Contacts of the strand formed by residues 162 - 168 (chain E) in PDB entry 1MDU
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 THR 162 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155E LEU* 4.0 16.6 - - + -
156E ASP 3.1 8.3 - - - +
157E SER* 2.7 25.3 + - - +
161E VAL* 1.3 73.6 - - - +
163E HIS* 1.3 66.2 + - - +
164E ASN* 5.3 3.7 - - - +
179E ARG* 3.6 2.8 - - - -
180E LEU* 2.9 44.8 + - + +
182E LEU 2.8 23.2 + - - -
263E LEU* 4.8 1.9 - - - +
276E ILE* 3.8 26.7 - - + -
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Residues in contact with HIS 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E HIC 4.7 0.7 - - - -
110E ALA* 4.4 5.8 - - + -
111E PRO* 3.7 38.7 + - + +
112E LEU* 5.8 0.2 - - + -
154E VAL 3.4 2.3 - - - +
155E LEU* 3.4 5.2 - - - +
156E ASP* 2.8 44.7 + - + +
161E VAL* 3.6 32.7 - - + +
162E THR* 1.3 75.8 - - - +
164E ASN* 1.3 63.5 + - - +
165E VAL* 3.8 15.7 - - + -
177E ILE* 4.2 7.0 - - + -
178E MET 3.4 13.9 - - - -
179E ARG* 3.0 42.0 + - + -
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Residues in contact with ASN 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E ILE* 4.6 4.1 - - + +
154E VAL 3.5 3.3 + - - -
155E LEU* 3.6 22.4 - - - +
162E THR* 5.3 3.7 - - - +
163E HIS* 1.3 72.0 - - - +
165E VAL* 1.3 60.8 + - - +
166E PRO* 3.7 3.3 - - - +
177E ILE* 3.3 7.1 - - - +
178E MET* 2.9 39.7 + - + +
179E ARG* 5.6 0.9 - - - -
180E LEU* 5.9 0.9 - - - +
279E THR* 2.5 33.4 + - - -
280E THR* 3.0 34.5 + - - +
283E SER* 4.0 13.7 - - - -
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Residues in contact with VAL 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E PRO* 3.8 22.2 - - + -
138E ILE* 5.5 1.3 - - + -
140E ALA* 3.7 33.7 - - + -
141E VAL* 5.3 0.9 - - + -
153E ILE* 3.5 5.6 - - - +
154E VAL* 2.9 32.0 + - + +
156E ASP* 5.7 0.2 - - + -
163E HIS* 3.8 13.5 - - + -
164E ASN* 1.3 77.9 - - - +
166E PRO* 1.4 64.9 - - - +
167E ILE* 3.6 11.5 + - + +
172E ALA* 4.0 21.1 - - + -
177E ILE* 3.9 20.6 - - + -
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Residues in contact with PRO 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E GLY 3.7 5.8 - - - +
153E ILE* 3.8 9.4 - - + -
164E ASN 3.7 3.4 - - - +
165E VAL* 1.4 83.6 - - - +
167E ILE* 1.3 59.6 + - - +
172E ALA* 3.4 3.8 - - - -
173E LEU* 2.9 33.5 + - + +
176E ALA* 3.6 28.5 - - + +
177E ILE* 4.0 7.0 - - + -
283E SER* 3.0 26.9 - - - +
287E CYS* 3.5 23.8 - - - -
295E LEU* 4.2 9.9 - - + -
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Residues in contact with ILE 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E ALA 3.9 10.1 - - - +
141E VAL* 3.9 31.4 - - + -
144E LEU* 3.5 30.3 - - + -
145E TYR* 5.8 0.2 - - + -
150E THR 3.6 9.2 - - - +
151E THR* 3.4 5.0 - - - +
152E GLY 2.7 34.3 + - - +
154E VAL* 4.0 8.7 - - + -
165E VAL* 3.8 19.5 - - + +
166E PRO* 1.3 80.3 - - - +
168E TYR* 1.3 64.3 + - - +
170E GLY* 3.8 5.4 - - - +
171E TYR 3.3 22.4 - - - +
172E ALA* 3.9 11.7 - - - +
173E LEU* 4.8 0.9 - - - -
295E LEU* 3.8 4.8 - - - +
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Residues in contact with TYR 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D VAL* 5.6 2.8 - - - +
151E THR* 3.7 14.8 - - + -
167E ILE* 1.3 74.3 - - - +
169E GLU* 1.3 104.9 + - + +
170E GLY 3.2 1.1 - - - -
171E TYR* 2.7 25.6 + - - +
173E LEU* 4.2 16.0 - - + +
291E ILE* 3.3 51.2 - - + +
294E ASP* 4.7 10.3 - - - -
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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