Contacts of the helix formed by residues 123 - 129 (chain C) in PDB entry 1WOH
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 VAL 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C VAL* 3.5 34.5 - - + +
38C PHE* 4.0 28.0 - - + +
97C HIS* 6.2 0.2 - - - -
100C ILE* 4.5 4.3 - - + -
118C GLY* 4.5 9.4 - - - -
120C ASP 3.2 20.4 - - - +
121C HIS 3.0 1.2 - - - -
122C SER* 1.3 76.6 - - - +
124C SER* 1.3 66.2 + - - +
125C TYR 3.1 0.4 + - - -
126C PRO* 3.2 11.8 - - - +
127C LEU* 3.0 37.0 + - + +
273C VAL* 3.8 21.1 - - + -
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Residues in contact with SER 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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121C HIS* 2.9 39.5 + - - -
123C VAL* 1.3 80.7 - - - +
125C TYR* 1.3 57.4 + - - +
127C LEU* 3.5 6.9 - - - +
128C LEU* 2.9 38.1 + - - +
162C PRO* 4.1 6.1 - - - -
163C PHE* 4.3 14.8 - - - -
227C SER* 3.7 0.3 + - - -
271C ASP* 3.1 26.1 + - - -
273C VAL* 4.3 2.3 - - - +
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Residues in contact with TYR 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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97C HIS* 4.2 14.8 - + - -
122C SER 3.3 7.7 + - - +
123C VAL 3.1 1.0 - - - -
124C SER* 1.3 81.4 - - - +
126C PRO* 1.3 78.1 - - + +
127C LEU 3.1 0.2 + - - -
128C LEU* 3.1 8.7 + - - +
129C ARG* 3.3 50.9 + - + +
157C TRP* 3.5 34.6 - + - -
162C PRO* 3.6 23.9 - - + +
165C ARG* 3.5 38.3 - - + -
166C ALA* 3.6 13.9 - - - -
169C ALA* 4.0 11.8 - - + +
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Residues in contact with PRO 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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97C HIS* 3.4 42.8 - - + +
100C ILE* 3.7 28.3 - - + -
101C THR* 2.5 30.7 + - - +
122C SER 3.2 14.1 - - - +
123C VAL* 3.2 15.5 - - - +
125C TYR* 1.3 101.0 - - + +
127C LEU* 1.3 58.7 + - - +
129C ARG* 3.5 13.4 + - - +
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Residues in contact with LEU 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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34C LEU* 5.2 1.1 - - + -
36C VAL* 4.4 9.4 - - + -
100C ILE* 3.3 28.3 - - + -
104C ALA* 4.1 17.2 - - + +
116C PHE* 3.5 46.0 - - + -
123C VAL* 3.0 33.3 + - + +
124C SER 3.5 4.5 - - - +
126C PRO* 1.3 78.2 - - - +
128C LEU* 1.3 63.2 + - - +
130C ALA* 3.1 22.3 + - - +
131C PHE* 3.4 11.4 - - - -
225C TYR* 3.7 15.9 - - - +
271C ASP* 4.0 9.2 - - + +
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Residues in contact with LEU 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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124C SER* 2.9 22.4 + - - +
125C TYR 3.1 4.2 + - - +
127C LEU* 1.3 70.5 - - - +
129C ARG* 1.3 60.7 + - - +
130C ALA 3.0 2.9 - - - -
131C PHE* 2.8 29.2 + - + +
137C LEU* 4.4 11.9 - - + -
139C VAL* 4.2 11.2 - - + -
163C PHE* 3.9 27.6 - - + -
166C ALA* 3.7 22.4 - - + -
170C LEU* 3.4 22.5 - - + +
173C LEU* 4.4 7.0 - - + -
225C TYR* 3.6 44.2 - - + -
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Residues in contact with ARG 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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97C HIS* 3.2 29.6 + - - +
98C ASP* 3.2 24.8 + - - +
101C THR* 3.0 37.7 + - + +
105C ARG* 4.9 6.0 + - - +
125C TYR* 3.3 50.0 + - + +
126C PRO* 3.7 10.6 - - - +
127C LEU 3.2 1.4 - - - -
128C LEU* 1.3 76.6 - - - +
130C ALA* 1.3 57.6 + - - +
131C PHE 3.0 4.0 + - - -
132C ALA* 3.3 17.3 + - - +
169C ALA* 5.1 5.2 - - + -
170C LEU* 4.0 19.0 - - + +
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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