Contacts of the helix formed by residues 134 - 145 (chain B) in PDB entry 6OGJ
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 SER 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B ARG* 1.3 80.0 + - - +
135B LYS* 1.3 64.7 + - - +
136B VAL* 3.4 12.9 - - - +
137B GLU* 3.2 25.8 + - - +
138B LEU* 3.2 16.1 + - - +
157B PHE* 3.3 22.4 - - - -
10C C 5.9 1.6 - - - -
11C C 4.0 30.1 - - - -
12C G 5.5 1.6 + - - -
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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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134B SER* 1.3 72.7 - - - +
136B VAL* 1.3 59.1 + - - +
138B LEU* 2.9 9.5 + - - +
139B ILE* 2.8 40.0 + - + +
152B PRO* 3.5 33.9 - - + +
153B ASN* 2.7 34.5 + - - +
155B PHE 6.0 0.2 - - - +
157B PHE* 3.4 20.4 - - + -
165B PRO* 4.7 14.4 - - + +
10C C 6.0 1.7 - - - +
11C C 3.5 31.6 + - - +
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER* 3.4 11.2 - - - +
135B LYS* 1.3 76.5 - - + +
137B GLU* 1.3 61.7 + - + +
139B ILE* 3.3 17.5 + - + +
140B ALA* 2.9 28.1 + - - +
11C C 3.8 50.5 - - + +
12C G 4.2 16.8 - - + +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ALA 4.5 2.8 - - - +
132B PHE* 3.7 16.4 - - + -
133B ARG* 2.9 67.3 + - - +
134B SER* 3.2 21.5 + - - +
135B LYS 3.2 0.4 - - - -
136B VAL* 1.3 76.1 - - + +
138B LEU* 1.3 64.8 + - - +
140B ALA* 3.3 3.8 + - - +
141B TYR* 3.1 23.4 + - - +
202B UNX 3.9 18.8 - - - -
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Residues in contact with LEU 138 (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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104B TRP* 3.6 30.7 - - + -
124B LEU* 4.6 0.4 - - + -
132B PHE* 3.6 23.6 - - + -
134B SER 3.2 7.8 + - - +
135B LYS* 2.9 9.5 + - - +
137B GLU* 1.3 78.3 - - - +
139B ILE* 1.3 64.5 + - - +
141B TYR* 3.2 3.4 + - - +
142B PHE* 2.9 44.6 + - + -
152B PRO* 4.4 11.4 - - + +
155B PHE* 3.5 31.9 - - + -
157B PHE* 3.4 34.5 - - + -
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Residues in contact with ILE 139 (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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135B LYS* 2.8 38.0 + - + +
136B VAL* 3.5 17.7 - - + +
138B LEU* 1.3 77.2 - - - +
140B ALA* 1.3 63.7 + - - +
142B PHE* 3.4 3.2 + - - +
143B GLU* 3.0 27.4 + - + +
152B PRO* 3.4 28.3 - - + -
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Residues in contact with ALA 140 (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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136B VAL 2.9 13.5 + - - +
137B GLU 3.3 7.6 + - - +
139B ILE* 1.3 77.5 - - - +
141B TYR* 1.3 62.3 + - - +
143B GLU* 3.5 6.3 + - - +
144B LYS* 3.2 22.0 + - - +
202B UNX 3.8 18.4 - - - -
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Residues in contact with TYR 141 (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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104B TRP* 6.2 1.3 - + - -
126B ASN* 4.1 12.2 + - - -
128B GLN* 3.9 17.8 + - - -
130B LYS* 3.8 22.9 - - + +
132B PHE* 3.5 39.5 - + + -
137B GLU 3.1 10.6 + - - +
138B LEU 3.7 2.7 - - - +
140B ALA* 1.3 74.3 - - - +
142B PHE* 1.3 82.8 + + - +
144B LYS* 3.2 9.9 + - + +
145B VAL* 3.0 54.7 + - + +
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Residues in contact with PHE 142 (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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104B TRP* 4.6 10.1 - + - -
138B LEU* 2.9 35.3 + - + +
139B ILE* 3.8 3.8 - - - +
141B TYR* 1.3 92.6 - + - +
143B GLU* 1.3 54.0 + - - +
145B VAL* 4.0 4.7 - - - -
146B GLY* 2.8 13.9 + - - -
147B ASP* 2.8 52.7 + - + +
150B LEU* 3.6 48.7 - - + -
152B PRO* 3.7 31.4 - - + -
155B PHE* 4.0 18.8 - + - -
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Residues in contact with GLU 143 (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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139B ILE* 3.0 22.1 + - + +
140B ALA* 3.6 7.6 - - - +
142B PHE* 1.3 75.2 - - - +
144B LYS* 1.3 63.0 + - - +
146B GLY* 3.2 13.8 + - - -
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Residues in contact with LYS 144 (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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140B ALA 3.2 11.1 + - - +
141B TYR* 3.5 13.0 - - + +
143B GLU* 1.3 79.7 - - - +
145B VAL* 1.3 62.7 + - + +
146B GLY* 3.5 0.7 + - - -
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Residues in contact with VAL 145 (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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141B TYR* 3.0 59.9 + - + +
142B PHE* 3.7 9.0 - - + +
144B LYS* 1.3 77.8 - - + +
146B GLY* 1.3 60.5 + - - +
147B ASP* 3.3 19.9 + - + +
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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