Contacts of the helix formed by residues 122 - 130 (chain A) in PDB entry 1V72
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 ASP 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A VAL* 3.8 1.7 - - - +
115A ASP 3.1 23.3 + - - +
116A GLY* 4.2 7.9 - - - -
117A PRO* 5.3 6.2 - - + +
120A LYS 3.3 2.1 + - - -
121A LEU* 1.3 70.9 - - - +
123A ILE* 1.3 60.5 + - - +
124A VAL* 2.9 18.2 + - - +
125A ARG* 2.8 34.6 + - + +
126A LEU* 2.9 28.3 + - - +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU 3.3 6.3 + - - +
122A ASP* 1.3 73.2 - - - +
124A VAL* 1.3 72.6 + - + +
126A LEU* 3.4 8.8 + - + +
127A ARG* 3.0 64.2 + - - +
161A GLU 5.3 0.2 - - - +
164A ALA* 3.7 27.6 - - + +
165A ILE* 4.0 17.7 - - + +
168A VAL* 3.7 27.6 - - + -
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ASP* 2.9 12.1 + - - +
123A ILE* 1.3 84.5 - - + +
125A ARG* 1.3 67.1 + - - +
127A ARG* 3.3 22.9 + - - +
128A GLU* 3.1 41.2 + - + +
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 3.6 22.6 - - + +
115A ASP* 4.7 5.2 - - + +
122A ASP* 2.8 27.1 + - + +
124A VAL* 1.3 71.0 - - - +
126A LEU* 1.3 62.1 + - - +
128A GLU* 3.0 42.8 + - - +
129A ARG* 2.8 66.6 + - + +
132A GLU* 4.1 8.1 + - - -
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A TYR* 4.0 22.0 - - + -
114A VAL* 3.5 19.4 - - + +
121A LEU* 4.4 10.8 - - + -
122A ASP 2.9 17.4 + - - +
123A ILE* 3.6 15.7 - - + +
125A ARG* 1.3 77.3 - - - +
127A ARG* 1.3 62.0 + - - +
129A ARG* 3.3 0.4 + - - -
130A THR* 3.0 56.4 + - + +
145A VAL* 4.2 14.1 - - + -
165A ILE* 3.8 36.8 - - + -
168A VAL* 4.4 12.3 - - + -
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Residues in contact with ARG 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ILE* 3.0 52.2 + - - +
124A VAL* 3.5 29.4 - - - +
126A LEU* 1.3 76.4 - - - +
128A GLU* 1.3 58.6 + - + +
130A THR* 3.4 11.8 + - - -
131A ARG* 3.1 29.7 + - - +
164A ALA* 5.2 6.7 + - - +
168A VAL* 3.8 25.9 - - + +
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A VAL* 3.1 29.0 - - + +
125A ARG* 3.0 37.8 + - - +
127A ARG* 1.3 76.3 - - + +
129A ARG* 1.3 64.7 + - - +
131A ARG* 3.2 45.5 + - - +
132A GLU* 3.5 11.6 - - - +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A TYR* 3.5 26.8 + - + -
112A MET* 3.7 30.6 - - - +
113A THR* 3.0 43.1 + - - +
114A VAL* 3.8 12.3 - - + -
125A ARG* 2.8 54.1 + - + +
126A LEU 4.0 2.5 - - - +
128A GLU* 1.3 71.5 - - - +
130A THR* 1.3 58.9 + - - +
131A ARG 3.0 5.2 + - - -
132A GLU* 3.1 52.8 + - - +
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Residues in contact with THR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A TYR* 4.0 20.2 - - + -
126A LEU* 3.0 41.3 + - + +
127A ARG 3.4 8.7 + - - -
128A GLU 3.3 0.2 - - - -
129A ARG* 1.3 75.3 - - - +
131A ARG* 1.3 57.0 + - - +
132A GLU 3.5 0.9 - - - -
134A VAL* 4.0 4.3 - - - +
142A PRO* 3.1 20.2 - - - +
145A VAL* 4.5 0.7 - - + -
168A VAL* 3.6 15.2 - - + +
172A SER* 4.2 15.2 + - - -
174A LEU* 3.6 30.5 - - + -
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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