Contacts of the strand formed by residues 139 - 146 (chain B) in PDB entry 2J3T
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 139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ARG* 4.5 3.4 - - - +
138B SER* 1.3 83.1 - - - +
140B VAL* 1.3 63.1 + - - +
141B THR* 3.9 20.0 + - + -
153B GLN 3.3 3.5 - - - +
155B VAL* 2.9 45.4 + - + +
157B PRO* 6.0 2.2 - - + -
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Residues in contact with VAL 140 (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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38B GLU* 5.4 4.2 - - - +
124B CYS* 3.5 41.4 - - + +
127B LEU* 4.0 18.8 - - + -
128B ARG* 3.9 36.4 - - + +
131B LEU* 4.3 0.9 - - + -
138B SER* 4.1 8.5 - - - +
139B VAL* 1.3 77.3 - - - +
141B THR* 1.3 72.5 + - - +
152B PHE* 4.5 2.9 - - + -
153B GLN 3.0 8.3 - - - +
154B VAL* 3.9 22.2 - - + -
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Residues in contact with THR 141 (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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124B CYS* 3.8 3.1 - - - -
139B VAL* 3.9 17.2 + - + -
140B VAL* 1.3 79.5 - - - +
142B ALA* 1.3 63.8 + - - +
151B LYS 4.0 0.2 - - - +
152B PHE* 3.3 5.4 - - - +
153B GLN* 2.6 64.6 + - - +
155B VAL* 5.8 0.5 - - - +
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Residues in contact with ALA 142 (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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120B LEU* 3.5 33.2 - - + +
124B CYS* 3.3 24.6 - - - -
141B THR* 1.3 77.0 - - - +
143B SER* 1.3 64.0 + - - +
150B CYS* 6.0 0.4 - - - -
151B LYS 3.7 4.5 - - - +
152B PHE* 4.0 10.3 - - + -
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Residues in contact with SER 143 (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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120B LEU* 4.5 0.6 - - - +
142B ALA* 1.3 78.5 - - - +
144B VAL* 1.3 66.1 + - - +
145B ALA 4.2 0.8 + - - -
149B VAL 4.5 0.3 - - - +
150B CYS* 3.4 3.0 - - - +
151B LYS* 3.0 51.9 + - - +
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Residues in contact with VAL 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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103B LEU* 3.9 11.2 - - + -
113B LEU* 3.6 22.4 - - + +
116B ALA* 4.5 8.7 - - + -
117B PRO* 5.4 7.0 - - + +
120B LEU* 3.4 25.3 - - + +
143B SER* 1.3 75.6 + - - +
145B ALA* 1.3 62.8 + - - +
146B ALA 3.7 14.4 - - - +
147B LEU* 3.8 23.6 - - + +
149B VAL 4.2 5.6 - - - +
150B CYS* 3.2 25.1 - - + -
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Residues in contact with ALA 145 (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 LEU* 5.5 1.0 - - - +
113B LEU* 3.2 24.2 - - - +
143B SER 4.2 1.2 + - - -
144B VAL* 1.3 74.1 - - - +
146B ALA* 1.3 64.5 + - + +
149B VAL 4.3 4.9 + - - +
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Residues in contact with ALA 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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109B GLY* 3.5 22.0 - - - +
110B LEU* 5.4 3.1 - - + -
113B LEU* 4.1 2.7 - - - -
144B VAL* 3.6 3.3 - - - -
145B ALA* 1.3 84.7 - - + +
147B LEU* 1.3 68.6 + - - +
149B VAL* 3.1 23.9 + - - +
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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