Contacts of the strand formed by residues 160 - 166 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109H PRO* 3.2 6.5 - - - +
110H LEU* 3.4 0.3 - - - +
153H MET* 3.5 19.7 - - - -
154H ASP 3.1 11.9 - - - +
155H SER* 2.9 20.1 + - - +
159H VAL* 1.3 74.0 - - - +
161H HIS* 1.3 64.4 + - - +
162H THR* 5.3 0.9 - - + -
177H ARG* 3.3 4.0 - - - -
178H LEU* 2.7 43.0 + - + -
180H LEU 2.8 22.6 + - - -
261H LEU* 5.0 0.3 - - - +
274H ILE* 3.4 28.1 - - + +
277H THR* 6.2 0.4 - - + -
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Residues in contact with HIS 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H PRO* 1.6 39.9 - - + +
110H LEU* 2.1 39.4 + - - -
136H ILE* 4.2 20.8 - - + +
138H ALA* 4.7 0.7 - - - +
152H VAL 3.7 1.2 - - - +
153H MET* 3.5 3.1 - - - -
154H ASP* 2.9 33.4 + - + +
160H THR* 1.3 75.1 + - - +
162H THR* 1.3 65.9 + - - +
163H VAL* 3.9 15.2 + - + -
175H ILE* 3.3 23.4 - - + +
176H LEU 3.0 16.6 - - - +
177H ARG* 3.3 14.9 - - + +
277H THR* 6.0 1.1 - - - -
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Residues in contact with THR 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H ILE* 4.3 4.9 - - + -
152H VAL 3.4 5.8 - - - +
153H MET* 3.6 18.8 - - + -
160H THR* 5.3 2.0 - - + -
161H HIS* 1.3 75.7 - - - +
163H VAL* 1.3 59.6 + - - +
175H ILE* 3.3 6.2 - - - -
176H LEU* 3.0 29.6 + - - +
274H ILE* 4.9 1.1 - - + +
277H THR* 3.4 24.9 + - + +
278H THR* 3.4 38.8 - - - +
281H SER* 3.0 24.9 + - - -
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Residues in contact with VAL 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H ILE* 5.4 2.5 - - + -
138H ALA* 5.0 7.2 - - + -
139H VAL* 3.6 33.7 - - + -
151H ILE* 3.2 22.3 - - - +
152H VAL* 3.2 16.6 + - + +
161H HIS* 3.9 20.4 - - + +
162H THR* 1.3 78.0 - - - +
164H PRO* 1.3 60.2 - - - +
165H ILE* 3.8 15.8 + - + +
170H ALA* 3.8 23.8 - - + -
175H ILE* 4.0 17.0 - - + -
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Residues in contact with PRO 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H GLY 3.8 5.8 - - - +
151H ILE* 4.0 7.0 - - + -
162H THR 4.1 0.2 - - - +
163H VAL* 1.3 83.7 - - - +
165H ILE* 1.3 56.0 + - - +
170H ALA* 3.5 2.3 - - - -
171H LEU* 2.7 42.7 + - + +
174H ALA* 3.5 31.0 - - + +
175H ILE* 4.1 2.5 - - + +
281H SER* 3.8 14.6 - - - -
285H CYS* 3.2 36.1 - - - -
293H LEU* 3.8 13.5 - - + -
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Residues in contact with ILE 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F VAL* 2.1 21.1 - - - +
44F MET* 1.3 112.0 - - + +
61F LYS* 3.1 4.7 - - - -
139H VAL* 5.3 3.6 - - + -
142H LEU* 1.5 58.3 - - + -
148H THR 3.4 1.3 - - - +
149H THR* 3.2 0.5 - - - +
150H GLY 2.9 17.1 + - - +
152H VAL* 4.1 5.4 - - + -
163H VAL* 3.9 21.1 - - + +
164H PRO* 1.3 74.7 - - - +
166H TYR* 1.3 56.2 + - - +
169H TYR 3.2 6.1 - - - +
170H ALA* 3.8 13.7 - - + -
171H LEU* 4.7 0.7 - - - -
293H LEU* 4.1 3.5 - - - +
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Residues in contact with TYR 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F TYR* 3.0 2.8 - - - -
57F GLU 2.1 27.6 - - - -
58F ALA* 1.5 50.2 - - - +
61F LYS* 0.8 358.7 - - + +
64F ILE* 3.0 20.0 - - + +
65F LEU* 2.3 45.1 - - + +
165H ILE* 1.3 62.3 - - - +
167H GLU* 1.3 71.2 + - + +
168H GLY 3.4 0.4 - - - -
169H TYR* 2.9 27.1 + - - +
289H ILE* 3.8 2.7 - - + -
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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