Contacts of the strand formed by residues 160 - 166 (chain E) in PDB entry 3LUE
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 160 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E PRO* 3.2 7.6 - - - +
110E LEU* 3.4 0.3 - - - +
153E MET* 3.5 19.1 - - - -
154E ASP 3.1 13.0 - - - +
155E SER* 2.9 19.3 + - - +
159E VAL* 1.3 73.6 - - - +
161E HIS* 1.3 64.2 + - - +
162E THR* 5.3 1.1 - - + -
177E ARG* 3.3 3.8 - - - -
178E LEU* 2.7 43.6 + - + -
180E LEU 2.8 22.7 + - - -
181E ALA* 4.1 0.2 - - - +
261E LEU* 5.0 0.5 - - - +
274E ILE* 3.4 27.9 - - + +
277E THR* 6.2 0.7 - - + -
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Residues in contact with HIS 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E PRO* 1.6 39.9 - - + +
110E LEU* 2.1 39.0 + - - -
136E ILE* 4.2 21.7 - - + +
138E ALA* 4.7 0.3 - - - +
152E VAL 3.7 1.4 - - - +
153E MET* 3.5 2.8 - - - -
154E ASP* 2.9 34.0 + - + +
160E THR* 1.3 74.7 - - - +
162E THR* 1.3 64.6 - - - +
163E VAL* 3.9 15.4 + - + -
175E ILE* 3.3 22.9 - - + +
176E LEU 3.0 18.4 - - - -
177E ARG* 3.3 14.4 - - + +
277E THR* 6.0 0.7 - - - -
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Residues in contact with THR 162 (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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151E ILE* 4.3 4.5 - - + -
152E VAL 3.4 4.5 - - - -
153E MET* 3.6 19.5 - - + -
160E THR* 5.3 1.8 - - + -
161E HIS* 1.3 77.6 - - - +
163E VAL* 1.3 61.1 + - - +
175E ILE* 3.3 6.2 - - - -
176E LEU* 3.0 29.0 + - - +
274E ILE* 4.9 1.3 - - + +
277E THR* 3.4 25.4 + - + +
278E THR* 3.4 38.4 - - - +
281E SER* 3.0 25.3 + - - -
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Residues in contact with VAL 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E ILE* 5.4 1.8 - - + -
138E ALA* 5.0 6.7 - - + -
139E VAL* 3.6 33.9 - - + -
151E ILE* 3.2 22.5 - - - +
152E VAL* 3.2 15.0 + - + +
161E HIS* 3.9 20.6 - - + +
162E THR* 1.3 77.1 - - - +
164E PRO* 1.3 59.8 - - - +
165E ILE* 3.8 16.4 + - + +
170E ALA* 3.8 23.3 - - + -
175E ILE* 4.0 18.2 - - + -
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Residues in contact with PRO 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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150E GLY 3.8 5.2 - - - +
151E ILE* 4.0 7.2 - - + -
162E THR 4.1 0.2 - - - +
163E VAL* 1.3 83.2 - - - +
165E ILE* 1.3 54.1 + - - +
170E ALA* 3.5 1.9 - - - -
171E LEU* 2.7 43.3 + - + +
174E ALA* 3.5 30.7 - - + +
175E ILE* 4.1 2.9 - - + +
281E SER* 3.8 14.6 - - - -
285E CYS* 3.2 36.3 - - - -
293E LEU* 3.8 13.7 - - + -
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Residues in contact with ILE 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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43C VAL* 2.1 21.5 - - - +
44C MET* 1.3 110.4 - - + +
61C LYS* 3.1 5.3 - - - -
139E VAL* 5.3 4.0 - - + -
142E LEU* 1.5 57.7 - - + -
148E THR 3.4 0.9 - - - +
149E THR* 3.5 0.3 - - - +
150E GLY 2.9 16.7 + - - +
152E VAL* 4.1 5.6 - - + -
163E VAL* 3.9 20.4 - - + +
164E PRO* 1.3 77.0 - - - +
166E TYR* 1.3 56.6 + - - +
169E TYR 3.2 6.3 - - - +
170E ALA* 3.8 13.0 - - + -
171E LEU* 4.7 0.7 - - - -
293E LEU* 4.1 2.5 - - - +
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Residues in contact with TYR 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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53C TYR* 3.0 2.8 - - - -
57C GLU 2.1 28.0 - - - -
58C ALA* 1.5 49.6 - - + +
61C LYS* 0.8 351.9 - - + +
64C ILE* 3.0 19.6 - - + +
65C LEU* 2.3 44.1 - - + +
165E ILE* 1.3 62.7 - - - +
167E GLU* 1.3 70.2 + - + +
168E GLY 3.4 0.4 - - - -
169E TYR* 2.9 28.3 + - - +
289E ILE* 3.8 2.5 - - + -
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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