Contacts of the strand formed by residues 176 - 184 (chain A) in PDB entry 1GQE
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 ILE 176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 4.9 2.0 - - + -
134A ALA* 3.5 5.0 - - - +
142A GLN* 3.0 28.5 + - - +
145A ALA* 3.6 22.1 - - + +
146A SER* 3.6 17.9 - - - +
149A GLU* 3.7 26.2 - - + +
168A GLU* 4.0 19.7 - - + +
169A SER 3.4 12.1 - - - +
170A GLU* 4.3 6.1 - - + +
171A GLY 3.6 1.1 - - - +
175A GLY* 1.3 79.5 - - - +
177A LYS* 1.3 60.7 + - - +
178A SER* 4.0 9.0 - - - +
179A VAL* 3.7 29.6 - - + -
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Residues in contact with LYS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLN* 3.0 16.2 + - - +
134A ALA* 2.9 33.2 + - + -
142A GLN* 4.1 14.4 - - - +
145A ALA* 5.2 0.2 - - - -
169A SER* 2.7 18.3 + - - +
170A GLU 3.7 20.0 - - - +
171A GLY* 4.0 5.2 - - - -
172A GLU* 2.7 44.4 + - - -
176A ILE* 1.3 76.1 - - - +
178A SER* 1.3 61.3 + - - +
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Residues in contact with SER 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE 3.2 12.6 - - - -
133A GLN* 3.7 15.3 - - - -
167A GLU* 2.9 17.4 + - - -
168A GLU* 3.4 3.1 - - - +
169A SER* 3.0 40.5 + - - +
176A ILE* 3.4 6.9 - - - +
177A LYS* 1.3 84.7 - - - +
179A VAL* 1.3 66.0 + - - +
273A GLN* 4.9 2.7 + - - -
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU 3.6 0.3 - - - +
131A ASP* 3.4 3.8 - - - +
132A ILE* 2.9 58.3 + - + +
149A GLU* 3.3 25.8 - - + +
165A ILE* 3.9 14.8 - - + -
167A GLU* 3.1 22.2 - - - +
168A GLU* 4.2 3.6 - - + -
176A ILE* 3.7 21.5 - - + -
178A SER* 1.3 77.9 - - - +
180A THR* 1.3 64.9 + - - +
181A ILE* 4.0 13.2 - - + -
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Residues in contact with THR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TYR* 4.4 10.5 - - + -
130A LEU 3.3 4.3 - - - +
131A ASP* 2.7 28.2 + - - +
165A ILE* 3.8 2.4 - - - -
166A ILE* 2.8 42.6 + - + -
167A GLU* 2.9 29.6 + - - +
179A VAL* 1.3 75.1 - - - +
181A ILE* 1.3 63.0 + - - +
223A TYR* 3.7 11.8 + - - +
273A GLN 4.9 1.9 + - - -
290A GLN* 4.2 12.4 + - - +
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Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TYR* 3.3 3.7 - - - -
130A LEU* 2.8 61.5 + - + +
132A ILE* 4.8 2.7 - - + -
149A GLU* 4.3 19.5 - - + +
152A TYR* 5.0 2.9 - - + -
153A LEU* 3.9 35.2 - - + +
163A THR* 4.0 4.0 - - - -
164A GLU 3.4 11.4 - - - +
165A ILE* 4.0 5.6 - - + -
179A VAL* 4.0 18.4 - - + -
180A THR* 1.3 80.8 - - - +
182A LYS* 1.3 64.0 + - - +
183A ILE* 3.3 27.4 + - + +
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Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 6.0 4.0 - - - +
127A ASP* 4.0 18.0 + - - +
128A CYS 3.5 6.2 + - - +
129A TYR* 3.2 45.1 + - + +
162A LYS 3.6 1.0 - - - +
163A THR* 3.3 6.8 - - - -
164A GLU* 2.9 37.1 + - + +
166A ILE* 4.0 16.6 - - + +
181A ILE* 1.3 71.7 - - - +
183A ILE* 1.3 61.4 + - - +
184A SER* 3.8 18.4 + - - +
225A GLU* 3.7 19.2 + - - +
286A GLN* 4.6 8.5 - - - +
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Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASP* 3.6 2.6 - - - +
128A CYS* 2.8 44.5 + - - +
130A LEU* 4.7 6.3 - - + -
152A TYR* 5.3 4.0 - - + +
153A LEU* 5.3 0.7 - - + -
155A TRP* 5.1 1.8 - - + -
156A ALA* 4.2 10.8 - - + -
161A PHE* 3.7 35.9 - - + -
162A LYS 3.4 2.0 - - - +
163A THR* 3.4 17.7 - - + -
181A ILE* 3.3 38.6 - - + +
182A LYS* 1.3 71.7 - - - +
184A SER* 1.3 61.7 + - - +
188A ALA* 3.7 8.4 - - + +
192A LEU* 4.0 24.9 - - + -
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Residues in contact with SER 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASP* 3.3 23.3 + - - -
160A GLY 4.6 0.3 - - - +
161A PHE* 3.3 6.4 - - - -
162A LYS* 2.8 54.4 + - - +
182A LYS* 3.8 22.3 + - - +
183A ILE* 1.3 75.4 - - - +
185A GLY* 1.3 58.5 + - - +
188A ALA* 4.5 0.2 - - - -
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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