Contacts of the strand formed by residues 131 - 138 (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 GLY 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ARG* 3.9 5.1 - - - +
129A GLY 4.0 1.6 + - - -
130A SER* 1.3 76.2 - - - +
132A TYR* 1.3 66.9 + - - -
147A THR 3.2 12.3 - - - -
149A ASN 3.7 12.3 - - - -
166A VAL* 2.9 31.2 + - - +
167A TRP* 3.4 15.6 + - - +
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Residues in contact with TYR 132 (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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82A CYS* 3.4 31.6 - - + +
83A HIS* 3.1 23.0 + + - -
86A PHE* 5.5 1.6 - - + -
124A ALA* 5.2 0.7 - - - -
127A ARG* 4.4 1.0 - - - +
131A GLY* 1.3 72.8 - - - -
133A GLY* 1.3 60.2 + - - +
134A TRP* 3.5 19.7 - + - +
146A SER* 3.2 11.1 - - - -
147A THR* 3.0 35.6 + - - +
149A ASN 3.2 25.8 - - - -
150A GLN* 2.6 30.4 + - - -
151A ASP 4.7 0.2 - - - -
163A VAL* 3.5 24.2 - - + -
164A ILE 3.2 4.5 - - - +
165A ASP* 3.5 38.6 + - + -
166A VAL* 4.2 5.6 - - - +
167A TRP* 3.7 5.6 - - - -
209A MN 3.9 0.3 + - - -
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Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 3.8 11.7 - - - +
124A ALA* 4.4 16.2 - - - +
132A TYR* 1.3 74.0 - - - +
134A TRP* 1.3 61.5 + - - -
145A MET 3.6 5.8 - - - -
146A SER* 4.4 1.3 - - - -
163A VAL* 3.3 7.6 - - - +
164A ILE* 2.9 44.9 + - - +
166A VAL* 4.8 0.4 - - - +
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Residues in contact with TRP 134 (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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81A TYR* 4.2 10.8 - + - -
82A CYS* 3.7 34.8 - - + -
85A LEU* 4.0 7.4 - - + -
120A LEU* 3.5 12.6 - - - +
132A TYR* 3.5 13.8 - - + +
133A GLY* 1.3 77.0 - - - -
135A LEU* 1.3 59.2 + - - +
136A VAL* 3.9 14.6 - - + -
144A VAL* 3.2 6.8 - - - -
145A MET* 2.7 45.5 + - + +
146A SER* 4.1 1.1 - - - -
147A THR* 2.9 34.0 + - + +
151A ASP 3.9 7.6 - - - -
152A THR* 4.2 0.4 - - - -
153A PRO* 3.6 26.0 - - + -
160A PRO* 3.7 34.8 - - + -
162A LEU 3.5 6.5 - - - -
163A VAL* 3.6 35.7 - - + -
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Residues in contact with LEU 135 (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* 5.6 0.7 - - + -
106A ILE* 4.7 11.9 - - + -
110A PHE* 4.2 6.1 - - + -
116A LEU* 4.0 35.7 - - + -
120A LEU* 4.3 6.9 - - + +
134A TRP* 1.3 74.0 - - - +
136A VAL* 1.3 64.1 + - - +
142A LEU* 4.2 20.9 - - + -
143A SER 3.5 19.1 - - - +
144A VAL* 4.4 2.0 - - + -
160A PRO* 3.7 0.9 - - - +
161A LEU* 2.9 48.1 + - + -
162A LEU* 2.9 36.0 + - + +
192A TRP* 5.2 0.7 - - + -
195A VAL* 4.9 7.0 - - + -
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Residues in contact with VAL 136 (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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134A TRP* 3.9 11.7 - - + -
135A LEU* 1.3 79.9 - - - +
137A LEU* 1.3 60.4 + - - +
138A ASP 4.9 0.2 - - - +
141A GLU 3.6 0.2 - - - +
142A LEU* 3.3 8.3 - - - +
143A SER* 2.9 56.4 + - - +
145A MET* 4.2 8.5 - - + -
153A PRO* 3.8 33.7 - - + -
158A LYS* 3.9 28.3 - - + -
159A ILE 3.2 11.9 - - - +
160A PRO* 4.2 4.7 - - + -
161A LEU* 4.5 5.4 - - - +
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Residues in contact with LEU 137 (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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136A VAL* 1.3 72.4 - - - +
138A ASP* 1.3 57.8 + - - +
139A GLY 3.4 23.0 + - - +
140A GLU* 3.8 11.0 - - - +
141A GLU 3.4 7.4 - - - +
142A LEU* 3.4 24.9 - - + -
157A GLY 4.6 0.7 - - - +
158A LYS* 3.5 4.0 - - - -
159A ILE* 2.8 50.7 + - + +
161A LEU* 4.4 8.7 - - + +
199A TYR* 3.8 14.1 - - + +
202A ALA* 3.6 31.9 - - + +
203A ILE* 4.0 19.7 - - + -
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Residues in contact with ASP 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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136A VAL 4.0 0.2 - - - -
137A LEU* 1.3 72.9 - - - +
139A GLY* 1.3 57.9 + - - +
140A GLU 3.4 0.2 + - - -
141A GLU* 2.8 36.4 + - + +
143A SER* 4.4 14.3 + - - +
156A GLU 5.6 0.3 - - - +
157A GLY 4.9 5.1 - - - +
158A LYS* 3.9 35.6 - - + +
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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