Contacts of the helix formed by residues 129 - 143 (chain A) in PDB entry 2OB1
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 TYR 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ASP* 1.3 108.9 + - - +
130A ASN* 1.3 67.7 + - - +
131A GLU* 3.5 27.4 - - + +
132A SER* 3.0 31.7 + - - -
133A VAL* 3.0 18.9 + - - -
174A CYS 3.5 13.3 + - - +
175A ASP* 5.6 2.9 - - - -
176A LEU* 6.0 0.2 - - - +
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Residues in contact with ASN 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASP 3.7 1.0 + - - -
129A TYR* 1.3 73.9 - - - +
131A GLU* 1.3 74.7 + - - +
133A VAL* 3.2 1.9 + - - +
134A GLU* 2.8 53.6 + - - +
173A ALA* 3.8 27.2 - - + +
174A CYS 4.7 1.4 - - - +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TYR* 3.3 25.7 - - + +
130A ASN* 1.3 91.2 + - - +
132A SER* 1.3 62.1 + - - +
134A GLU* 3.5 6.5 + - - +
135A LEU* 3.1 24.1 + - - +
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A CYS* 5.4 0.2 - - - -
107A GLY* 3.9 14.0 + - - -
128A ASP* 2.9 27.3 + - - +
129A TYR* 3.0 36.2 + - - -
131A GLU* 1.3 78.9 - - - +
133A VAL* 1.3 58.6 + - - +
135A LEU* 3.3 6.4 + - - +
136A LYS* 3.0 27.8 + - - +
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A CYS* 4.5 1.8 - - - -
127A ILE 4.3 0.2 - - - -
128A ASP* 3.4 40.8 - - + +
129A TYR 3.0 9.6 + - - +
130A ASN 3.2 12.8 - - - +
132A SER* 1.3 78.6 - - - +
134A GLU* 1.3 55.7 + - + +
136A LYS* 4.3 5.2 - - - -
137A ASN* 2.8 32.2 + - - +
163A LEU* 3.3 14.5 - - + +
171A LEU* 3.7 25.7 - - + +
172A ALA 3.5 7.9 - - - +
173A ALA* 3.5 31.6 - - + +
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASN* 2.8 46.2 + - - +
131A GLU* 3.7 7.2 - - - +
133A VAL* 1.3 76.7 - - - +
135A LEU* 1.3 57.4 + - - +
137A ASN* 3.5 7.1 + - - +
138A SER* 2.9 32.9 + - - -
156A ASP* 4.9 3.8 - - - +
163A LEU* 3.4 32.9 - - + +
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A TYR* 3.3 39.9 - - + +
48A TYR* 5.4 1.1 - - - +
52A LEU* 3.9 13.0 - - + -
55A PHE* 3.9 28.7 - - + +
56A SER* 5.4 3.4 - - - -
59A ALA* 5.4 0.2 - - + -
131A GLU 3.1 17.7 + - - +
132A SER* 3.8 4.9 - - - +
134A GLU* 1.3 78.0 - - - +
136A LYS* 1.3 65.0 + - - +
138A SER* 3.2 5.3 + - - -
139A ILE* 3.0 40.3 + - + +
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Residues in contact with LYS 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR* 3.7 21.5 + - + +
106A CYS* 3.8 6.8 - - - +
107A GLY 3.0 26.6 + - - +
108A SER 4.2 4.9 - - - -
109A ASP 2.6 31.5 + - - +
110A LEU* 4.5 4.5 - - - -
112A MET* 3.8 12.8 - - - -
126A ASP* 2.8 32.5 + - - +
132A SER 3.0 16.8 + - - +
133A VAL* 3.7 6.1 - - - +
135A LEU* 1.3 77.3 - - - +
137A ASN* 1.3 52.8 + - - +
139A ILE* 3.2 2.5 + - - +
140A LEU* 2.8 50.7 + - + +
169A TYR* 4.2 0.7 - - - +
171A LEU* 4.2 13.7 - - + -
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Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A VAL 2.8 21.5 + - - +
134A GLU* 3.6 6.9 + - - +
136A LYS* 1.3 70.9 - - - +
138A SER* 1.3 67.4 + - - +
141A ARG* 2.7 48.3 + - - +
156A ASP* 3.1 33.9 + - - -
163A LEU* 3.5 27.7 + - + +
164A ILE* 3.1 19.9 - - - +
171A LEU* 3.7 14.0 - - + +
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Residues in contact with SER 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 3.6 34.0 - - - -
134A GLU* 2.9 18.7 + - - -
135A LEU* 3.4 12.2 - - - -
137A ASN* 1.3 79.6 + - - +
139A ILE* 1.3 57.3 + - - +
141A ARG* 3.9 3.5 - - - +
142A GLU* 3.0 31.7 + - - +
156A ASP* 5.5 3.8 + - - -
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR* 3.5 58.1 - - + +
51A THR* 3.7 31.8 - - + +
52A LEU* 3.8 23.8 - - + +
55A PHE* 4.1 7.4 - - + -
135A LEU* 3.0 39.4 + - + +
136A LYS 3.7 5.2 - - - +
138A SER* 1.3 74.1 - - - +
140A LEU* 1.3 66.9 + - - +
143A SER* 3.1 22.9 + - - -
146A LEU* 3.8 7.0 - - + -
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR* 4.5 4.5 - - + -
110A LEU* 4.3 20.6 - - + -
112A MET* 4.1 5.2 - - + -
113A LEU* 5.1 0.9 - - + -
136A LYS* 2.8 42.0 + - + +
137A ASN 4.0 2.5 - - - +
139A ILE* 1.3 74.0 - - - +
141A ARG* 1.3 60.6 + - - +
143A SER 3.5 1.9 - - - +
146A LEU* 4.1 27.6 - - + -
147A ARG* 3.1 31.0 + - - -
150A LEU* 4.0 20.4 - - + -
152A LEU* 4.1 12.6 - - + -
164A ILE* 3.7 22.2 - - + -
169A TYR* 3.9 13.9 - - - +
171A LEU* 4.4 0.4 - - + -
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Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASN* 2.7 37.2 + - - +
138A SER* 4.0 3.4 - - - +
140A LEU* 1.3 77.4 - - - +
142A GLU* 1.3 59.5 + - - +
147A ARG* 2.8 36.4 + - - -
152A LEU* 3.8 17.7 - - + +
153A SER* 2.9 30.8 + - - +
154A LYS* 3.6 20.5 - - - +
155A GLU 3.2 5.1 + - - -
156A ASP* 3.6 28.7 - - - +
157A THR* 3.0 28.6 + - - +
158A ALA* 3.9 6.1 - - - +
163A LEU 2.8 23.2 + - - -
164A ILE* 3.6 18.2 - - - +
165A ASP 5.0 0.2 - - - +
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Residues in contact with GLU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A THR* 3.7 11.9 - - + -
54A LYS* 3.4 33.8 + - + +
55A PHE* 3.5 26.0 - - + -
138A SER 3.0 19.3 + - - +
139A ILE 3.2 0.2 + - - -
141A ARG* 1.3 77.2 - - - +
143A SER* 1.3 67.5 + - - +
144A GLU 3.3 1.7 + - - -
147A ARG* 3.1 11.2 + - - +
154A LYS* 3.2 32.0 + - - +
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER* 2.5 29.6 + - - -
51A THR* 3.5 15.2 - - - +
139A ILE 3.1 7.3 + - - -
140A LEU 3.5 0.5 - - - +
142A GLU* 1.3 77.9 - - - +
144A GLU* 1.3 58.9 + - - +
145A ILE* 3.4 2.8 - - - +
146A LEU* 3.2 35.2 + - - +
147A ARG* 2.8 33.4 + - - +
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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