Contacts of the helix formed by residues 124 - 134 (chain C) in PDB entry 4BVH
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 SER 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C LYS 3.8 1.3 + - - -
123C LEU* 1.3 74.9 - - - +
125C LEU* 1.3 64.7 + - - +
126C GLN* 3.4 10.7 + - - +
127C ASP* 3.0 39.5 + - - +
128C VAL* 3.2 17.0 + - - +
360C VAL* 4.0 4.9 - - - +
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Residues in contact with LEU 125 (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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124C SER* 1.3 71.7 - - - +
126C GLN* 1.3 60.1 + - - +
128C VAL* 3.2 5.8 + - + +
129C ALA* 2.9 25.8 + - - +
341C LEU* 3.8 39.0 - - + -
343C ILE* 5.4 1.1 - - + -
360C VAL* 4.0 8.9 - - + +
362C GLN* 3.6 34.8 - - + +
369C GLY 4.4 1.1 - - - +
372C SER* 3.9 12.3 - - - -
373C LEU* 3.8 31.7 - - + +
376C LEU* 3.7 21.8 - - + -
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Residues in contact with GLN 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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124C SER* 3.1 10.4 + - - +
125C LEU* 1.3 80.7 - - - +
127C ASP* 1.3 59.8 + - - +
129C ALA* 3.1 3.6 + - - +
130C GLU* 2.8 49.3 + - + +
376C LEU* 3.8 36.4 - - + +
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Residues in contact with ASP 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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122C LYS 4.4 1.2 - - - +
123C LEU* 3.2 30.6 - - + +
124C SER* 3.0 41.4 + - - +
126C GLN* 1.3 79.7 - - - +
128C VAL* 1.3 62.3 + - - +
130C GLU* 3.3 7.4 + - - +
131C LEU* 3.0 30.6 + - + +
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Residues in contact with VAL 128 (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* 5.0 7.2 - - + -
124C SER 3.2 12.6 + - - +
125C LEU* 3.2 8.0 + - - +
127C ASP* 1.3 76.0 - - - +
129C ALA* 1.3 66.6 + - - +
131C LEU* 3.2 10.4 + - + +
132C ILE* 3.1 27.9 + - + +
314C LEU* 4.1 34.1 - - + -
316C LEU* 4.9 0.2 - - + -
339C PRO* 5.1 4.7 - - + -
341C LEU* 4.1 30.3 - - + -
360C VAL* 3.8 26.9 - - + -
373C LEU* 4.9 1.8 - - + -
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Residues in contact with ALA 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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125C LEU 2.9 11.6 + - - +
126C GLN 3.1 6.9 + - - +
128C VAL* 1.3 76.0 - - - +
130C GLU* 1.3 53.4 + - + +
132C ILE* 3.2 1.1 + - - -
133C ARG* 2.7 37.9 + - - +
373C LEU* 3.9 12.9 - - + +
376C LEU* 3.5 45.3 - - + +
377C LEU* 3.3 16.3 - - + +
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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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126C GLN* 2.8 41.4 + - + +
127C ASP* 3.9 6.7 - - - +
128C VAL 3.2 0.2 - - - -
129C ALA* 1.3 74.3 - - - +
131C LEU* 1.3 59.2 + - - +
133C ARG* 2.7 46.7 + - - +
134C ALA* 3.0 32.4 + - - +
376C LEU 4.0 11.4 - - - +
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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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123C LEU* 5.0 5.6 - - + -
127C ASP* 3.0 21.3 + - + +
128C VAL* 3.2 14.6 + - + +
130C GLU* 1.3 78.2 - - - +
132C ILE* 1.3 57.5 + - - +
134C ALA* 4.7 0.4 - - - -
135C ARG 3.4 1.2 + - - -
136C ALA* 2.9 43.8 + - + +
137C CYS* 3.0 27.1 + - - -
314C LEU* 5.8 0.2 - - + -
339C PRO* 4.1 16.4 - - + -
358C ARG* 4.0 18.4 - - - +
1396C EDO 3.6 29.4 - - - +
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Residues in contact with ILE 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 VAL* 3.1 23.1 + - + +
129C ALA* 3.6 5.6 - - - +
131C LEU* 1.3 72.6 - - - +
133C ARG* 1.3 60.1 + - - +
135C ARG* 2.7 34.0 + - - -
137C CYS* 4.1 13.0 - - + +
140C VAL* 5.2 2.9 - - + -
212C PHE* 5.2 2.0 - - + -
216C LEU* 4.4 11.2 - - + -
221C LEU* 3.8 25.0 - - + +
314C LEU* 3.7 30.7 - - + -
316C LEU* 5.2 4.7 - - + -
373C LEU* 4.8 10.8 - - + -
377C LEU* 3.6 27.8 - - + -
379C TRP* 3.9 11.2 - - + -
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Residues in contact with ARG 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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129C ALA 2.7 20.9 + - - +
130C GLU* 2.7 48.9 + - - +
132C ILE* 1.3 74.6 - - - +
134C ALA* 1.3 59.7 + - - +
135C ARG* 3.0 27.3 + - - +
376C LEU 4.6 2.7 - - - -
377C LEU* 3.9 32.2 + - + +
378C GLY* 5.9 0.8 - - - -
379C TRP* 5.5 2.7 - - - +
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Residues in contact with ALA 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 GLU 3.0 19.1 + - - +
131C LEU* 3.9 5.2 - - - +
132C ILE 3.1 0.4 - - - -
133C ARG* 1.3 76.2 - - - +
135C ARG* 1.3 67.3 + - - +
136C ALA* 3.3 11.6 + - + +
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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