Contacts of the strand formed by residues 141 - 148 (chain A) in PDB entry 1XRE
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 GLU 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A TYR* 3.6 25.4 - - + +
136A VAL 3.6 0.3 - - - +
137A LEU* 3.4 3.5 - - - -
138A ASP* 2.8 44.5 + - + +
139A GLY 3.4 0.2 - - - -
140A GLU* 1.3 77.7 - - - +
142A LEU* 1.3 79.0 + - - +
143A SER* 3.9 10.3 + - - +
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Residues in contact with LEU 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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102A VAL* 4.5 3.6 - - + -
105A VAL* 3.5 50.0 - - + +
106A ILE* 3.8 19.5 - - + +
109A TYR* 3.7 18.9 - - + +
110A PHE* 3.9 22.3 - - + -
135A LEU* 4.2 13.5 - - + -
136A VAL 3.3 3.4 - - - +
137A LEU* 3.4 29.4 - - + -
141A GLU* 1.3 85.0 - - - +
143A SER* 1.3 59.5 + - - +
161A LEU* 3.8 20.0 - - + -
199A TYR* 4.3 3.8 - - + -
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Residues in contact with SER 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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110A PHE* 4.2 4.9 - - - -
135A LEU* 3.5 6.7 - - - +
136A VAL* 2.9 50.0 + - - +
138A ASP* 4.4 12.5 + - - +
141A GLU* 3.9 11.9 + - - -
142A LEU* 1.3 75.1 - - - +
144A VAL* 1.3 68.0 + - - +
145A MET* 5.7 0.3 - - - +
158A LYS* 4.9 6.4 + - - -
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Residues in contact with VAL 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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110A PHE* 4.2 11.9 - - + -
116A LEU* 3.8 28.7 - - + -
119A GLN* 3.7 17.5 - - + +
120A LEU* 3.7 20.0 - - + +
123A ALA* 3.5 28.5 - - + -
134A TRP 3.2 12.6 - - - +
135A LEU* 4.4 2.9 - - + -
143A SER* 1.3 81.8 - - - +
145A MET* 1.3 67.6 + - - +
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Residues in contact with MET 145 (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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123A ALA* 4.3 9.1 - - - +
133A GLY* 3.6 2.4 - - - -
134A TRP* 2.7 46.8 + - + +
136A VAL* 4.2 9.2 - - + -
143A SER* 5.9 0.2 - - - +
144A VAL* 1.3 78.5 - - - +
146A SER* 1.3 73.9 + - - +
147A THR* 3.9 15.9 - - + -
153A PRO* 4.0 17.7 - - + -
156A GLU* 3.4 27.1 - - - +
158A LYS* 3.7 36.8 - - - +
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Residues in contact with SER 146 (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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123A ALA* 3.7 26.3 + - - +
126A SER 5.6 0.2 - - - -
127A ARG* 3.0 37.3 + - - +
132A TYR 3.2 15.7 - - - -
134A TRP* 4.1 0.9 - - - -
145A MET* 1.3 86.1 - - - +
147A THR* 1.3 69.0 + - - +
148A PRO* 4.8 0.3 - - - +
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Residues in contact with THR 147 (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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127A ARG* 3.5 10.0 + - - +
131A GLY* 3.2 3.8 - - - -
132A TYR* 3.0 34.4 + - - +
134A TRP* 2.9 30.4 + - + +
145A MET* 3.9 14.1 - - + -
146A SER* 1.3 77.9 - - - +
148A PRO* 1.4 70.3 + - + +
151A ASP* 2.7 34.8 + - + +
152A THR 4.1 11.9 - - - +
156A GLU* 5.4 1.1 - - - +
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Residues in contact with PRO 148 (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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127A ARG* 3.5 25.3 - - - +
128A PHE 6.1 0.2 - - - +
130A SER 3.5 8.1 - - - +
147A THR* 1.4 89.5 - - + +
149A ASN* 1.3 80.8 + - - +
150A GLN 3.3 0.2 + - - -
151A ASP* 3.0 38.3 + - + +
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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