Contacts of the strand formed by residues 166 - 174 (chain B) in PDB entry 1RGQ
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 VAL 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B PRO* 5.2 8.7 - - + -
133B ARG 3.5 12.6 - - - +
134B PRO* 4.6 7.6 - - + -
161B VAL 3.9 0.2 - - - +
162B CYS* 3.5 1.5 - - - -
163B THR* 3.0 50.7 + - - +
164B ARG* 4.9 6.7 - - + +
165B GLY* 1.3 84.6 - - - +
167B THR* 1.3 63.8 + - - +
168B LYS* 4.1 15.8 + - + +
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Residues in contact with THR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.4 13.0 - - - +
132B PRO* 3.5 3.3 - - - +
133B ARG 2.8 31.6 + - - -
135B ILE* 3.9 21.5 - - + -
138B LEU* 3.4 24.7 - - + +
160B ALA* 3.8 17.5 - - + -
161B VAL 3.3 9.4 - - - -
162B CYS* 3.5 30.5 - - - -
166B VAL* 1.3 73.1 - - - +
168B LYS* 1.3 61.5 + - - +
169B ALA 4.4 4.5 - - - -
170B VAL* 5.4 1.0 - - - +
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Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B SER* 3.7 5.0 - - - -
129B LEU* 2.8 39.1 + - - +
132B PRO* 4.2 20.4 - - + -
161B VAL* 3.5 6.9 + - + +
163B THR* 3.9 24.0 + - + +
166B VAL* 4.1 14.0 + - + +
167B THR* 1.3 75.3 - - - +
169B ALA* 1.3 56.4 + - + +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ARG* 4.7 8.5 - - - +
127B GLY 3.4 13.5 - - - +
128B SER* 4.1 7.4 - - - +
129B LEU* 4.4 0.9 - - - +
160B ALA* 3.7 2.9 - - - +
161B VAL* 2.8 51.4 + - + +
167B THR* 3.7 2.1 - - - -
168B LYS* 1.3 84.4 - - + +
170B VAL* 1.3 65.0 + - - +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 4.5 11.9 - - + -
119B VAL* 3.9 26.9 - - + -
126B ARG* 3.4 9.6 - - - -
127B GLY* 2.8 44.8 + - - +
129B LEU* 4.1 23.6 - - + -
138B LEU* 5.2 5.6 - - + -
146B LEU* 4.7 8.1 - - + -
157B PHE* 3.7 29.6 - - + -
159B ALA 3.6 3.6 - - - +
160B ALA* 4.5 3.6 - - + +
161B VAL* 5.0 1.1 - - - -
167B THR* 5.4 0.9 - - - +
169B ALA* 1.3 78.5 - - - +
171B ASP* 1.3 60.6 + - - +
172B PHE* 4.4 4.2 + - + -
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Residues in contact with ASP 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B SER* 3.5 13.8 + - - +
126B ARG* 2.9 31.1 + - - +
157B PHE* 3.9 3.6 - - - -
158B ARG* 3.0 49.0 + - - -
159B ALA* 2.6 35.4 + - + +
170B VAL* 1.3 74.9 - - - +
172B PHE* 1.3 70.1 + - - +
194B AKP 4.3 12.5 - - + +
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Residues in contact with PHE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 3.8 24.5 - - + -
121B ARG* 3.8 30.3 - - - -
124B ASP 3.6 19.3 - - - -
125B SER* 3.0 30.5 + - - -
126B ARG 3.6 31.0 - - - -
127B GLY* 4.0 4.9 - - - -
146B LEU* 4.0 23.6 - - + -
154B VAL* 4.6 6.7 - - + -
155B GLY* 4.3 7.0 - - - -
156B LEU 3.3 19.1 - - - +
157B PHE* 4.4 0.7 - - + -
158B ARG* 4.2 4.8 - - - +
170B VAL* 4.5 4.5 - - + -
171B ASP* 1.3 82.2 - - - +
173B ILE* 1.3 76.8 + - - +
174B PRO* 3.8 7.2 - - + +
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B VAL* 3.9 19.3 - - + -
83B GLN 3.9 16.4 - - - +
84B ASP 3.5 25.4 - - - +
85B LEU* 4.0 26.0 - - + -
155B GLY* 3.2 2.1 - - - -
156B LEU* 2.9 51.4 + - + +
158B ARG* 4.0 18.2 - - + -
172B PHE* 1.3 75.4 - - - +
174B PRO* 1.4 66.7 - - + +
177B ASN* 4.0 23.6 - - + +
178B LEU* 5.1 2.2 - - + -
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Residues in contact with PRO 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ARG* 4.2 4.7 - - - +
124B ASP* 4.0 28.9 - - - +
125B SER* 4.3 11.2 - - - -
154B VAL 3.6 8.5 - - - +
155B GLY* 4.1 0.7 - - - -
172B PHE* 3.8 12.8 - - + +
173B ILE* 1.4 85.3 - - - +
175B VAL* 1.3 59.6 + - - +
176B GLU* 3.2 22.9 - - + +
177B ASN* 2.9 53.8 + - - +
178B LEU* 3.7 4.2 + - - +
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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