Contacts of the helix formed by residues 126 - 137 (chain B) in PDB entry 2O07
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 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B SER* 2.5 30.7 + - - -
48B TYR* 3.7 15.7 - - + +
49B GLN* 2.9 33.9 + - - +
51B ILE* 4.2 0.2 - - - +
124B GLU* 2.8 22.8 + - - +
125B ILE* 1.3 79.1 - - + +
127B GLU* 1.3 62.0 + - - +
128B ASP* 3.2 21.7 + - - +
129B VAL* 3.1 25.5 + - + +
130B ILE 3.8 0.7 + - - -
501B MTA 3.7 2.0 - - - +
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Residues in contact with GLU 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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48B TYR* 5.6 0.4 - - - -
124B GLU* 4.7 1.5 - - - +
125B ILE 3.9 2.2 + - - -
126B ASP* 1.3 72.0 + - - +
128B ASP* 1.3 64.4 + - - +
129B VAL 3.3 0.2 - - - -
130B ILE* 3.2 23.5 + - + +
131B GLN* 3.1 26.8 + - + +
151B LEU* 5.6 4.2 - - + +
153B VAL* 3.7 41.3 - - + +
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Residues in contact with ASP 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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45B ARG 4.9 0.9 - - - +
46B SER* 3.5 21.5 - - - -
47B ARG 5.0 0.6 + - - -
51B ILE* 3.8 16.7 - - + +
126B ASP* 3.2 12.7 + - - +
127B GLU* 1.3 76.7 - - - +
129B VAL* 1.3 64.0 + - - +
131B GLN* 3.3 7.8 + - - +
132B VAL* 3.0 29.8 + - + +
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Residues in contact with VAL 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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49B GLN* 3.4 28.9 - - - +
51B ILE* 3.9 13.9 - - + -
63B LEU* 4.2 19.3 - - + -
65B LEU* 3.9 9.2 - - + -
103B GLY* 4.0 13.5 - - - -
126B ASP* 3.1 18.0 + - - +
128B ASP* 1.3 76.3 - - - +
130B ILE* 1.3 57.2 - - - +
132B VAL* 3.5 4.1 + - - +
133B SER* 2.9 42.4 + - - +
501B MTA 3.3 27.1 - - + +
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Residues in contact with ILE 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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103B GLY* 3.8 9.2 - - - +
124B GLU* 3.8 28.3 - - + +
126B ASP 4.3 0.7 - - - +
127B GLU* 3.2 22.3 + - + +
129B VAL* 1.3 77.6 - - - +
131B GLN* 1.3 77.2 + - - +
133B SER* 3.4 1.6 + - - -
134B LYS* 3.0 42.9 + - - +
144B TYR* 3.3 28.0 - - + +
151B LEU* 3.8 39.5 - - + -
153B VAL* 6.3 0.7 - - + -
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Residues in contact with GLN 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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127B GLU* 3.1 14.6 + - + +
128B ASP* 3.3 9.8 + - - +
130B ILE* 1.3 88.9 - - - +
132B VAL* 1.3 62.4 + - + +
134B LYS* 3.4 35.1 + - - +
135B LYS* 3.3 20.6 + - - +
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Residues in contact with VAL 132 (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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42B HIS* 3.5 35.7 - - + +
51B ILE* 4.0 17.9 - - + -
53B VAL* 3.4 33.0 - - + -
63B LEU* 4.4 6.1 - - + -
128B ASP* 3.0 21.7 + - + +
129B VAL 3.9 3.1 - - - +
131B GLN* 1.3 73.8 - - + +
133B SER* 1.3 59.4 + - - +
135B LYS* 3.2 3.1 + - - -
136B PHE* 2.8 40.7 + - + +
137B LEU* 6.3 0.4 - - + -
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Residues in contact with SER 133 (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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63B LEU* 4.2 3.5 - - - +
103B GLY 3.6 5.0 + - - -
104B ASP* 3.3 39.1 + - - +
129B VAL* 2.9 26.4 + - - +
130B ILE 3.8 2.2 - - - -
132B VAL* 1.3 73.5 - - - +
134B LYS* 1.3 62.4 + - - +
137B LEU* 2.9 52.6 + - - +
141B ALA* 3.4 4.5 - - - +
144B TYR* 5.3 0.2 - - - -
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Residues in contact with LYS 134 (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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130B ILE* 3.0 32.0 + - - +
131B GLN* 3.5 35.9 + - - +
132B VAL 3.3 0.2 - - - -
133B SER* 1.3 75.2 - - - +
135B LYS* 1.3 60.2 - - - +
138B PRO* 4.5 12.3 - - - +
141B ALA* 3.6 19.1 - - + +
144B TYR* 3.8 28.3 - - + +
151B LEU* 5.9 2.2 - - - +
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Residues in contact with LYS 135 (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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131B GLN 3.3 9.4 + - - +
132B VAL* 3.2 7.7 + - - +
133B SER 3.1 0.6 - - - -
134B LYS* 1.3 82.2 - - - +
136B PHE* 1.3 100.0 + - + +
137B LEU 3.7 0.2 - - - -
138B PRO* 4.2 8.1 - - - +
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Residues in contact with PHE 136 (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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41B LEU* 3.7 47.6 - - + -
42B HIS* 3.8 26.0 - + + -
53B VAL* 3.7 25.4 - - + -
61B ASN* 2.6 36.6 + - - +
73B GLU* 3.8 0.7 - - - +
132B VAL* 2.8 40.0 + - + +
135B LYS* 1.3 114.5 - - + +
137B LEU* 1.3 61.6 + - + +
138B PRO* 3.3 10.0 - - - +
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Residues in contact with LEU 137 (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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53B VAL* 6.0 2.9 - - + -
61B ASN* 4.2 15.5 - - + +
62B VAL 5.3 0.4 - - - -
63B LEU* 4.0 20.6 - - + +
71B CYS* 3.8 27.6 - - - +
72B THR 5.5 0.2 - - - -
73B GLU* 3.9 24.7 - - + +
104B ASP* 3.9 7.9 - - + -
133B SER* 2.9 39.2 + - - +
136B PHE* 1.3 88.8 - - + +
138B PRO* 1.3 65.9 - - - +
139B GLY 3.2 2.9 - - - -
140B MET* 2.9 30.6 + - + -
141B ALA 2.9 10.2 + - - -
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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