Contacts of the strand formed by residues 149 - 156 (chain B) in PDB entry 2W9T
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 HIS 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B LEU* 3.8 18.3 - - + +
26B ASN* 2.7 39.2 + - - +
111B THR* 4.1 12.6 - - + -
112B VAL 3.0 12.6 - - - +
113B ILE* 4.3 9.4 - - + -
114B ASP 4.9 0.4 - - - +
138B GLU* 3.7 6.9 - - - +
139B GLY* 2.8 45.8 + - - -
141B LEU* 3.9 11.5 - - + +
145B ASN* 4.0 9.4 - - + -
147B ILE 2.9 23.0 + - - +
148B PRO* 1.3 74.7 - - - +
150B THR* 1.3 59.3 + - - +
151B PHE* 3.4 28.5 - + - -
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Residues in contact with THR 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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110B ILE 3.5 1.9 - - - +
111B THR* 3.3 4.9 - - - +
112B VAL* 2.7 45.9 + - - +
136B SER* 3.6 15.5 - - - +
137B VAL 3.2 20.8 + - - +
138B GLU* 4.5 7.6 - - - +
149B HIS* 1.3 75.4 + - - +
151B PHE* 1.3 62.2 + - - +
152B LEU* 3.4 29.0 + - + -
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Residues in contact with PHE 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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26B ASN* 3.8 22.7 - - + -
27B ASP* 3.6 12.3 - - - -
30B HIS* 3.6 41.5 - + + +
110B ILE 3.7 2.2 - - - -
111B THR* 3.3 28.9 - - + -
135B SER* 3.8 3.6 + - - +
136B SER* 3.5 4.0 + - - -
137B VAL* 2.8 51.2 + - + +
139B GLY* 3.7 13.0 - - - -
149B HIS* 3.4 32.5 - + - -
150B THR* 1.3 68.8 - - - +
152B LEU* 1.3 65.1 + - - +
153B HIS 4.1 0.2 + - - -
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Residues in contact with LEU 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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30B HIS* 5.5 1.6 + - - -
109B TYR* 3.4 6.2 - - - +
110B ILE* 2.7 48.9 + - + +
112B VAL* 3.4 27.1 - - + -
126B TYR* 4.3 13.5 - - + +
133B VAL* 5.5 2.2 - - + -
135B SER 3.5 2.5 - - - +
136B SER* 3.8 14.4 - - - +
150B THR* 3.4 28.3 - - + -
151B PHE* 1.3 73.3 - - - +
153B HIS* 1.3 61.4 + - - +
154B LEU* 3.9 26.0 - - + -
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Residues in contact with HIS 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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107B ASP* 2.6 43.7 + - + -
108B MET 3.3 9.7 + - - -
109B TYR* 3.4 35.8 + + + -
134B GLU* 2.7 67.6 + - + +
135B SER* 2.8 28.9 + - - +
152B LEU* 1.3 74.7 - - - +
154B LEU* 1.3 64.1 + - - +
155B VAL* 3.7 10.7 - - + +
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Residues in contact with LEU 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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107B ASP* 3.1 6.4 - - - +
108B MET* 2.9 41.6 + - + +
110B ILE* 3.9 16.2 - - + -
126B TYR* 3.4 40.4 - - + -
131B TRP* 4.1 24.1 - - + -
132B GLU 3.1 7.0 - - - +
133B VAL* 4.0 28.0 - - + +
152B LEU* 3.9 23.6 - - + -
153B HIS* 1.3 81.0 + - - +
155B VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 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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106B ASP 3.6 7.4 - - - +
107B ASP* 4.1 4.3 - - + +
131B TRP* 3.4 3.7 - - - -
132B GLU* 2.8 55.4 + - + +
134B GLU* 3.8 17.5 - - + -
153B HIS* 3.7 25.1 - - + +
154B LEU* 1.3 78.1 - - - +
156B ARG* 1.3 66.8 + - - +
157B ARG* 3.4 0.4 + - - -
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Residues in contact with ARG 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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102B ILE 2.8 27.1 + - - -
103B ASP* 3.1 30.8 + - - +
104B GLN 5.0 1.2 + - - -
105B VAL 2.9 24.1 + - - +
106B ASP* 3.0 17.9 + - - +
130B ASP* 3.5 19.6 - - - +
131B TRP* 3.4 30.0 - - + -
155B VAL* 1.3 77.3 - - - +
157B ARG* 1.3 72.5 + - - +
158B LYS* 3.2 34.9 + - + +
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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