Contacts of the strand formed by residues 142 - 150 (chain F) in PDB entry 3RBQ
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 GLN 142 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95F ASP* 3.7 5.7 + - - +
96F MET* 2.9 54.1 + - + +
97F ASP* 4.5 2.4 + - - +
140F LEU 3.7 0.4 - - - -
141F ARG* 1.3 112.3 + - - +
143F VAL* 1.3 66.7 + - - +
193F ILE* 3.6 23.5 - - + +
194F TYR 3.3 10.3 - - - +
195F ASP* 2.8 29.5 + - - +
196F PHE* 4.8 0.2 - - - -
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Residues in contact with VAL 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F ILE* 3.8 19.1 - - + -
94F ARG 3.2 12.6 - - - +
95F ASP* 4.5 0.7 - - - -
96F MET* 3.7 5.0 - - - +
102F LEU* 4.2 7.9 - - + -
137F PHE* 5.0 2.0 - - + -
140F LEU* 3.8 28.9 - - + -
142F GLN* 1.3 80.8 - - - +
144F GLY* 1.3 59.7 + - - +
192F HIS 3.8 0.5 - - - +
193F ILE* 3.6 3.3 - - - +
194F TYR* 2.9 59.0 + - + -
196F PHE* 3.8 16.4 - - + -
500L DAO 4.2 12.6 - - + -
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Residues in contact with GLY 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F LYS 3.4 1.9 - - - +
93F ILE* 3.3 5.3 - - - -
94F ARG* 2.8 45.4 + - - +
96F MET* 3.5 20.2 - - - +
143F VAL* 1.3 72.9 - - - +
145F ALA* 1.3 59.6 + - - -
146F THR 3.9 0.4 + - - -
191F GLU* 4.2 0.9 - - - -
192F HIS 3.4 5.6 - - - -
193F ILE* 4.2 7.0 - - - -
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Residues in contact with ALA 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F PHE* 3.7 30.7 - - + -
92F LYS 3.3 4.9 - - - -
93F ILE* 4.4 3.8 - - + +
143F VAL 4.2 0.2 - - - -
144F GLY* 1.3 72.6 - - - -
146F THR* 1.3 60.8 + - - +
147F VAL* 3.9 3.4 + - + +
190F CYS 3.7 0.7 - - - +
191F GLU* 3.3 4.9 + - - -
192F HIS* 2.6 50.3 + - + +
194F TYR* 3.8 20.6 - - + -
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Residues in contact with THR 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ARG* 3.8 19.1 - - - +
91F PHE* 3.4 4.5 + - - -
92F LYS* 2.8 53.2 + - + +
94F ARG* 4.1 8.1 + - - -
144F GLY 3.9 0.2 + - - -
145F ALA* 1.3 70.2 - - - +
147F VAL* 1.3 64.1 + - - +
148F GLU* 4.9 0.9 - - + +
189F THR* 3.9 22.2 - - + -
190F CYS 3.5 5.6 - - - +
191F GLU* 3.7 16.9 + - + +
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Residues in contact with VAL 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F PHE* 3.3 38.1 - - + -
90F ARG 3.3 11.0 - - - +
91F PHE* 3.6 24.7 - - + -
145F ALA 4.2 4.0 - - - +
146F THR* 1.3 79.2 - - - +
148F GLU* 1.3 64.4 + - - +
149F PHE* 4.3 5.8 - - + -
179F PHE* 5.2 1.1 - - + -
189F THR* 3.2 5.4 - - - +
190F CYS* 2.9 37.1 + - + +
192F HIS* 4.1 27.4 - - + +
502L ALA* 4.1 11.7 - - + -
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Residues in contact with GLU 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F PHE* 3.5 4.5 - - - +
89F VAL* 2.8 33.3 + - + +
90F ARG* 2.6 63.6 + - + +
146F THR* 4.9 2.4 - - + +
147F VAL* 1.3 80.1 - - - +
149F PHE* 1.3 61.3 + - - +
187F LYS* 3.4 31.2 + - - +
188F ASN 3.2 7.2 - - - +
189F THR* 3.8 21.9 + - + +
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Residues in contact with PHE 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F ILE* 4.1 9.9 - - + -
87F ASP 3.2 16.2 - - - +
88F PHE* 3.7 26.2 - + + -
89F VAL* 4.2 1.6 - - - +
147F VAL* 4.3 2.5 - - + -
148F GLU* 1.3 80.2 - - - +
150F THR* 1.3 62.6 + - - +
151F VAL* 3.9 20.0 - - + -
159F PHE* 3.9 8.5 - + - -
179F PHE* 3.7 32.5 - + + -
182F CYS* 3.9 24.7 - - - -
187F LYS* 3.3 2.5 - - - -
188F ASN* 2.6 71.8 + - + +
189F THR 4.1 12.3 - - - -
190F CYS* 4.4 1.3 - - + -
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Residues in contact with THR 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F LYS 3.4 2.8 + - - +
86F ILE* 3.3 4.9 - - - -
87F ASP* 2.9 45.9 + - - +
89F VAL* 4.3 14.4 - - + +
149F PHE* 1.3 78.1 - - - +
151F VAL* 1.3 68.2 + - - +
186F SER 3.3 9.0 - - - +
187F LYS* 4.0 22.9 - - + -
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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