Contacts of the strand formed by residues 152 - 159 (chain A) in PDB entry 1MPU
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 TYR 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A SER* 1.3 89.5 + - - +
153A HIS* 1.3 77.1 + - - +
191A LEU* 3.9 31.5 - - + +
192A TYR 3.6 2.9 - - - -
193A ALA* 4.3 6.5 - - + -
199A TYR* 3.3 59.4 + + - -
207A ASN* 5.0 5.9 - - - +
208A THR* 3.2 10.4 + - - +
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Residues in contact with HIS 153 (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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113A PHE* 6.3 2.9 - - + -
149A VAL* 3.4 27.5 - - + +
150A LYS 2.6 26.4 + - - -
151A SER* 4.2 10.5 - - - -
152A TYR* 1.3 81.0 + - - +
154A TRP* 1.3 61.7 + - - +
191A LEU* 3.0 7.8 - - - -
192A TYR* 2.5 44.8 + + + +
208A THR* 2.7 38.2 + - + +
209A TYR* 4.2 1.9 + - - -
210A ILE* 3.7 31.3 - - + +
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Residues in contact with TRP 154 (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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118A LYS 3.1 27.2 + - - -
120A TRP* 3.3 33.2 - + + +
123A SER* 3.7 20.9 - - - +
134A LEU* 3.9 8.8 - - + +
135A LEU* 4.8 0.9 - - - +
153A HIS* 1.3 73.7 - - - +
155A MET* 1.3 60.0 + - - +
189A CYS* 3.6 27.1 - - + -
190A ALA 3.4 24.5 - - - -
191A LEU* 3.5 15.4 - - + +
201A GLU* 3.6 13.5 - - + -
202A ASN 3.2 22.7 - - - -
203A CYS 4.2 0.2 - - - -
205A THR 3.2 20.8 + - - -
207A ASN* 3.7 26.2 - - + +
208A THR 3.0 8.8 + - - -
209A TYR* 3.6 11.4 - - + +
210A ILE* 3.5 23.6 + - - +
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Residues in contact with MET 155 (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 TRP* 3.1 19.6 + - - -
134A LEU* 3.6 9.4 - - - -
135A LEU* 3.5 18.8 - - + +
137A VAL* 4.6 4.7 - - - -
153A HIS 3.6 0.2 + - - -
154A TRP* 1.3 74.6 - - - +
156A GLY* 1.3 60.0 + - - +
157A LEU* 3.0 17.1 + - + +
168A TRP* 4.1 21.3 - - - -
179A LEU* 4.3 13.9 - - + -
190A ALA* 3.3 24.1 + - + +
191A LEU 3.5 23.8 - - - +
192A TYR* 3.6 32.5 - - + +
197A LYS 3.8 3.1 - - - +
198A GLY* 3.6 19.3 - - - -
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Residues in contact with GLY 156 (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 TRP* 4.5 0.9 - - - -
134A LEU* 3.4 9.8 - - - +
135A LEU 3.2 10.9 + - - -
155A MET* 1.3 73.8 - - - +
157A LEU* 1.3 57.8 + - - +
158A VAL* 3.7 2.0 + - - -
168A TRP* 3.0 17.2 - - - -
169A GLU* 2.9 55.9 + - - -
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Residues in contact with LEU 157 (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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155A MET* 3.0 14.7 + - + +
156A GLY* 1.3 74.1 - - - +
158A VAL* 1.3 69.6 + - - +
166A TRP* 3.9 24.5 - - + -
167A GLN* 3.5 26.0 - - - +
168A TRP* 3.5 30.4 - - + -
174A LEU* 4.4 13.0 - - + -
179A LEU* 4.4 16.4 - - + -
181A ILE* 4.4 22.7 - - + -
189A CYS* 3.5 0.9 - - - +
190A ALA* 3.2 40.6 + - + -
198A GLY* 5.4 1.1 - - - -
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Residues in contact with VAL 158 (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 TRP* 3.4 39.5 - - + +
156A GLY 4.6 0.2 - - - +
157A LEU* 1.3 82.4 - - - +
159A HIS* 1.3 59.8 + - - +
160A ILE* 4.4 13.7 - - + -
166A TRP* 3.4 7.4 - - - -
167A GLN* 2.8 48.1 + - + +
168A TRP 4.3 1.1 - - - -
169A GLU* 4.1 20.6 - - + +
188A ASP 3.2 14.4 - - - +
189A CYS* 4.0 6.5 - - - -
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Residues in contact with HIS 159 (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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158A VAL* 1.3 72.6 - - - +
160A ILE* 1.3 80.4 + - - +
161A PRO* 3.7 16.1 - - + +
163A ASN* 5.0 1.4 + - - -
164A GLY 3.3 27.0 + - - -
165A SER 3.7 9.4 - - - -
166A TRP* 3.5 41.7 + + + -
187A GLY 5.3 0.2 + - - -
188A ASP* 2.9 43.9 + - - +
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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