Contacts of the strand formed by residues 147 - 153 (chain B) in PDB entry 5WWT
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
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Residue Dist Surf HB Arom Phob DC
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110B GLN* 3.5 44.4 + - + +
112B CYS* 4.4 5.9 - - - +
145B GLY 3.5 6.5 + - - +
146B ASP* 1.3 69.7 - - - +
148B ILE* 1.3 62.4 + - - +
174B ASN* 4.7 10.1 - - + +
175B GLY 3.8 8.5 - - - +
176B ILE* 4.6 16.4 - - + +
199B THR* 5.5 3.8 - - - +
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLN* 4.5 0.9 - - - -
112B CYS* 3.2 38.1 - - - +
113B GLU* 4.9 0.2 - - - -
114B ALA* 3.7 7.2 - - + -
142B MET* 3.6 24.0 - - + -
146B ASP* 3.2 20.6 - - + +
147B VAL* 1.3 74.6 - - - +
149B SER* 1.3 66.1 + - - +
150B VAL* 4.0 1.1 + - + -
174B ASN* 3.3 6.2 - - - +
175B GLY 2.9 42.7 + - - +
177B SER* 4.1 8.5 - - - -
196B ILE* 3.6 42.8 - - + -
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Residues in contact with SER 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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109B LYS* 3.7 1.2 - - - -
110B GLN* 2.7 34.4 + - - +
112B CYS 2.9 10.7 + - - -
113B GLU* 3.5 1.2 - - - -
114B ALA 3.0 22.7 + - - -
148B ILE* 1.3 72.5 - - - +
150B VAL* 1.3 60.7 + - - +
151B TYR* 3.4 21.7 - - - -
171B PHE* 3.6 13.5 - - - -
173B GLY 3.7 0.2 - - - -
174B ASN* 2.6 23.6 + - - -
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Residues in contact with VAL 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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114B ALA 3.5 6.5 - - - +
116B VAL* 3.9 28.5 - - + -
124B VAL* 5.4 0.4 - - + -
130B VAL* 4.3 8.7 - - + -
148B ILE* 4.6 5.8 - - + +
149B SER* 1.3 73.8 - - - +
151B TYR* 1.3 66.2 + - - +
171B PHE* 3.9 1.6 - - - -
172B LEU* 3.0 42.2 + - + -
173B GLY 2.9 13.9 + - - +
196B ILE* 3.9 29.2 - - + -
198B MET* 3.8 28.9 - - + -
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Residues in contact with TYR 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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109B LYS* 3.6 34.3 - - + +
110B GLN 4.7 1.4 + - - -
113B GLU* 3.7 34.7 + - + +
114B ALA 2.8 13.4 + - - +
115B ILE* 3.4 7.5 - - + -
116B VAL* 3.1 27.2 + - - +
149B SER* 3.4 31.4 - - - -
150B VAL* 1.3 74.3 - - - +
152B SER* 1.3 60.7 + - - +
169B LYS* 3.9 42.4 - - + -
170B VAL 3.3 4.0 - - - -
171B PHE* 3.8 34.8 - + + -
172B LEU* 4.1 3.1 - - - -
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Residues in contact with SER 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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115B ILE* 4.9 0.9 - - - -
116B VAL* 4.1 4.3 - - - -
118B ALA* 3.8 18.0 - - - -
121B GLY* 3.9 9.1 - - - -
151B TYR* 1.3 73.8 - - - +
153B ASP* 1.3 61.2 + - - +
154B ILE* 3.0 24.8 + - - +
168B THR 3.6 0.2 - - - +
169B LYS* 3.5 7.1 - - - -
170B VAL* 2.8 29.0 + - - -
172B LEU* 3.7 30.9 - - - +
335B MET* 3.9 6.1 - - - +
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Residues in contact with ASP 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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115B ILE* 3.8 16.0 - - + +
116B VAL 3.1 21.1 + - - +
117B GLY* 4.9 2.1 - - - -
118B ALA* 3.4 15.1 + - - +
136B VAL* 5.2 2.7 - - + +
151B TYR 4.0 0.8 + - - -
152B SER* 1.3 70.2 + - - +
154B ILE* 1.3 58.9 + - - +
155B LYS* 3.8 3.8 + - - +
156B GLY* 2.9 23.6 + - - -
157B LYS 2.8 30.5 + - - -
158B CYS* 2.8 23.3 + - + +
165B PHE* 3.3 18.3 - - + -
168B THR 4.0 5.7 - - - +
169B LYS* 5.3 0.4 - - - +
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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