Contacts of the helix formed by residues 123 - 133 (chain C) in PDB entry 1V14
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 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C LEU 5.4 1.1 - - - +
26C ALA 3.3 2.6 + - - -
27C GLY* 3.6 16.8 - - - +
87C THR* 4.2 3.6 - - - -
88C PRO* 5.5 0.9 - - + -
91C GLN* 2.6 49.1 + - + +
99C TYR* 3.4 27.8 - - + +
100C GLU* 4.4 0.2 - - - -
122C THR* 1.3 74.4 - - - +
124C PRO* 1.3 74.8 - - - +
126C ARG* 3.3 12.1 + - - +
127C HIS* 2.8 21.7 + - - +
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Residues in contact with PRO 124 (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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87C THR* 3.6 13.5 - - + -
91C GLN 3.7 7.4 - - - +
92C GLN* 4.4 0.4 - - - -
93C VAL* 3.9 12.3 - - + +
96C ARG* 3.3 35.2 - - + +
97C LYS 3.9 3.6 - - - +
98C VAL 3.4 22.2 - - - +
100C GLU* 3.6 29.4 - - + +
123C THR* 1.3 83.7 - - - +
125C LYS* 1.3 63.4 + - - +
127C HIS* 3.2 2.8 + - + +
128C ILE* 2.9 30.2 + - + +
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Residues in contact with LYS 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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16A LYS* 5.6 6.1 - - - +
17A PRO* 4.5 30.5 + - - -
18A VAL* 6.0 1.0 - - - +
90C ASN 3.6 20.5 + - - +
91C GLN* 3.0 38.6 + - - +
92C GLN 4.5 2.7 - - - +
93C VAL* 3.7 16.6 - - + -
123C THR 3.1 0.2 + - - -
124C PRO* 1.3 75.1 - - - +
126C ARG* 1.3 63.1 + - - +
128C ILE* 3.7 2.5 + - - +
129C ASP* 2.9 43.4 + - - +
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Residues in contact with ARG 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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26C ALA 3.7 10.3 - - - +
27C GLY 3.3 33.2 - - - +
28C LYS* 3.9 2.0 - - - +
29C ASP* 3.0 40.1 + - - +
91C GLN* 4.4 0.4 - - - +
122C THR* 4.7 2.2 - - + -
123C THR* 3.0 19.3 + - - +
125C LYS* 1.3 79.5 - - - +
127C HIS* 1.3 59.1 + - - +
129C ASP* 3.1 22.4 + - - +
130C ILE* 2.8 62.9 + - + +
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Residues in contact with HIS 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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96C ARG* 3.7 22.1 + - - +
100C GLU* 4.2 16.6 - - + +
102C HIS* 3.6 18.5 - + + -
122C THR* 3.5 22.3 - - - +
123C THR 2.8 15.4 + - - +
124C PRO* 3.5 7.9 - - + +
126C ARG* 1.3 77.7 - - - +
128C ILE* 1.3 64.5 + - + +
130C ILE* 3.6 10.8 + - - +
131C HIS* 3.4 28.2 + + + +
1134C MG 2.2 30.6 - - - -
5I T 4.4 9.6 - - - -
6I C 3.4 12.2 + - - -
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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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93C VAL* 3.9 18.8 - - + -
96C ARG* 3.4 36.1 - - - +
124C PRO* 2.9 21.5 + - + +
125C LYS* 3.8 5.6 - - - +
127C HIS* 1.3 76.7 - - + +
129C ASP* 1.3 61.8 + - - +
131C HIS* 3.3 8.2 + - - +
132C ARG* 3.1 51.1 + - + +
13J T 4.5 5.6 - - - +
14J C 3.7 34.3 - - - +
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Residues in contact with ASP 129 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C LYS* 2.9 40.0 + - - +
126C ARG* 3.1 24.3 + - - +
128C ILE* 1.3 80.2 - - - +
130C ILE* 1.3 66.6 + - - +
131C HIS 3.1 2.5 + - - -
132C ARG* 3.3 32.5 + - - +
133C GLY 3.9 8.7 + - - +
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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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29C ASP 3.5 17.3 - - - +
30C SER* 4.5 6.5 - - - +
102C HIS* 3.7 32.5 - - + +
122C THR* 4.0 24.9 - - + -
126C ARG* 2.8 47.4 + - + +
127C HIS* 3.7 6.5 - - - +
129C ASP* 1.3 76.3 - - - +
131C HIS* 1.3 64.8 + - - +
133C GLY 3.4 12.2 - - - +
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Residues in contact with HIS 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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102C HIS* 5.3 8.1 - + - -
127C HIS* 3.4 20.0 + - + +
128C ILE* 3.3 11.4 + - - +
130C ILE* 1.3 83.2 - - + +
132C ARG* 1.3 70.8 + - + +
133C GLY 4.2 1.2 - - - +
4I A 5.4 0.9 - - - -
5I T 4.2 28.0 - - - -
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Residues in contact with ARG 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 ILE* 3.1 32.3 + - + +
129C ASP* 3.3 22.8 + - - +
131C HIS* 1.3 83.1 - - + +
133C GLY* 1.3 60.5 + - - +
14J C 3.5 39.2 + - - +
15J G 3.4 39.4 + - - +
16J C 5.2 19.1 + - - +
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Residues in contact with GLY 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 ASP 3.9 6.4 + - - +
130C ILE 3.4 18.9 - - - +
131C HIS 4.2 0.9 - - - +
132C ARG* 1.3 81.9 - - - +
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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