Contacts of the strand formed by residues 176 - 183 (chain B) in PDB entry 5E0T
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 GLY 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLU 3.1 12.6 - - - -
117A LYS* 4.1 15.5 - - - -
154B ILE* 3.7 7.3 - - - +
172B SER* 3.5 0.7 - - - -
173B GLY 2.9 29.3 + - - +
174B GLU 3.3 3.8 + - - -
175B LEU* 1.3 82.6 - - - +
177B ASN* 1.3 66.4 + - - +
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Residues in contact with ASN 177 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ILE* 5.8 0.4 - - - +
114A TYR* 3.4 4.5 - - - +
115A GLU* 2.8 48.7 + - - +
117A LYS* 5.7 3.8 - - - +
154B ILE* 3.8 5.8 - - - -
171B ALA 3.1 15.5 - - - +
172B SER* 3.4 17.7 - - - -
176B GLY* 1.3 76.7 - - - -
178B GLY* 1.3 60.6 + - - +
179B ASN* 5.7 2.9 + - - -
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Residues in contact with GLY 178 (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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113A ASP 3.1 12.6 - - - -
114A TYR* 3.4 18.6 - - - -
151B LEU* 4.3 4.2 - - - +
154B ILE* 3.9 4.6 - - - +
169B PHE 4.1 0.2 - - - +
170B SER* 3.5 1.6 - - - -
171B ALA* 2.9 33.0 + - - +
177B ASN* 1.3 77.0 - - - +
179B ASN* 1.3 67.8 + - - +
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Residues in contact with ASN 179 (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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111A VAL 4.0 0.5 - - - +
112A SER* 3.3 2.4 - - - -
113A ASP* 2.8 59.7 + - - +
114A TYR* 4.6 1.2 - - - -
151B LEU* 4.9 0.4 - - - -
168B LYS* 4.2 17.7 - - + +
169B PHE 3.0 7.2 - - - +
170B SER* 3.2 25.0 + - - +
177B ASN* 5.7 2.8 + - - -
178B GLY* 1.3 76.9 - - - -
180B ILE* 1.3 64.7 + - - +
181B LYS* 4.0 21.3 - - - +
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Residues in contact with ILE 180 (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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110A LYS* 4.0 24.0 - - + -
111A VAL 3.5 2.9 - - - +
112A SER* 3.6 22.2 - - - +
114A TYR* 3.7 20.4 - - - +
147B ILE* 4.2 39.7 - - + +
150B ASP* 4.6 8.5 - - + +
151B LEU* 3.9 23.8 - - + -
168B LYS* 3.3 2.6 - - - -
169B PHE* 2.8 45.1 + - + +
179B ASN* 1.3 79.6 - - - +
181B LYS* 1.3 62.6 + - - +
182B LEU* 4.7 3.6 - - + -
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Residues in contact with LYS 181 (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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109A GLU 3.7 1.2 - - - +
110A LYS* 3.5 3.8 - - - +
111A VAL* 2.9 44.3 + - + +
113A ASP* 6.1 1.8 - - - -
167B VAL 3.5 6.3 - - - +
168B LYS* 3.9 34.5 - - + +
179B ASN* 4.0 14.1 - - - +
180B ILE* 1.3 72.1 - - - +
182B LEU* 1.3 62.4 + - - +
183B SER* 5.0 3.6 + - - +
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Residues in contact with LEU 182 (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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109A GLU 3.4 3.4 - - - +
110A LYS* 3.7 24.7 - - + -
137B VAL* 5.2 0.2 - - + -
139B MET* 3.7 38.1 - - + -
143B GLU* 3.2 25.4 - - - +
147B ILE* 4.2 9.4 - - + -
166B GLY* 3.4 5.4 - - - -
167B VAL* 2.9 43.9 + - + +
169B PHE* 4.2 17.9 - - + -
180B ILE* 4.1 2.4 + - + -
181B LYS* 1.3 72.3 - - - +
183B SER* 1.3 64.8 + - - +
195B VAL* 4.1 23.6 - - + -
197B ILE* 3.7 1.8 - - - +
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Residues in contact with SER 183 (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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109A GLU* 2.9 45.8 + - - +
165B ASP 4.5 7.2 - - - -
166B GLY* 4.8 1.8 - - - -
181B LYS* 5.0 4.0 + - - +
182B LEU* 1.3 76.9 + - - +
184B GLN* 1.3 63.7 + - - +
185B THR 3.6 1.6 + - - -
195B VAL* 3.9 12.0 - - - +
197B ILE* 4.1 5.8 - - - -
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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