Contacts of the helix formed by residues 133 - 141 (chain C) in PDB entry 2W4V
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 133 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C PRO* 3.8 26.7 - - + +
132C TYR* 1.3 90.8 - - + +
134C ASP* 1.3 59.4 + - - +
135C SER* 2.3 32.7 + - - +
136C VAL* 2.4 37.7 + - - +
137C ILE* 2.4 18.1 - - - +
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Residues in contact with ASP 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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133C THR* 1.3 77.5 - - - +
135C SER* 1.3 70.3 + - - +
137C ILE* 3.0 27.6 - - - +
138C ALA* 3.2 7.3 + - - +
195C LYS* 3.0 31.4 + - + +
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Residues in contact with SER 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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9C ASP* 4.3 14.1 - - - +
133C THR* 2.3 28.9 + - - +
134C ASP* 1.3 89.0 - - - +
136C VAL* 1.3 70.6 + - - +
138C ALA* 3.3 17.2 - - - +
139C LYS* 3.7 5.4 + - - +
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Residues in contact with VAL 136 (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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9C ASP* 3.7 32.8 - - + +
13C LEU* 5.2 1.3 - - + -
130C PRO 4.0 10.5 - - - +
131C ILE* 3.1 30.1 - - + +
132C TYR* 3.3 2.9 - - - +
133C THR* 2.4 57.2 - - - +
135C SER* 1.3 84.1 + - - +
137C ILE* 1.3 65.6 + - + +
139C LYS* 3.2 15.9 + - - +
140C TYR* 3.3 13.0 + - - +
153C PHE* 4.6 4.9 - - + -
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Residues in contact with ILE 137 (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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132C TYR 3.7 8.5 - - - +
133C THR 2.4 36.6 - - - +
134C ASP* 3.0 15.3 - - - +
136C VAL* 1.3 76.9 - - + +
138C ALA* 1.3 72.3 + - - +
140C TYR* 3.1 32.5 + - + +
141C ARG* 3.3 7.6 + - - +
153C PHE* 4.3 20.6 - - + -
192C TYR* 6.2 1.3 - - - -
195C LYS* 3.0 36.8 - - + +
196C VAL* 3.8 27.6 - - + -
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Residues in contact with ALA 138 (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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134C ASP 3.2 7.6 + - - +
135C SER* 3.3 14.1 - - - +
136C VAL 3.1 0.2 - - - -
137C ILE* 1.3 92.6 - - + +
139C LYS* 1.3 59.6 + - - +
140C TYR 3.6 0.2 + - - -
141C ARG* 3.6 17.8 - - - +
143C LYS* 4.3 5.5 + - - -
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Residues in contact with LYS 139 (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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5C PHE* 4.7 9.4 - - - +
7C ASP* 2.7 34.1 + - + -
9C ASP* 3.2 21.3 - - - +
10C PHE* 5.0 3.4 - - - +
135C SER 3.7 3.7 + - - +
136C VAL* 3.2 10.9 + - - +
138C ALA* 1.3 80.8 - - - +
140C TYR* 1.3 58.3 + - - +
143C LYS* 2.8 31.5 - - - +
148C ILE* 4.6 13.0 - - + +
149C PRO* 5.2 14.5 - - + +
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Residues in contact with TYR 140 (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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136C VAL 3.3 7.9 + - - +
137C ILE* 3.1 17.2 + - + +
139C LYS* 1.3 77.7 - - - +
141C ARG* 1.3 79.0 + - + +
142C GLY 3.2 0.9 + - - -
143C LYS* 3.2 20.5 + - - +
148C ILE* 5.0 7.2 - - + +
151C HIS* 6.0 1.8 - - + -
153C PHE* 2.3 75.4 - + + -
154C SER* 3.5 7.7 - - - +
157C ASP* 2.8 32.1 + - + +
192C TYR* 3.1 31.0 - + + -
196C VAL* 3.8 21.2 - - + +
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Residues in contact with ARG 141 (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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137C ILE* 3.3 9.6 + - - +
138C ALA* 3.6 15.0 - - - +
139C LYS 3.3 1.0 - - - -
140C TYR* 1.3 96.7 - - + +
142C GLY* 1.3 58.7 + - - +
143C LYS* 2.8 32.1 + - - +
157C ASP* 4.2 1.6 - - - +
195C LYS 4.5 3.4 + - - -
196C VAL* 2.4 57.6 + - + +
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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