Contacts of the strand formed by residues 147 - 157 (chain B) in PDB entry 5XOU
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 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ARG 3.5 0.2 - - - +
138B GLU* 2.8 41.0 + - - +
146B ARG* 1.3 77.7 - - - +
148B LEU* 1.3 59.7 + - - +
171B TYR* 5.1 11.9 - - + -
172B ARG 4.1 2.0 - - - -
173B ILE* 5.7 0.2 - - - +
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Residues in contact with LEU 148 (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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128B TRP* 5.7 1.6 - - + -
135B TYR* 3.9 18.3 - - + -
136B ARG 5.5 0.2 - - - +
137B ARG 3.7 3.4 - - - -
146B ARG* 4.1 2.0 - - + +
147B VAL* 1.3 73.2 - - - +
149B GLY* 1.3 60.6 + - - +
171B TYR* 3.0 12.5 - - - +
172B ARG* 2.7 58.9 + - + +
174B LEU* 5.9 4.9 - - + -
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Residues in contact with GLY 149 (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 TYR* 3.2 4.8 - - - -
136B ARG* 2.8 30.6 + - - +
137B ARG* 2.7 26.5 + - - +
148B LEU* 1.3 73.3 - - - +
150B GLY* 1.3 58.6 + - - -
170B ALA 3.5 3.1 - - - -
171B TYR* 4.1 11.2 - - - -
289B ARG* 4.2 11.9 - - - -
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Residues in contact with GLY 150 (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 VAL* 3.0 14.6 - - - -
135B TYR* 3.9 1.3 - - - -
136B ARG* 4.7 5.2 - - - -
149B GLY* 1.3 75.7 - - - -
151B ALA* 1.3 57.3 + - - +
169B PRO* 3.0 9.9 - - - +
170B ALA 2.6 35.5 + - - -
289B ARG* 4.8 4.4 + - - +
293B ILE* 3.6 18.9 - - - +
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Residues in contact with ALA 151 (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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132B LEU 3.9 1.0 - - - +
133B ALA* 3.4 6.6 - - - +
134B VAL* 3.2 30.8 + - + +
135B TYR* 4.9 1.4 - - - -
150B GLY* 1.3 75.3 - - - +
152B VAL* 1.3 63.3 + - - +
153B LEU* 3.9 11.7 + - + +
167B VAL* 3.7 22.7 - - + -
168B ASP 3.1 21.8 - - - +
169B PRO* 3.8 2.0 - - + -
170B ALA* 3.7 6.4 + - - +
293B ILE* 4.2 10.5 - - + -
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Residues in contact with VAL 152 (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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132B LEU* 4.0 9.2 - - + +
133B ALA* 4.7 11.2 - - + +
135B TYR* 5.5 1.3 - - - +
151B ALA* 1.3 75.5 - - - +
153B LEU* 1.3 71.1 + - - +
166B GLU 3.8 0.7 - - - +
167B VAL* 3.7 1.2 - - - -
168B ASP* 2.8 39.9 + - + +
170B ALA* 4.3 15.9 - - + -
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Residues in contact with LEU 153 (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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117B LEU* 3.8 17.9 - - + -
121B LEU* 3.6 29.2 - - + -
132B LEU* 3.0 37.4 + - - +
134B VAL* 4.2 5.4 - - + -
151B ALA* 4.0 12.8 - - + +
152B VAL* 1.3 87.8 - - - +
154B ASP* 1.3 65.8 + - - +
165B LEU* 4.7 4.0 - - + -
166B GLU 3.3 3.4 - - - +
167B VAL* 3.8 33.7 - - + -
297B ILE* 3.6 34.8 - - + -
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Residues in contact with ASP 154 (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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114B ARG* 2.7 47.4 + - - +
117B LEU* 3.8 6.7 - - - +
132B LEU* 4.8 1.3 - - - +
153B LEU* 1.3 79.3 - - - +
155B LEU* 1.3 67.3 + - - +
156B TRP* 3.9 26.1 - - + -
164B LEU 4.2 0.2 - - - -
165B LEU* 3.1 12.6 - - - +
166B GLU* 2.9 39.3 + - + +
7F A 4.7 1.2 + - - -
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Residues in contact with LEU 155 (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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16B LEU* 4.3 9.9 - - + -
110B SER 3.5 0.7 - - - +
113B ALA* 3.5 26.5 - - - +
114B ARG* 3.3 22.0 - - - +
116B LEU* 4.5 4.3 - - + -
117B LEU* 3.6 32.8 - - + +
154B ASP* 1.3 79.5 + - - +
156B TRP* 1.3 64.1 + - - +
163B PHE* 4.1 18.6 - - + -
164B LEU 3.2 22.7 - - - +
165B LEU* 3.3 28.7 - - + +
303B LEU* 3.6 26.2 - - + -
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Residues in contact with TRP 156 (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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13B ARG* 3.5 38.9 - - + +
106B ARG* 4.2 12.1 - - - +
110B SER* 3.1 23.8 - - - +
113B ALA* 4.0 3.6 - - - -
114B ARG* 5.9 0.2 - - + -
154B ASP* 3.9 20.9 - - + -
155B LEU* 1.3 80.8 - - - +
157B VAL* 1.3 84.5 + - - +
158B SER* 5.6 0.2 - - - +
163B PHE* 3.5 8.0 - - - -
164B LEU* 2.8 56.7 + - + +
166B GLU* 3.5 50.0 - - + -
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Residues in contact with VAL 157 (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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19B LEU* 3.5 39.5 - - + -
67B TRP* 5.2 0.2 - - + -
100B PRO* 5.5 0.2 - - + -
106B ARG* 2.7 54.3 + - + +
109B LEU* 3.5 37.7 - - + +
110B SER* 3.4 13.2 - - - +
113B ALA* 4.4 6.3 - - + -
156B TRP* 1.3 84.7 - - - +
158B SER* 1.3 61.0 + - - +
161B GLY* 5.3 0.7 - - - -
162B ALA 3.4 4.3 - - - +
163B PHE* 4.7 1.8 - - + -
164B LEU* 4.1 1.8 - - - -
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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