Contacts of the helix formed by residues 125 - 135 (chain C) in PDB entry 2WWR
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 ARG 125 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C THR 3.4 5.2 + - - -
122C THR 3.3 15.8 + - - +
123C CYS 4.2 4.9 - - - +
124C ARG* 1.3 79.8 - - - +
126C LEU* 1.3 60.8 + - - +
127C PRO* 3.5 4.7 - - - -
128C GLU* 3.1 47.5 + - + +
129C ALA* 3.1 28.8 + - - +
146C LEU* 3.4 22.7 - - + +
147C CYS* 3.1 48.9 + - - +
148C GLY* 4.2 2.5 - - - -
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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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120C LEU 4.4 1.8 - - - +
121C THR* 3.0 29.9 + - - +
124C ARG* 3.6 31.2 - - + +
125C ARG* 1.3 72.8 - - - +
127C PRO* 1.3 62.6 - - - +
129C ALA* 3.2 5.8 + - - +
130C ILE* 2.8 39.5 + - + +
114D LEU* 4.0 14.4 - - + -
117D SER* 3.5 37.0 - - - +
118D LEU* 4.3 4.5 - - - +
121D THR* 3.8 17.3 - - + +
291D LEU* 3.8 17.7 - - + +
294D ILE* 4.1 4.5 - - + -
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Residues in contact with PRO 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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121C THR* 3.2 20.0 - - + +
122C THR* 5.3 0.2 - - - -
125C ARG* 3.6 3.4 - - - -
126C LEU* 1.3 92.3 - - + +
128C GLU* 1.3 61.0 + - - +
130C ILE* 3.4 11.0 + - + +
131C GLU* 3.2 27.0 + - - +
286C LYS 5.8 3.4 - - - +
289C VAL* 3.8 22.7 - - + -
130D ILE* 3.7 33.4 - - + -
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Residues in contact with GLU 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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125C ARG* 3.1 50.9 + - + +
126C LEU 3.3 0.6 - - - -
127C PRO* 1.3 80.5 - - - +
129C ALA* 1.3 61.7 + - - +
131C GLU* 3.6 5.9 + - - +
132C GLU* 3.2 31.9 + - + +
146C LEU* 3.9 11.3 - - + +
286C LYS* 3.8 53.7 + - + +
287C ASN* 5.2 3.5 + - - +
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Residues in contact with ALA 129 (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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125C ARG 3.1 18.7 + - - +
126C LEU* 3.2 5.1 + - - +
128C GLU* 1.3 75.6 - - - +
130C ILE* 1.3 65.1 + - - +
132C GLU* 3.1 11.8 + - - +
133C VAL* 3.2 17.8 + - - +
146C LEU* 3.8 22.4 - - + +
291D LEU* 4.5 2.0 - - + -
292D PRO* 3.6 24.8 - - + +
294D ILE* 4.1 14.4 - - + -
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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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126C LEU* 2.8 30.0 + - + +
127C PRO* 3.8 9.2 - - + +
129C ALA* 1.3 74.3 - - - +
131C GLU* 1.3 65.1 + - - +
133C VAL* 3.0 25.9 - - + +
134C LYS* 3.4 31.8 + - + +
121D THR* 5.3 2.5 - - + +
127D PRO* 4.2 26.0 - - + -
289D VAL* 3.8 24.2 - - + -
290D ILE 3.7 23.3 - - - +
291D LEU* 3.9 10.1 - - + -
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Residues in contact with GLU 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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127C PRO 3.2 16.1 + - - +
128C GLU* 3.8 6.3 - - - +
130C ILE* 1.3 82.9 - - - +
132C GLU* 1.3 56.8 + - + +
134C LYS* 3.1 32.9 + - - +
135C ASN* 2.9 44.5 + - - +
131D GLU* 5.6 1.6 - - - +
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Residues in contact with GLU 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 GLU* 3.2 20.4 + - + +
129C ALA* 3.1 12.0 + - - +
131C GLU* 1.3 78.7 - - - +
133C VAL* 1.3 59.4 + - - +
135C ASN* 3.2 21.5 + - - +
136C GLY 3.7 0.2 - - - -
137C GLY* 2.8 40.9 + - - +
138C TRP* 3.2 6.8 + - - -
145C TRP* 3.1 42.7 + - + -
146C LEU* 4.4 7.6 - - + -
286C LYS* 4.9 10.8 + - - -
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Residues in contact with VAL 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 ALA 3.2 12.2 + - - +
130C ILE* 3.0 19.7 - - + +
132C GLU* 1.3 76.9 - - - +
134C LYS* 1.3 63.3 + - + +
135C ASN 3.6 0.2 + - - -
136C GLY* 3.9 0.9 + - - -
138C TRP* 3.7 30.9 - - + +
276D LEU* 4.8 6.2 - - + +
278D THR* 3.7 16.5 - - - +
283D LEU* 3.8 32.7 - - + +
290D ILE* 3.7 21.8 - - + +
291D LEU 4.1 1.8 - - - -
292D PRO* 3.7 28.9 - - + -
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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 ILE* 3.4 33.7 + - + +
131C GLU* 3.1 33.2 + - - +
133C VAL* 1.3 87.7 - - + +
135C ASN* 1.3 57.0 + - - +
136C GLY 3.6 0.6 + - - -
127D PRO* 6.3 0.8 - - - +
278D THR* 4.0 14.6 - - - +
283D LEU* 4.3 32.1 - - + +
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Residues in contact with ASN 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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131C GLU* 2.9 29.7 + - - +
132C GLU* 3.2 22.8 + - - +
134C LYS* 1.3 77.0 - - + +
136C GLY* 1.3 60.7 + - - +
137C GLY* 3.2 13.1 + - - -
278D THR* 4.3 2.7 - - - -
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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