Contacts of the helix formed by residues 121 - 128 (chain C) in PDB entry 3V81
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 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C THR* 3.7 9.6 + - - +
8C VAL 3.9 8.2 - - - +
9C PRO* 4.1 6.7 - - - +
10C VAL* 3.6 39.3 + - + +
120C LEU* 1.3 83.7 - - + +
122C GLU* 1.3 92.9 + - - +
123C ASP* 3.8 12.1 + - - +
124C PHE* 3.0 37.5 + - + +
125C ARG* 3.1 13.6 + - - +
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Residues in contact with GLU 122 (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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7C THR* 3.0 32.9 + - - +
120C LEU 3.8 2.3 + - - +
121C ASP* 1.3 91.4 - - - +
123C ASP* 1.3 75.5 + - - +
124C PHE 3.0 3.1 + - - -
125C ARG* 3.0 40.8 + - - +
126C LYS 4.9 0.2 + - - -
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Residues in contact with ASP 123 (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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10C VAL 6.1 0.2 - - - +
121C ASP* 3.3 10.3 + - - +
122C GLU* 1.3 95.1 - - - +
124C PHE* 1.3 59.3 + - - +
125C ARG 3.4 0.4 - - - -
126C LYS* 3.1 33.1 + - - +
127C TYR* 4.0 3.3 - - - -
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Residues in contact with PHE 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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10C VAL* 3.8 20.2 - - + -
11C LYS* 3.5 27.1 - - - -
12C LEU* 3.8 24.0 - - + -
80C LEU* 4.1 18.4 - - + -
84C THR* 3.9 9.2 - - + -
120C LEU* 4.6 11.0 - - + -
121C ASP* 3.0 28.8 + - + +
123C ASP* 1.3 77.3 - - - +
125C ARG* 1.3 67.3 + - - +
126C LYS 2.9 4.9 + - - -
127C TYR* 3.1 24.6 + + + -
128C THR* 5.0 4.8 - - + +
153C TRP* 3.2 38.6 - + - -
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Residues in contact with ARG 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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119C PRO* 4.9 5.9 - - - +
120C LEU* 3.9 26.2 + - + +
121C ASP 3.1 9.5 + - - +
122C GLU* 3.0 42.3 + - - +
123C ASP 3.4 0.4 - - - -
124C PHE* 1.3 76.3 - - - +
126C LYS* 1.3 55.3 + - - +
127C TYR 3.0 2.9 + - - -
128C THR* 2.4 32.4 + - - +
145C GLN* 4.1 24.9 - - - +
146C TYR 2.7 24.3 + - - +
147C ASN* 3.3 43.2 + - - +
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Residues in contact with LYS 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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54C ASN* 3.4 33.6 - - - +
56C TYR* 3.0 28.1 - - - +
122C GLU 4.9 0.2 + - - -
123C ASP* 3.1 30.2 + - - +
124C PHE 2.9 1.8 + - - -
125C ARG* 1.3 76.8 - - - +
127C TYR* 1.3 90.5 + - + +
128C THR* 3.2 3.6 + - - -
129C ALA* 4.6 1.9 + - - +
145C GLN* 4.5 13.2 + - - +
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Residues in contact with TYR 127 (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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12C LEU* 3.4 29.5 - - + +
17C ASP* 2.9 26.6 + - - -
18C GLY* 3.5 21.1 - - - -
19C PRO* 4.6 5.9 - - - +
56C TYR* 3.6 28.7 - + - +
58C THR* 5.3 2.8 - - - +
80C LEU* 3.8 31.8 - - + +
123C ASP 4.0 9.3 + - - -
124C PHE* 3.1 32.1 + + + +
125C ARG 3.0 2.2 + - - -
126C LYS* 1.3 108.3 - - + +
128C THR* 1.3 61.9 + - - +
129C ALA 3.6 3.0 + - - +
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Residues in contact with THR 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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58C THR* 4.8 5.1 + - - +
77C PHE* 6.2 1.3 - - + -
80C LEU* 4.4 16.2 - - + -
120C LEU* 4.6 10.8 - - + -
124C PHE* 5.0 5.6 - - + +
125C ARG 2.4 26.5 + - - +
126C LYS 3.2 1.8 - - - -
127C TYR* 1.3 79.5 - - + +
129C ALA* 1.3 64.7 + - - +
130C PHE* 3.8 2.6 + - - +
144C TYR* 4.2 12.5 + - - -
145C GLN* 3.6 3.7 - - - +
146C TYR* 2.9 53.8 + - + -
150C PRO* 4.7 7.2 - - + -
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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