Contacts of the strand formed by residues 140 - 146 (chain A) in PDB entry 1U54
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 VAL 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ACP 3.7 63.0 - - + +
131A LYS* 3.5 1.4 - - - -
132A LEU* 3.2 31.1 + - + -
133A GLY 2.8 27.9 + - - +
134A ASP 4.1 0.9 - - - -
138A GLY 5.7 0.2 - - - +
139A VAL* 1.3 83.3 - - - +
141A ARG* 1.3 69.5 + - - +
156A ALA* 4.8 0.7 - - + -
157A VAL 3.5 13.7 - - - +
158A LYS* 4.4 20.9 - - + +
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Residues in contact with ARG 141 (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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128A LEU* 4.4 36.0 - - + +
129A LEU 3.5 25.8 + - - +
130A GLU 3.2 7.2 - - - +
131A LYS* 3.5 36.5 - - - +
132A LEU* 3.7 6.5 - - - +
139A VAL* 4.1 11.7 - - + +
140A VAL* 1.3 78.8 - - - +
142A ARG* 1.3 62.3 + - - +
156A ALA* 3.8 0.7 - - - -
157A VAL* 2.9 39.0 + - - +
159A CYS* 4.9 8.3 - - - -
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Residues in contact with ARG 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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128A LEU* 4.1 0.6 - - - -
129A LEU* 2.6 51.7 + - - +
130A GLU* 3.0 40.4 + - - +
132A LEU* 3.4 26.6 - - + +
141A ARG* 1.3 72.1 - - - +
143A GLY* 1.3 58.9 + - - +
154A SER* 3.2 28.5 + - - -
155A VAL 3.7 10.8 - - - +
157A VAL* 4.7 0.4 - - - -
207A LEU* 3.9 27.0 - - + +
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Residues in contact with GLY 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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126A LEU* 5.5 0.7 - - - -
127A ARG 3.4 12.1 - - - -
128A LEU* 4.5 0.9 - - - -
129A LEU* 4.3 3.6 - - - -
141A ARG 4.0 0.4 + - - -
142A ARG* 1.3 79.7 + - - +
144A GLU* 1.3 67.2 + - - +
153A VAL 3.5 1.9 - - - +
154A SER* 3.6 7.6 + - - -
155A VAL* 2.9 40.7 + - - +
157A VAL* 4.2 7.9 - - - -
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Residues in contact with GLU 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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125A ASP 3.4 1.6 - - - +
126A LEU* 3.4 9.1 - - - +
127A ARG* 3.2 51.1 + - + +
129A LEU* 4.2 23.2 - - + +
143A GLY* 1.3 77.0 - - - +
145A TRP* 1.3 60.1 + - - +
146A ASP* 3.8 2.1 + - - +
152A THR* 4.3 27.2 - - + +
153A VAL 3.4 5.8 - - - +
154A SER* 5.2 5.2 - - - +
155A VAL* 4.2 0.2 - - - +
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Residues in contact with TRP 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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115A GLN* 5.6 8.1 - - - -
117A LEU* 6.0 4.7 - - + -
119A CYS* 4.0 16.4 - - - -
121A ILE* 3.2 44.6 - - + +
125A ASP* 3.4 14.1 - - + +
126A LEU* 3.5 11.0 - - + -
144A GLU* 1.3 70.1 - - - +
146A ASP* 1.3 59.4 + - - +
147A ALA* 2.6 41.8 + - + +
148A PRO* 3.5 23.5 - - + +
151A LYS 3.3 0.5 - - - +
152A THR* 4.2 0.2 - - - -
153A VAL* 2.8 43.2 + - + +
155A VAL* 3.6 19.5 - - + +
193A TYR* 3.9 44.9 - + + -
204A VAL* 4.7 1.6 - - + -
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Residues in contact with ASP 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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124A LYS 5.0 3.8 - - - +
125A ASP* 2.9 41.4 + - + +
144A GLU 3.8 1.9 + - - -
145A TRP* 1.3 69.2 + - - +
147A ALA* 1.3 67.3 + - - +
148A PRO* 4.5 0.9 - - - +
150A GLY 4.8 5.0 - - - +
151A LYS 3.7 4.3 - - - -
152A THR* 2.4 35.4 + - - -
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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