Contacts of the strand formed by residues 160 - 166 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G PRO* 3.2 7.3 - - - +
110G LEU* 3.4 0.3 - - - +
153G MET* 3.5 19.1 - - - -
154G ASP 3.1 12.3 - - - +
155G SER* 2.9 19.7 + - - +
159G VAL* 1.3 74.3 - - - +
161G HIS* 1.3 62.9 + - - +
162G THR* 5.3 0.9 - - + -
177G ARG* 3.3 4.0 - - - -
178G LEU* 2.7 43.3 + - + +
180G LEU 2.8 22.5 + - - -
261G LEU* 5.0 0.3 - - - +
274G ILE* 3.4 28.7 - - + +
277G THR* 6.2 0.4 - - + -
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Residues in contact with HIS 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G PRO* 1.6 39.4 - - + +
110G LEU* 2.1 39.2 + - - -
136G ILE* 4.2 20.7 - - + +
138G ALA* 4.7 0.7 - - - +
152G VAL 3.7 1.2 - - - +
153G MET* 3.5 2.9 - - - -
154G ASP* 2.9 34.0 + - + +
160G THR* 1.3 75.4 - - - +
162G THR* 1.3 65.3 + - - +
163G VAL* 3.9 14.8 - - + +
175G ILE* 3.3 23.4 - - + +
176G LEU 3.0 18.2 - - - +
177G ARG* 3.3 13.5 - - + +
277G THR* 6.0 0.9 - - - -
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Residues in contact with THR 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G ILE* 4.3 4.9 - - + -
152G VAL 3.4 5.2 - - - +
153G MET* 3.6 19.5 - - + -
160G THR* 5.3 1.6 - - + -
161G HIS* 1.3 77.5 - - - +
163G VAL* 1.3 60.1 + - - +
164G PRO* 4.3 0.2 - - - -
175G ILE* 3.3 6.2 - - - +
176G LEU* 3.0 28.9 + - - +
274G ILE* 4.9 0.9 - - + +
277G THR* 3.4 25.6 + - + +
278G THR* 3.4 38.4 - - + +
281G SER* 3.0 24.9 + - - -
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Residues in contact with VAL 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G ILE* 5.4 2.2 - - + -
138G ALA* 5.0 6.5 - - + -
139G VAL* 3.6 34.3 - - + -
151G ILE* 3.2 23.3 - - - +
152G VAL* 3.2 17.0 + - + +
161G HIS* 3.9 20.6 - - + +
162G THR* 1.3 77.7 - - - +
164G PRO* 1.3 61.5 - - - +
165G ILE* 3.8 16.3 + - + +
170G ALA* 3.8 23.3 - - + -
175G ILE* 4.0 18.2 - - + -
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Residues in contact with PRO 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G GLY 3.8 5.2 - - - +
151G ILE* 4.0 6.7 - - + -
162G THR 4.1 0.2 - - - +
163G VAL* 1.3 83.4 - - - +
165G ILE* 1.3 55.2 + - - +
170G ALA* 3.5 2.1 - - - -
171G LEU* 2.7 42.8 + - + +
174G ALA* 3.5 31.6 - - + +
175G ILE* 4.1 2.7 - - + +
281G SER* 3.8 13.7 - - - -
285G CYS* 3.2 37.5 - - - -
293G LEU* 3.8 12.8 - - + -
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Residues in contact with ILE 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E VAL* 2.1 19.7 - - - +
44E MET* 1.3 111.7 - - + +
61E LYS* 3.1 5.5 - - - -
139G VAL* 5.3 4.0 - - + -
142G LEU* 1.5 58.1 - - + -
148G THR 3.4 0.9 - - - +
149G THR* 3.2 0.3 - - - +
150G GLY 2.9 16.4 + - - +
152G VAL* 4.1 5.4 - - + -
163G VAL* 3.9 20.9 - - + +
164G PRO* 1.3 74.9 - - - +
166G TYR* 1.3 56.0 + - - +
169G TYR 3.2 6.3 - - - +
170G ALA* 3.8 13.9 - - + -
171G LEU* 4.7 0.7 - - - -
293G LEU* 4.1 3.5 - - - +
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Residues in contact with TYR 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E TYR* 3.0 2.8 - - - -
57E GLU 2.1 27.4 - - - -
58E ALA* 1.5 49.8 - - - +
61E LYS* 0.8 351.3 - - + +
64E ILE* 3.0 19.3 - - + +
65E LEU* 2.3 43.1 - - + +
165G ILE* 1.3 61.6 - - - +
167G GLU* 1.3 71.6 + - + +
168G GLY 3.4 0.4 - - - -
169G TYR* 2.9 27.0 + - - +
171G LEU* 4.2 0.2 - - - +
289G ILE* 3.8 2.0 - - + -
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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