1.3 64.7 + - - +
130C ILE* 3.3 8.1 + - - +
131C LEU* 3.1 24.5 + - + +
139C VAL* 5.1 4.3 - - + -
141C ILE* 4.7 4.9 - - + -
150C ARG* 3.7 27.8 - - + -
153C PHE* 3.7 25.6 - - + -
154C MET* 3.8 29.6 - - + -
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Residues in contact with ARG 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C MET* 3.3 56.0 + - + +
125C VAL* 4.0 7.2 - - - +
127C ILE* 1.3 72.7 - - - +
129C TYR* 1.3 61.1 + - - +
131C LEU* 4.1 0.9 - - - +
132C GLU* 2.9 39.2 + - - +
153C PHE* 4.2 20.7 - - + -
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Residues in contact with TYR 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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115C THR* 5.3 11.4 - - + -
125C VAL* 3.3 12.2 + - + +
126C PRO* 3.2 15.7 - - + +
128C ARG* 1.3 78.5 - - - +
130C ILE* 1.3 61.4 + - + +
132C GLU* 3.8 6.8 + - - +
133C THR* 2.7 68.3 + - + +
135C SER* 4.6 3.8 - - - -
64D GLN* 3.7 22.4 - - - -
67D ARG* 4.2 7.8 + - - -
111D HIS* 3.3 35.1 + + - -
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Residues in contact with ILE 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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81C ALA* 3.7 27.1 - - + -
83C VAL* 4.3 17.9 - - + -
115C THR* 5.0 7.0 - - + +
126C PRO* 2.9 22.4 + - + +
127C ILE* 3.3 7.8 + - - +
129C TYR* 1.3 82.9 - - + +
131C LEU* 1.3 59.9 + - + +
133C THR* 4.0 6.1 - - - -
134C GLY* 2.7 34.5 + - - -
135C SER* 3.3 8.5 + - - +
136C ALA* 3.7 28.3 - - + +
139C VAL* 4.1 20.9 - - + -
159C MET* 4.7 5.8 - - + +
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Residues in contact with LEU 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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127C ILE* 3.1 39.6 + - + +
128C ARG 4.2 2.2 - - - +
130C ILE* 1.3 87.5 - - + +
132C GLU* 1.3 62.9 - - - +
134C GLY* 3.4 9.3 + - - -
139C VAL* 5.4 0.2 - - + -
153C PHE* 3.8 16.6 - - + -
154C MET* 4.0 6.5 - - + -
157C ARG* 3.3 51.8 + - + +
159C MET* 3.8 38.4 - - + -
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Residues in contact with GLU 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 ARG* 2.9 25.6 + - - +
129C TYR* 3.8 5.2 - - - +
131C LEU* 1.3 80.5 - - - +
133C THR* 1.3 60.2 + - - +
134C GLY* 3.6 0.3 + - - -
157C ARG* 5.4 3.3 - - - +
19D ARG* 4.0 19.9 + - + +
20D PRO* 5.7 3.5 - - - +
62D GLY 4.9 3.5 - - - +
64D GLN* 3.0 30.5 + - - +
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Residues in contact with THR 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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71C ARG* 4.2 9.0 + - - -
129C TYR* 2.7 58.2 + - + +
130C ILE 3.7 0.9 - - - +
132C GLU* 1.3 75.8 - - - +
134C GLY* 1.3 64.5 + - - +
135C SER* 3.2 32.3 + - - +
19D ARG* 3.5 34.5 + - - +
64D GLN* 4.9 6.6 + - - +
65D PRO 5.3 0.2 + - - -
67D ARG* 5.1 6.2 - - - +
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Residues in contact with GLY 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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71C ARG* 4.0 3.3 + - - -
75C GLY 4.8 1.7 - - - +
77C THR* 3.2 19.8 - - - +
130C ILE 2.7 14.9 + - - -
131C LEU* 3.4 7.8 + - - -
132C GLU 3.2 3.2 + - - -
133C THR* 1.3 79.2 - - - +
135C SER* 1.3 54.7 + - - -
136C ALA 3.3 8.5 - - - +
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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