Contacts of the strand formed by residues 144 - 151 (chain B) in PDB entry 5J63
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 ILE 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B LEU* 3.1 33.9 - - + +
109B PRO* 4.4 1.1 - - + -
131B THR* 3.8 22.0 - - + -
133B HIS* 3.9 5.2 - - + -
142B GLY 4.3 0.2 - - - +
143B ALA* 1.3 68.0 - - - +
145B VAL* 1.3 62.3 + - - +
146B ALA* 3.8 14.8 - - - +
147B GLN* 4.0 14.8 - - + +
186B LEU 4.1 1.2 - - - +
188B ILE* 2.7 44.1 + - + +
189B ALA 5.7 0.2 - - - +
190B GLN* 3.5 34.5 - - + +
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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
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101B PHE* 4.1 20.4 - - + -
132B LEU* 3.2 14.7 + - + +
133B HIS* 4.4 2.2 - - - -
134B ARG* 4.5 5.2 - - + +
143B ALA 3.1 11.9 + - - +
144B ILE* 1.3 72.9 - - - +
146B ALA* 1.3 60.4 + - + +
176B THR* 4.0 25.1 - - + -
179B ALA* 6.5 1.3 - - + -
180B ILE* 4.7 7.9 - - + -
185B ILE* 3.9 28.5 - - + -
186B LEU* 3.7 20.2 - - - +
187B GLU* 5.1 3.8 - - + -
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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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131B THR* 3.5 3.8 - - - +
132B LEU 3.0 30.2 + - - +
144B ILE* 3.5 4.9 - - - -
145B VAL* 1.3 82.7 - - + +
147B GLN* 1.3 62.4 + - - +
172B LEU* 3.7 14.1 - - + -
175B GLN* 5.4 2.2 - - + +
176B THR* 3.7 23.6 - - + +
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Residues in contact with GLN 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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107B LEU* 3.2 34.8 - - + +
108B LEU* 3.0 33.5 + - - +
130B VAL 3.4 6.7 - - - +
131B THR* 2.9 23.9 + - - +
144B ILE* 4.0 16.2 - - + +
146B ALA* 1.3 77.6 - - - +
148B LEU* 1.3 65.2 + - - +
149B ARG* 4.5 10.3 + - - +
172B LEU* 5.0 1.1 - - - -
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Residues in contact with LEU 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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107B LEU* 4.5 2.9 - - - -
129B GLY* 3.0 3.7 - - - -
130B VAL* 2.8 49.0 + - + +
147B GLN* 1.3 76.8 - - - +
149B ARG* 1.3 76.0 + - - +
150B ILE* 4.7 1.8 - - + -
168B ALA* 3.6 33.7 - - + +
171B GLN* 4.2 19.5 - - + +
172B LEU* 4.0 20.6 - - + +
175B GLN* 4.3 16.4 - - - +
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Residues in contact with ARG 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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107B LEU* 3.7 27.8 - - + +
127B GLU* 3.3 36.1 + - - +
128B THR 3.6 12.3 - - - +
147B GLN* 4.5 12.3 + - - +
148B LEU* 1.3 84.7 - - - +
150B ILE* 1.3 75.7 - - - +
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Residues in contact with ILE 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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127B GLU* 3.4 9.8 - - - +
128B THR* 2.8 53.5 + - + +
129B GLY* 4.0 3.6 - - - -
148B LEU* 4.7 2.0 - - + -
149B ARG* 1.3 86.0 - - - +
151B ALA* 1.3 62.9 + - - +
161B LEU* 4.0 14.6 - - + -
164B LYS* 3.8 30.7 - - + +
165B LEU* 3.5 28.9 - - + -
168B ALA* 4.3 20.2 - - + -
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Residues in contact with ALA 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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126B THR 3.8 7.2 - - - +
127B GLU* 4.1 11.7 + - + +
150B ILE* 1.3 76.0 - - - +
152B ILE* 1.3 63.7 + - - +
153B ALA* 5.0 1.1 - - + +
161B LEU* 4.9 1.0 - - - +
164B LYS* 3.4 28.5 + - - +
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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