Contacts of the helix formed by residues 125 - 135 (chain C) in PDB entry 2V5Q
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 HIS 125 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C ALA 3.5 6.1 - - - +
89C MET 3.2 28.8 + - - -
90C THR* 3.5 11.3 - - - -
91C GLY* 3.4 25.0 - - - -
120C ALA* 2.8 11.6 + - - +
123C GLU* 3.4 29.3 + - + +
124C GLY* 1.3 74.8 + - - +
126C LEU* 1.3 59.0 - - - +
127C GLU 3.3 2.9 - - - -
128C ILE* 3.1 23.3 + - + +
129C VAL* 3.0 26.2 + - - +
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Residues in contact with LEU 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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121C ALA 5.1 1.3 - - - +
124C GLY* 3.1 22.8 + - - +
125C HIS* 1.3 70.6 - - - +
127C GLU* 1.3 60.1 - - - +
129C VAL* 3.3 19.6 + - + +
130C GLU* 3.0 22.7 + - - +
117D LEU* 3.4 23.3 - - + -
118D HIS* 3.4 37.7 - - + +
121D ALA* 3.8 27.4 - - + -
129D VAL* 6.0 0.9 - - + -
139D VAL* 3.7 34.9 - - + +
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Residues in contact with GLU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 4.3 17.1 - - + +
125C HIS 3.3 0.8 - - - -
126C LEU* 1.3 72.5 - - - +
128C ILE* 1.3 68.1 + - + +
130C GLU* 3.6 12.4 + - - +
131C VAL* 3.2 26.7 + - - +
139D VAL* 3.8 18.8 - - + -
140D ASN* 3.3 29.8 + - - +
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Residues in contact with ILE 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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88C ALA* 3.8 15.5 - - + +
91C GLY* 3.8 28.3 - - - +
92C HIS 3.9 2.7 - - - +
93C LEU* 3.4 46.7 - - + +
96C VAL* 4.2 12.3 - - + -
120C ALA* 3.7 11.9 - - + -
125C HIS* 3.1 15.5 + - + +
127C GLU* 1.3 78.1 - - + +
129C VAL* 1.3 55.0 + - - +
131C VAL* 3.1 5.5 + - + +
132C LEU* 2.9 51.8 + - + +
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU* 3.8 22.7 - - + +
120C ALA* 3.9 5.2 - - + -
121C ALA* 3.7 37.9 - - + +
125C HIS 3.0 17.4 + - - +
126C LEU* 3.3 21.8 - - + +
128C ILE* 1.3 76.1 - - - +
130C GLU* 1.3 61.5 + - - +
132C LEU* 3.3 2.3 + - - +
133C LEU* 3.0 30.8 + - + +
121D ALA* 6.0 0.4 - - + -
126D LEU* 5.8 0.9 - - + -
129D VAL* 3.7 29.2 - - + -
133D LEU* 4.7 2.2 - - + -
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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 LEU 3.0 11.5 + - - +
127C GLU* 3.6 14.6 - - - +
129C VAL* 1.3 77.4 - - - +
131C VAL* 1.3 58.6 + - + +
133C LEU* 3.4 4.5 + - - +
134C LYS* 2.9 34.1 + - - +
133D LEU* 3.5 36.1 - - + +
137D ALA 4.6 3.6 - - - +
139D VAL* 3.5 34.9 + - + +
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Residues in contact with VAL 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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93C LEU* 3.8 22.9 - - + -
96C VAL* 3.8 27.4 - - + -
97C GLU* 4.5 17.5 - - + +
100C LEU* 4.5 1.6 - - + -
127C GLU 3.2 12.4 + - - +
128C ILE* 3.1 9.8 + - - +
130C GLU* 1.3 80.1 - - + +
132C LEU* 1.3 63.8 + - - +
134C LYS* 3.4 17.9 + - - +
135C TYR* 3.2 42.7 + - + -
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Residues in contact with LEU 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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84C LEU* 4.1 27.1 - - + -
88C ALA* 4.0 2.9 - - + -
96C VAL* 4.1 12.8 - - + -
100C LEU* 4.5 3.8 - - + -
106C VAL* 3.6 23.5 - - + +
116C PRO* 3.7 11.2 - - + +
117C LEU* 3.6 33.2 - - + +
120C ALA* 4.3 2.5 - - + -
128C ILE* 2.9 39.3 + - + +
129C VAL 3.8 3.6 - - - +
131C VAL* 1.3 76.4 - - - +
133C LEU* 1.3 55.4 + - - +
135C TYR 3.3 1.6 + - - -
136C GLY 3.2 6.6 + - - -
137C ALA* 2.8 39.9 + - + +
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Residues in contact with LEU 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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117C LEU* 4.1 15.0 - - + -
129C VAL* 3.0 28.5 + - + +
130C GLU* 3.6 4.5 - - - +
132C LEU* 1.3 78.3 - - - +
134C LYS* 1.3 61.5 + - - +
136C GLY* 3.1 13.9 + - - -
137C ALA* 3.8 20.8 + - + +
139C VAL* 3.8 24.0 - - + -
129D VAL* 4.6 3.1 - - + -
130D GLU* 4.1 29.8 - - + +
133D LEU* 3.7 28.7 - - + -
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Residues in contact with LYS 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* 2.9 20.1 + - - +
131C VAL* 3.5 18.1 - - + +
133C LEU* 1.3 75.0 - - - +
135C TYR* 1.3 94.9 + - + +
136C GLY 3.4 0.7 + - - -
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Residues in contact with TYR 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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97C GLU* 5.3 11.2 + - + -
100C LEU* 3.9 32.9 - - + +
106C VAL* 3.6 14.6 - - + +
131C VAL* 3.2 36.3 + - + +
132C LEU 3.6 4.7 - - - +
133C LEU 3.2 0.8 - - - -
134C LYS* 1.3 108.0 + - + +
136C GLY* 1.3 56.9 + - - +
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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