Contacts of the strand formed by residues 141 - 146 (chain A) in PDB entry 1UCU
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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134A VAL* 4.9 5.7 - - - +
139A GLN* 3.3 28.8 + - + +
140A ASP* 1.3 76.8 - - - +
142A THR* 1.3 78.9 + - - +
143A LEU* 2.9 29.8 + - - +
157A ILE 3.6 0.5 - - - +
158A ASP* 4.7 0.2 - - - -
159A LEU* 2.7 49.7 + - + +
160A LYS* 5.8 1.0 - - - +
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Residues in contact with THR 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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141A ASN* 1.3 85.1 + - - +
143A LEU* 1.3 61.2 + - - +
144A THR* 3.8 8.8 + - + +
156A ASP* 3.7 35.7 - - + +
157A ILE 3.4 4.9 - - - +
158A ASP* 2.7 28.6 + - - +
160A LYS* 5.8 0.7 + - - -
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Residues in contact with LEU 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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73A ILE* 4.4 26.2 - - + -
134A VAL* 4.1 22.9 - - + -
141A ASN* 2.9 35.4 - - - +
142A THR* 1.3 70.8 - - - +
144A THR* 1.3 62.8 + - - +
145A ILE* 3.8 14.7 + - + +
155A ILE 3.7 1.2 - - - +
156A ASP* 3.3 3.5 - - - -
157A ILE* 2.8 50.1 + - + +
159A LEU* 4.0 21.3 - - + -
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Residues in contact with THR 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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142A THR* 3.8 10.7 + - + +
143A LEU* 1.3 74.0 - - - +
145A ILE* 1.3 64.9 + - - +
146A GLN 4.1 1.3 + - - -
154A THR* 4.2 13.8 - - - +
156A ASP* 3.4 31.9 - - - +
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Residues in contact with ILE 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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66A ASN* 3.3 42.8 - - + +
69A ASP* 5.4 2.9 - - + -
70A GLY* 4.6 8.7 - - - +
73A ILE* 5.0 6.5 - - + -
143A LEU* 4.2 26.0 - - + +
144A THR* 1.3 79.5 - - - +
146A GLN* 1.3 64.5 + - - +
147A VAL* 3.2 7.5 + - + +
154A THR* 3.1 5.9 - - - -
155A ILE 2.9 38.5 + - - +
157A ILE* 4.4 17.5 - - + -
432A PHE* 4.5 10.5 - - + -
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Residues in contact with GLN 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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59A GLY 5.9 0.9 - - - +
63A ALA* 3.9 4.6 - - + -
66A ASN* 3.5 31.7 + - - +
144A THR 4.1 1.0 + - - -
145A ILE* 1.3 68.5 - - - +
147A VAL* 1.3 58.5 + - - +
148A GLY 2.7 24.5 + - - +
149A ALA 3.8 3.8 + - - -
150A ASN 2.7 36.2 + - - +
151A ASP* 4.6 3.6 - - - +
152A GLY 4.3 5.7 + - - -
153A GLU 3.6 8.3 + - - -
154A THR* 3.7 16.4 - - + +
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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