Contacts of the strand formed by residues 137 - 144 (chain A) in PDB entry 1AR4
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 ARG 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A PHE* 3.5 58.9 + - + +
131A TRP* 3.4 12.8 - - - -
132A ASP* 2.8 50.8 + - - +
135A GLY* 4.0 10.5 + - - +
136A LYS* 1.3 79.3 - - - +
138A ILE* 1.3 58.5 + - - +
139A ASN* 2.9 31.5 - - - +
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 4.3 11.9 - - + -
99A ALA* 4.0 18.6 - - + -
100A ILE* 4.6 8.5 - - + -
103A PHE* 3.6 25.9 - - + +
104A PHE* 3.6 20.6 - - + -
129A LEU* 3.6 34.5 - - + -
130A VAL 3.3 11.7 - - - +
131A TRP* 3.9 17.0 - - + -
137A ARG* 1.3 76.1 + - - +
139A ASN* 1.3 69.3 + - - +
157A LEU* 4.1 15.3 - - + -
195A PHE* 3.9 20.6 - - + -
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Residues in contact with ASN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PHE* 4.2 4.5 - - - -
128A SER 3.7 0.2 - - - +
129A LEU* 3.4 5.9 - - - +
130A VAL* 2.9 40.8 + - + +
132A ASP* 3.7 26.3 - - - +
137A ARG* 2.9 37.1 + - - +
138A ILE* 1.3 79.7 + - - +
140A THR* 1.3 68.9 + - - +
141A LEU* 5.1 6.3 - - + -
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Residues in contact with THR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PHE* 3.7 27.7 - - + -
110A MET 5.0 1.1 - - - +
113A GLN* 2.8 35.1 + - + +
114A PHE* 4.3 25.6 - - + +
117A ALA* 5.2 8.2 - - - +
128A SER 3.1 5.2 - - - -
129A LEU* 3.8 13.5 - - + -
139A ASN* 1.3 75.9 - - - +
141A LEU* 1.3 69.6 + - - +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ALA* 5.0 4.9 - - - +
126A TRP 3.8 0.3 - - - +
127A ALA* 3.7 2.4 - - - -
128A SER* 2.7 36.0 + - - +
130A VAL* 3.5 29.6 - - + -
139A ASN* 5.1 6.5 - - + -
140A THR* 1.3 81.3 - - - +
142A GLN* 1.3 61.7 + - - +
143A PHE* 3.7 28.7 - - + -
149A ASN 4.6 6.7 - - - +
150A LEU* 4.1 2.2 - - + -
151A PRO* 3.7 35.0 - - + -
154A SER* 3.9 6.3 - - - +
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Residues in contact with GLN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ALA 4.8 0.2 + - - -
117A ALA* 2.9 36.5 + - + +
120A GLY* 4.1 5.9 + - - +
121A ILE* 3.6 40.3 - - + +
122A GLN 5.4 0.7 + - - -
126A TRP 3.4 3.4 - - - +
127A ALA* 5.0 0.4 - - - +
141A LEU* 1.3 73.7 - - - +
143A PHE* 1.3 65.1 + - - +
144A TYR* 3.4 25.4 + - + -
149A ASN* 2.7 37.7 + - - +
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Residues in contact with PHE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ASN* 4.0 20.2 - - - -
121A ILE* 4.2 4.0 - - - +
125A GLY* 3.1 4.7 - - - -
126A TRP* 2.9 54.2 + - + +
128A SER* 3.5 18.6 - - - -
130A VAL* 4.4 8.1 - - + -
141A LEU* 3.7 23.1 - - + -
142A GLN* 1.3 78.3 - - - +
144A TYR* 1.3 64.6 + - - +
146A HIS 4.1 11.7 - - - +
148A ASN 3.2 8.3 - - - +
149A ASN 4.1 0.9 - - - -
150A LEU* 3.6 43.7 - - + -
154A SER* 5.7 0.7 - - - -
156A PRO* 5.7 0.9 - - + -
159A GLN* 3.1 24.2 - - - -
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Residues in contact with TYR 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 4.9 8.5 - - + -
122A GLN 6.0 2.7 - - - -
124A SER 3.6 5.2 - - - +
142A GLN* 3.4 28.9 + - + -
143A PHE* 1.3 77.3 - - - +
145A ASP* 1.3 73.7 + - + +
146A HIS* 3.0 5.4 + - - -
148A ASN* 2.9 40.0 + - + +
149A ASN* 3.5 37.5 + - + -
63B LYS* 3.4 29.8 + - - -
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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