Contacts of the strand formed by residues 143 - 149 (chain B) in PDB entry 3TJK
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LYS* 5.0 0.2 - - - +
110B TYR* 3.2 30.5 - - + +
112B VAL* 3.9 13.2 - - + -
138B PHE* 3.0 54.8 + - + +
139B ARG* 3.4 11.2 + - - +
141B ILE* 3.0 14.2 + - - +
142B ASN* 1.3 74.2 - - - +
144B GLU* 1.3 76.1 + - - +
232B VAL* 3.4 13.5 - - + +
236B GLN* 3.4 4.2 + - - -
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Residues in contact with GLU 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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106B TYR* 3.5 38.0 - - + -
109B LYS* 2.9 42.5 + - + +
110B TYR 2.9 9.5 + - - +
111B LEU* 3.5 3.9 - - + -
112B VAL 2.9 24.8 + - - -
135B LEU* 4.9 1.9 - - - +
139B ARG* 3.0 47.7 + - - +
143B THR* 1.3 80.1 - - - +
145B VAL* 1.3 68.5 + - - +
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 4.2 0.2 - - - -
112B VAL* 3.3 14.6 - - + +
114B PHE* 3.6 29.8 - - + -
131B PHE* 4.2 10.3 - - + -
135B LEU* 3.8 17.7 - - + +
138B PHE* 3.8 37.7 - - + -
144B GLU* 1.3 83.3 + - - +
146B VAL* 1.3 72.0 + - - +
174B ILE* 3.6 25.1 - - + +
175B PRO* 3.4 17.7 - - - +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TRP* 4.1 11.4 - - + -
101B LEU* 4.2 10.5 - - + -
106B TYR* 3.1 41.7 - - + +
111B LEU* 3.9 9.4 - - + +
112B VAL 2.9 7.4 + - - +
113B PHE* 3.5 31.4 - - + -
114B PHE* 3.0 29.7 + - - +
145B VAL* 1.3 78.9 - - - +
147B ALA* 1.3 71.8 + - - +
175B PRO* 4.0 13.7 - - + +
177B LEU* 4.3 5.6 - - + -
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Residues in contact with ALA 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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114B PHE* 3.3 36.8 - - + -
116B TYR* 4.0 9.2 - - + -
128B ILE* 4.5 2.2 - - + -
146B VAL* 1.3 75.2 - - - +
148B CYS* 1.3 55.1 + - - +
174B ILE* 4.0 5.9 - - + +
175B PRO 3.1 9.3 + - - +
176B LEU* 3.5 22.7 - - + -
177B LEU* 2.8 34.8 + - - +
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Residues in contact with CYS 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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113B PHE* 4.2 10.8 - - + -
114B PHE 2.9 11.3 + - - +
115B PHE* 3.1 37.9 - - + +
116B TYR* 2.9 29.5 + - - -
147B ALA* 1.3 76.4 - - - +
149B SER* 1.3 63.6 + - - +
177B LEU* 3.4 32.5 - - + -
179B ASP* 3.7 24.9 - - - -
184B ILE* 4.7 1.6 - - - -
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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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115B PHE* 5.4 1.8 - - - -
116B TYR* 3.1 38.3 + - - -
117B PRO 3.9 3.4 - - - -
148B CYS* 1.3 72.7 - - - +
150B VAL* 1.3 61.9 + - - +
151B ASP* 2.5 31.3 + - - +
156B HIS* 3.2 15.8 - - - -
177B LEU 3.3 8.1 + - - +
179B ASP* 2.9 27.3 + - - +
185B SER* 5.6 0.4 - - - -
198B THR* 5.3 2.7 - - - -
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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