Contacts of the helix formed by residues 123 - 131 (chain B) in PDB entry 2W93
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ASP* 2.7 20.1 + - - +
122B PHE* 1.3 84.1 - - + +
124B VAL* 1.3 59.1 + - - +
125B PHE 3.4 2.0 - - - -
126B HIS* 3.3 15.2 + - - +
127B ARG* 2.9 50.0 + - - +
138B MET* 6.2 0.2 - - - -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ASN* 3.9 28.3 - - + +
117B LEU* 4.1 24.5 - - + +
121B ASP* 3.5 25.1 + - + +
122B PHE 3.5 0.6 - - - -
123B THR* 1.3 79.3 + - - +
125B PHE* 1.3 86.8 + - + +
127B ARG* 3.2 26.5 + - - +
128B MET* 2.9 34.1 + - - +
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Residues in contact with PHE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 4.9 2.5 - - + -
412A TRP* 3.5 25.4 - + - -
74B PHE* 3.6 34.5 - + + -
75B GLY* 3.6 7.0 - - - -
78B GLU* 3.3 38.2 - - + +
79B LEU* 3.9 34.9 - - + +
115B HIS 3.6 10.8 - - - -
116B THR* 4.5 1.6 - - - -
117B LEU* 4.1 20.9 - - + -
121B ASP 5.3 0.7 - - - -
122B PHE 5.1 0.2 + - - -
123B THR 3.4 0.2 - - - -
124B VAL* 1.3 94.3 - - + +
126B HIS* 1.3 67.2 + - - +
128B MET* 3.2 12.7 + - - +
129B SER* 3.0 25.5 + - - -
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Residues in contact with HIS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PHE 5.2 2.1 + - - +
123B THR* 3.3 17.8 + - - +
125B PHE* 1.3 79.1 - - - +
127B ARG* 1.3 60.7 + - + +
129B SER* 3.2 3.3 + - - -
130B ALA* 2.9 26.9 + - + +
136B THR* 2.7 33.8 + - + -
137B ALA* 4.5 0.6 + - - -
138B MET* 3.9 40.4 - - + +
164B TYR* 3.6 40.9 + + + +
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ASN* 2.9 28.9 + - - +
121B ASP* 2.9 27.5 + - - -
123B THR* 2.9 31.5 + - - +
124B VAL* 3.2 22.1 + - - +
126B HIS* 1.3 78.4 - - + +
128B MET* 1.3 63.9 + - - +
130B ALA* 3.3 16.7 + - - +
131B ASN* 3.1 15.9 + - - -
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LEU* 3.7 26.2 - - + -
128A MET* 3.6 32.6 - - + +
131A ASN* 3.6 31.9 - - + +
132A ILE* 4.1 25.4 - - + -
79B LEU* 3.9 25.1 - - + -
82B LEU* 4.5 9.9 - - + -
124B VAL* 2.9 20.2 + - - +
125B PHE* 3.5 13.9 - - - +
127B ARG* 1.3 76.8 - - - +
129B SER* 1.3 60.8 + - - +
131B ASN* 3.2 27.2 + - - +
132B ILE 4.4 0.2 + - - -
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLU* 4.8 1.4 + - - -
82B LEU* 3.3 27.8 - - - +
85B ILE* 5.6 1.3 - - - +
97B HIS* 4.7 2.6 + - - -
125B PHE 3.0 14.7 + - - -
126B HIS 3.7 2.0 - - - -
128B MET* 1.3 71.5 - - - +
130B ALA* 1.3 65.2 + - - +
131B ASN 3.0 2.7 - - - -
132B ILE* 3.0 19.0 + - - +
133B SER* 2.7 23.2 + - - -
136B THR* 4.9 0.2 - - - -
164B TYR* 3.4 36.7 - - - -
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B HIS* 2.9 14.7 + - + +
127B ARG* 3.6 13.9 - - - +
128B MET 3.2 0.8 - - - -
129B SER* 1.3 77.0 - - - +
131B ASN* 1.3 61.4 + - - +
132B ILE 3.3 0.9 + - - -
133B SER* 3.5 16.2 + - - +
136B THR* 3.8 25.5 - - + +
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Residues in contact with ASN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 4.0 12.5 - - - +
124A VAL* 3.8 18.3 - - + +
127A ARG* 2.8 32.2 + - - +
128A MET* 3.7 23.2 - - + +
131A ASN* 5.2 3.4 - - - +
89B TYR* 5.2 4.0 - - - -
127B ARG 3.1 24.2 + - - -
128B MET* 3.2 14.1 + - - +
129B SER 3.0 1.2 - - - -
130B ALA* 1.3 77.9 - - - +
132B ILE* 1.3 61.7 + - - +
133B SER 3.6 0.9 - - - -
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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