Contacts of the strand formed by residues 143 - 148 (chain B) in PDB entry 1DWQ
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 THR 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B THR* 3.7 34.5 - - + +
136B PHE 3.2 7.6 - - - +
137B THR* 4.1 9.7 + - - +
141B GLY 3.7 3.2 + - - -
142B GLU* 1.3 71.7 - - - +
144B ILE* 1.3 58.4 + - - +
145B THR* 4.0 3.8 + - - +
182B ASN* 3.2 21.8 + - - +
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Residues in contact with ILE 144 (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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52B ASN 4.3 0.2 - - - +
135B THR* 3.1 5.2 - - - -
136B PHE* 2.6 65.6 + - + +
138B ASN* 3.7 35.2 - - + +
142B GLU* 4.3 2.2 - - + -
143B THR* 1.3 77.6 - - - +
145B THR* 1.3 61.5 + - - +
146B THR 3.8 0.5 + - - -
178B SER* 3.2 26.2 - - - +
180B PHE* 3.8 22.7 - - + -
182B ASN* 4.2 6.5 - - - +
183B VAL* 3.6 31.2 - - + -
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Residues in contact with THR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B TYR* 4.1 23.1 - - + -
134B PHE 3.3 11.7 - - - +
135B THR* 3.3 16.5 - - + +
143B THR* 4.0 4.4 + - - +
144B ILE* 1.3 75.8 - - - +
146B THR* 1.3 70.0 + - - +
147B MET* 5.7 4.1 - - + +
178B SER* 2.8 22.5 + - - -
179B LEU 4.5 1.4 + - - -
180B PHE* 5.1 0.6 + - - +
182B ASN* 5.1 3.4 - - - +
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Residues in contact with THR 146 (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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48B ILE* 3.7 27.8 - - + -
49B GLU* 4.9 0.9 + - - +
133B TYR* 3.2 6.4 - - - +
134B PHE* 2.8 55.2 + - - +
135B THR 5.4 0.2 - - - -
136B PHE* 3.5 37.4 - - + -
144B ILE 4.6 0.2 - - - +
145B THR* 1.3 79.7 - - - +
147B MET* 1.3 61.5 + - - +
176B LYS* 4.0 9.9 + - - +
177B GLY 3.2 10.8 - - - +
178B SER* 4.1 3.4 - - - -
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Residues in contact with MET 147 (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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12B ILE* 4.2 12.3 - - + -
13B CYS* 4.2 10.6 - - - -
128B TRP* 3.7 23.3 - - + -
131B THR* 3.8 10.8 - - + -
132B GLU 3.1 10.8 - - - +
133B TYR* 3.9 16.6 - - + -
134B PHE* 4.3 3.4 - - - -
145B THR* 5.7 3.1 - - + +
146B THR* 1.3 77.5 - - - +
148B LYS* 1.3 61.2 + - - +
149B LEU* 3.7 24.2 - - + -
176B LYS* 3.3 9.1 - - - +
177B GLY 2.9 32.7 + - - +
178B SER* 5.1 0.9 - - - -
179B LEU* 4.2 35.4 - - + +
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Residues in contact with LYS 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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131B THR* 3.3 3.2 - - - +
132B GLU* 2.8 49.2 + - + +
134B PHE* 3.8 20.1 - - + -
147B MET* 1.3 75.5 - - - +
149B LEU* 1.3 71.0 + - - +
150B GLY* 4.5 0.2 - - - -
151B PHE* 6.3 1.6 - - + -
175B ARG 5.3 3.6 - - - +
176B LYS* 4.0 35.8 - - + +
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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