Contacts of the strand formed by residues 141 - 150 (chain A) in PDB entry 1UXU
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 ASN 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A VAL* 3.7 8.1 - - - +
133A ASP* 2.8 59.4 + - + +
134A VAL* 4.8 0.8 - - - +
136A TYR 3.0 21.8 + - - -
137A PHE 4.1 1.4 + - - -
138A PRO* 3.3 29.0 - - - +
139A PHE 3.6 0.8 - - - +
140A ASP* 1.3 91.8 + - - +
142A GLN* 1.3 67.2 + - - +
178A TRP* 4.5 3.1 - - - -
207A LEU* 3.7 19.0 - - + +
208A LEU 3.0 13.1 - - - +
209A LYS* 4.2 0.2 - - - -
210A ARG* 5.5 2.3 + - - -
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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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45A MET* 3.9 24.0 - - - +
47A GLU* 3.0 29.7 + - - +
50A GLN* 2.8 41.4 + - - -
130A CYS* 3.6 7.8 - - - +
131A VAL 3.6 5.9 - - - -
132A VAL* 3.5 12.9 - - - +
141A ASN* 1.3 74.0 + - - +
143A GLN* 1.3 60.6 + - - +
144A CYS* 3.8 5.8 + - - -
178A TRP* 3.4 23.5 - - + -
206A LEU 3.5 3.5 - - - +
207A LEU* 3.6 3.6 - - - +
208A LEU* 2.9 40.6 + - + +
210A ARG* 4.8 0.6 - - - +
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Residues in contact with GLN 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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130A CYS* 3.2 2.9 - - - -
131A VAL* 2.8 44.9 + - + +
133A ASP* 5.0 10.7 + - + +
136A TYR* 6.0 3.8 - - - -
141A ASN* 4.2 1.0 - - - +
142A GLN* 1.3 71.7 - - - +
144A CYS* 1.3 61.1 + - - +
145A ASN* 4.0 5.0 + - - +
205A THR* 3.6 30.6 - - + +
206A LEU 3.8 2.2 - - - -
207A LEU* 4.0 14.6 - - + +
2215A NAG 2.9 46.4 + - - +
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Residues in contact with CYS 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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45A MET* 4.0 11.4 - - - -
52A LEU* 3.7 27.1 - - + -
128A SER* 5.4 1.6 - - - +
129A SER 4.4 2.0 - - - +
130A CYS* 2.1 47.8 - - - -
142A GLN* 4.2 5.6 - - - -
143A GLN* 1.3 74.1 - - - +
145A ASN* 1.3 66.9 + - - +
146A LEU* 3.7 3.0 + - - +
204A PHE 3.6 0.7 - - - +
206A LEU* 2.8 41.7 + - + +
208A LEU* 4.2 11.2 - - - -
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Residues in contact with ASN 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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96A ASN* 2.9 27.8 + - - +
128A SER* 3.9 4.5 + - - -
129A SER 4.4 5.9 + - - +
143A GLN* 3.9 5.3 + - - -
144A CYS* 1.3 73.8 - - - +
146A LEU* 1.3 65.7 + - - +
147A THR* 4.5 3.8 + - - +
203A THR* 3.9 8.8 - - + +
204A PHE 3.4 1.1 - - - -
205A THR* 2.8 28.8 + - - +
2215A NAG 1.4 64.5 + - - +
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Residues in contact with LEU 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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37A ILE* 5.3 0.2 - - + -
52A LEU* 4.9 8.3 - - + -
54A ALA* 5.4 0.7 - - + -
56A LEU* 4.4 23.3 - - + -
94A LEU* 4.1 11.7 - - + -
96A ASN* 4.0 1.1 - - - -
126A THR* 4.1 15.7 - - - +
128A SER* 3.3 26.9 - - - +
144A CYS 4.3 6.5 - - - +
145A ASN* 1.3 75.8 - - - +
147A THR* 1.3 61.2 + - - +
148A PHE* 3.7 21.5 - - + -
183A MET* 3.8 27.8 - - + -
202A VAL 3.7 1.9 - - - +
203A THR* 3.3 1.4 - - - -
204A PHE* 2.8 41.8 + - + +
206A LEU* 5.0 11.7 - - + -
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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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94A LEU* 3.5 5.6 - - - +
95A TYR* 2.8 44.3 + - + -
96A ASN* 3.0 21.0 + - - +
145A ASN* 4.5 5.4 + - - +
146A LEU* 1.3 73.6 - - - +
148A PHE* 1.3 58.2 + - - +
201A ASP* 3.6 25.1 - - + +
202A VAL 3.5 2.9 - - - -
203A THR* 2.8 29.7 + - - +
1213A MLK 4.0 15.0 - - + +
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Residues in contact with PHE 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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35A LEU* 3.8 21.8 - - + -
37A ILE* 3.7 28.7 - - + -
56A LEU* 3.9 16.8 - - + -
58A ILE* 4.0 20.6 - - + -
92A ILE* 4.0 8.5 - - + -
93A VAL* 3.2 20.2 - - - +
94A LEU* 3.8 26.9 - - + -
95A TYR* 4.2 4.3 - - - -
126A THR* 4.9 2.7 - - + -
146A LEU* 3.7 30.3 - - + -
147A THR* 1.3 73.9 - - - +
149A GLY* 1.3 59.4 + - - +
160A ILE* 4.0 1.4 - - - +
201A ASP* 3.2 4.5 - - - -
202A VAL* 2.8 35.7 + - + +
204A PHE* 3.9 16.6 - + - -
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Residues in contact with GLY 149 (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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92A ILE* 3.9 6.7 - - - +
93A VAL* 2.9 32.4 + - - +
95A TYR* 3.1 19.5 - - - -
148A PHE* 1.3 76.1 - - - +
150A SER* 1.3 64.3 + - - -
160A ILE* 4.3 12.6 - - - -
200A PRO 4.3 6.1 - - - -
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Residues in contact with SER 150 (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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90A PRO* 6.3 0.2 - - - -
91A ASP* 2.7 28.7 + - - -
92A ILE* 4.0 11.6 - - - +
95A TYR* 2.6 23.9 + - - -
149A GLY* 1.3 71.2 - - - -
151A TRP* 1.3 61.3 + - - +
153A TYR* 2.9 45.4 + - - +
158A VAL* 4.8 14.1 - - - -
160A ILE* 5.3 1.4 - - - +
200A PRO 5.0 1.4 + - - -
1213A MLK 3.7 4.5 - - - +
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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