Contacts of the strand formed by residues 139 - 148 (chain A) in PDB entry 1UB6
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 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A PRO* 4.3 16.6 - - + -
134A THR 5.3 2.2 - - - +
135A THR* 4.2 32.3 - - + +
136A GLY 4.6 6.7 - - - +
138A SER* 1.3 75.2 - - - +
140A THR* 1.3 74.4 + - - +
141A LEU* 3.8 6.0 + - + +
184A VAL 3.7 0.2 - - - +
185A THR* 3.1 25.1 - - - -
186A VAL* 2.7 24.5 + - + +
188A SER* 5.1 1.6 - - - +
191A TRP* 3.5 34.8 - - + -
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Residues in contact with THR 140 (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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129A PRO* 4.6 1.4 - - - +
139A VAL* 1.3 81.3 - - - +
141A LEU* 1.3 66.9 + - - +
183A SER* 4.2 19.7 - - - -
184A VAL 3.4 9.9 - - - +
185A THR* 3.5 15.6 - - + +
119B THR* 4.8 6.6 + - - -
121B SER* 3.3 27.9 + - - +
123B PHE* 3.3 21.9 - - + -
140B PHE* 4.2 13.5 - - + -
142B ASN* 4.7 6.5 - - - +
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Residues in contact with LEU 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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127A ALA 3.7 1.6 - - - -
128A ALA* 3.9 4.0 - - + -
129A PRO* 3.4 23.3 - - + -
139A VAL* 3.8 8.2 + - + +
140A THR* 1.3 77.6 - - - +
142A GLY* 1.3 55.4 + - - +
183A SER* 3.2 4.4 - - - -
184A VAL* 2.5 52.9 + - + -
186A VAL* 5.0 4.9 - - + -
191A TRP* 3.2 41.7 - - + -
196A VAL* 3.7 37.7 - - + -
213A LEU* 3.3 24.0 - - + -
123B PHE* 5.1 2.2 - - - -
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Residues in contact with GLY 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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126A PRO 3.6 0.5 - - - -
127A ALA* 2.6 49.2 + - - +
141A LEU* 1.3 78.9 - - - +
143A CYS* 1.3 60.0 + - - -
157A TRP* 3.4 10.5 - - - -
182A SER 3.0 13.2 - - - -
183A SER* 4.0 2.5 - - - -
213A LEU* 3.6 4.5 - - - +
123B PHE* 5.0 0.2 - - - -
140B PHE* 5.0 4.0 - - - -
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Residues in contact with CYS 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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124A VAL* 4.3 10.3 - - + -
125A TYR 3.4 4.9 - - - +
126A PRO* 4.5 9.4 - - - -
127A ALA* 5.2 0.7 - - - -
142A GLY* 1.3 80.6 - - - -
144A LEU* 1.3 60.1 + - - +
145A VAL* 3.9 8.0 + - + +
155A VAL* 5.3 2.9 - - + -
157A TRP* 3.7 7.3 - - + -
181A SER* 3.6 3.0 - - - -
182A SER* 2.9 32.0 + - - -
198A CYS* 2.0 53.6 - - + -
200A VAL* 5.2 1.8 - - + -
211A LYS* 4.5 2.7 - - - -
213A LEU* 4.2 9.4 - - - -
140B PHE* 5.8 0.8 - - - -
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Residues in contact with LEU 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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123A SER 3.4 2.8 - - - +
124A VAL* 3.4 2.3 - - - -
125A TYR* 2.6 60.5 + - + +
127A ALA* 5.0 5.5 - - + +
143A CYS* 1.3 73.3 - - - +
145A VAL* 1.3 64.0 + - - +
146A LYS* 4.2 17.9 - - + -
179A THR* 3.9 20.0 - - + -
180A MET 3.8 9.6 - - - +
181A SER* 4.1 15.0 - - - +
129B GLN* 4.8 2.2 - - - +
136B SER* 3.5 25.6 - - - +
138B VAL* 4.2 20.4 - - + -
183B THR* 5.0 5.4 - - + +
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Residues in contact with VAL 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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122A PRO* 3.4 31.6 - - + -
123A SER 3.4 4.5 - - - +
124A VAL* 4.5 4.3 - - + -
143A CYS* 4.3 8.3 - - + +
144A LEU* 1.3 77.2 - - - +
146A LYS* 1.3 60.2 + - - +
148A TYR* 3.5 12.8 - - + -
153A VAL* 4.7 4.9 - - + -
155A VAL* 4.4 3.6 - - + -
179A THR* 3.3 2.6 - - - -
180A MET* 2.9 59.0 + - - +
200A VAL* 3.7 38.1 - - + -
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Residues in contact with LYS 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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122A PRO 3.8 0.2 - - - -
123A SER* 2.8 39.7 + - - -
125A TYR* 3.6 34.8 - - + +
144A LEU* 4.2 11.0 - - + -
145A VAL* 1.3 74.4 - - - +
147A GLY* 1.3 63.2 + - - +
148A TYR* 3.5 3.4 - - - -
174A GLN* 4.5 11.9 - - - +
178A TYR 3.6 5.6 - - - -
179A THR* 3.2 29.1 + - + +
129B GLN* 3.8 21.1 - - - +
136B SER* 4.9 0.4 - - - +
185B THR* 4.6 13.5 - - + +
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Residues in contact with GLY 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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120A THR* 2.7 17.4 + - - -
121A PRO 3.1 10.7 - - - +
123A SER* 5.1 3.2 + - - -
146A LYS* 1.3 80.9 - - - +
148A TYR* 1.3 59.5 + - - +
177A LEU* 3.6 31.1 - - - +
178A TYR 3.2 6.1 + - - -
179A THR* 4.1 1.8 + - - -
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Residues in contact with TYR 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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120A THR* 3.3 17.3 - - - +
122A PRO* 3.7 19.3 - - + -
145A VAL* 3.5 37.5 - - + -
146A LYS 4.1 1.6 - - - -
147A GLY* 1.3 79.4 - - - +
149A PHE* 1.3 59.2 + - - +
150A PRO 3.8 3.8 - - - -
151A GLU* 3.3 24.2 + - - -
153A VAL* 3.3 14.4 - - + +
171A ALA* 3.3 16.8 - - - +
177A LEU* 3.6 4.0 - - - -
178A TYR* 2.7 73.5 + - + +
179A THR 4.0 0.2 - - - -
180A MET* 3.1 23.1 - - - +
202A HIS* 3.6 21.5 - + - +
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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