Contacts of the strand formed by residues 131 - 138 (chain A) in PDB entry 1XUQ
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* 4.1 5.6 - - - +
129A GLY 4.0 1.6 + - - -
130A SER* 1.3 74.6 - - - +
132A TRP* 1.3 61.5 + - - -
147A THR 3.2 11.7 - - - -
149A ASN 3.7 13.2 - - - -
166A VAL* 2.8 36.8 + - - +
167A TRP* 3.4 15.7 + - - +
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Residues in contact with TRP 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 ASN* 3.6 40.1 - - + +
83A HIS* 3.8 16.4 - + - -
85A PHE* 5.4 0.7 - + - -
86A PHE* 3.7 30.1 - + + -
127A ARG* 4.4 1.0 - - - +
131A GLY* 1.3 78.3 - - - -
133A ALA* 1.3 59.0 + - - +
134A TRP* 3.4 40.7 - + + +
146A SER* 3.1 9.2 - - - -
147A THR* 2.9 34.6 + - - +
149A ASN 3.4 15.8 + - - -
150A GLN* 2.9 21.1 + - - +
163A GLY 4.6 1.3 - - - -
164A LEU 3.4 14.4 - - - -
165A ASP* 3.4 53.6 + - + -
166A VAL* 3.9 4.7 - - - +
167A TRP* 4.2 0.8 - - - +
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Residues in contact with ALA 133 (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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120A PHE* 3.5 25.1 - - + +
123A ALA* 4.6 3.8 - - + -
124A GLY* 3.9 31.9 - - - +
132A TRP* 1.3 74.3 - - - +
134A TRP* 1.3 61.6 + - - +
145A THR 3.6 7.0 - - - +
146A SER* 4.4 1.1 - - - +
163A GLY* 3.1 4.5 - - - -
164A LEU* 2.8 37.0 + - + +
166A VAL* 4.6 2.8 - - + +
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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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82A ASN* 3.5 32.5 - - + -
85A PHE* 3.9 26.2 - + + -
120A PHE* 3.7 7.5 - - - -
132A TRP* 3.4 39.5 - + + +
133A ALA* 1.3 78.0 - - - +
135A LEU* 1.3 60.5 + - - +
136A VAL* 3.7 10.8 - - + -
144A VAL* 3.3 10.6 - - - +
145A THR* 2.9 53.9 + - - +
147A THR* 2.9 30.1 + - + -
152A SER* 5.5 0.2 - - - -
153A PRO* 3.5 29.3 - - + +
160A PRO* 3.8 20.6 - - + -
162A ILE 3.4 19.3 - - - +
163A GLY* 3.8 7.9 - - - -
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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 LEU* 4.4 8.5 - - + -
106A ILE* 4.3 19.3 - - + -
110A PHE* 4.1 19.3 - - + -
116A PHE* 3.8 36.8 - - + -
120A PHE* 3.9 1.4 - - - -
134A TRP* 1.3 72.3 - - - +
136A VAL* 1.3 61.4 - - - +
142A LEU* 4.0 20.4 - - + -
143A GLU 3.6 14.1 - - - +
144A VAL* 4.5 0.4 - - + +
160A PRO* 3.8 0.3 - - - +
161A VAL* 2.8 45.5 + - + +
162A ILE* 2.9 28.1 + - + +
192A TRP* 4.9 1.8 - - + -
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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* 3.7 21.8 - - + -
135A LEU* 1.3 79.0 - - - +
137A VAL* 1.3 64.0 - - - +
142A LEU* 3.3 10.1 - - - +
143A GLU* 2.9 62.2 + - + +
145A THR* 4.0 7.9 - - + +
153A PRO* 3.9 25.1 - - + -
158A LYS* 4.0 23.1 - - + -
159A THR 3.2 14.1 - - - +
160A PRO* 4.2 3.8 - - + -
161A VAL* 4.3 1.3 - - - +
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Residues in contact with VAL 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 73.7 - - - +
138A ASN* 1.3 60.0 + - - +
139A ASN 4.0 2.5 + - - +
140A GLY* 3.6 34.1 - - - +
141A GLU 3.4 3.6 - - - +
142A LEU* 4.0 7.0 - - + -
157A GLY 4.6 0.3 - - - +
158A LYS* 3.5 4.5 - - - -
159A THR* 2.9 34.5 + - - +
161A VAL* 3.7 22.7 - - + -
199A TYR* 3.8 24.2 - - + +
202A ALA* 4.2 28.3 - - + -
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Residues in contact with ASN 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 1.1 - - + -
137A VAL* 1.3 71.4 - - - +
139A ASN* 1.3 91.0 + - - +
141A GLU* 2.8 28.9 + - + +
143A GLU* 2.9 30.0 - - + +
156A GLU 5.2 1.2 + - - -
157A GLY 4.5 4.4 + - - -
158A LYS* 3.5 33.5 + - + +
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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