Contacts of the strand formed by residues 171 - 177 (chain A) in PDB entry 1G0X
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 TRP 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LYS* 3.3 10.1 - - - +
136A GLU* 2.9 49.6 + - + +
137A GLY 6.1 0.2 - - - -
169A ARG* 3.4 63.3 + - + +
170A TRP* 1.3 78.8 - - - +
172A TYR* 1.3 62.9 + - - +
191A LEU* 3.8 35.7 - - + -
192A LEU 3.4 2.7 - - - -
193A GLU* 2.7 40.4 + - + -
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Residues in contact with TYR 172 (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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104A LEU* 3.8 10.5 - - + -
120A LEU* 3.8 14.4 - - + -
133A LEU* 3.7 30.5 - - + -
134A CYS 3.3 4.7 - - - -
135A LYS* 3.7 38.5 - - + +
136A GLU* 4.6 1.1 - - - +
161A VAL* 3.6 31.2 - - + +
170A TRP* 3.3 52.4 - - + -
171A TRP* 1.3 74.3 - - - +
173A ARG* 1.3 69.6 + - - +
191A LEU* 3.5 1.3 - - - +
192A LEU* 2.7 43.8 + - + +
194A LEU* 4.2 15.5 - - + -
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Residues in contact with ARG 173 (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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17A THR* 5.2 9.5 - - - +
104A LEU* 3.8 3.8 - - - -
133A LEU* 3.8 1.1 - - - +
134A CYS* 2.9 31.1 + - - +
136A GLU* 3.1 38.7 + - - +
172A TYR* 1.3 80.7 - - - +
174A CYS* 1.3 61.9 + - - +
175A TYR* 4.1 14.5 + - + -
188A PRO* 3.2 40.9 - - + +
189A SER* 3.5 17.1 + - - +
191A LEU* 3.9 25.0 - - + +
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Residues in contact with CYS 174 (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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102A PRO* 3.6 11.9 - - - +
104A LEU* 3.8 26.4 - - + +
122A CYS* 2.0 55.4 - - + -
132A ILE 3.1 13.2 - - - +
133A LEU* 4.3 6.7 - - + -
159A PHE* 5.3 0.4 - - + -
173A ARG* 1.3 73.7 - - - +
175A TYR* 1.3 66.8 + - - +
188A PRO* 3.9 0.5 - - - +
189A SER* 3.0 31.3 + - - -
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Residues in contact with TYR 175 (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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15A VAL* 4.3 10.0 - - + +
17A THR* 5.9 1.6 - - - +
96A THR* 3.6 21.3 + - + +
102A PRO* 4.2 4.3 - - - -
122A CYS* 4.4 0.2 - - - -
131A PHE* 3.4 8.3 - - - -
132A ILE* 2.8 38.0 + - + +
134A CYS* 3.7 27.6 - - + -
136A GLU* 4.9 2.0 + - - -
173A ARG* 4.1 24.3 + - + +
174A CYS* 1.3 79.6 - - - +
176A ALA* 1.3 60.1 + - - +
177A TYR* 5.2 0.2 - - - -
185A TRP* 3.6 40.4 - + + -
186A SER* 3.1 29.2 - - - +
188A PRO* 3.3 37.5 - - + +
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Residues in contact with ALA 176 (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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99A TYR* 3.9 1.7 - - - -
100A ILE 5.4 1.1 - - - +
102A PRO* 4.3 6.2 - - + +
124A SER* 4.7 5.2 - - - -
128A PHE* 3.7 30.3 - - + -
130A GLY 3.3 6.3 - - - +
131A PHE* 3.7 20.6 - - + -
175A TYR* 1.3 74.6 - - - +
177A TYR* 1.3 64.5 + - - +
185A TRP* 3.8 0.9 - - - +
186A SER* 3.0 38.7 + - - +
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Residues in contact with TYR 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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99A TYR* 4.0 8.1 - - - -
128A PHE* 3.6 13.0 - - - +
129A ASP* 3.3 1.0 - - - +
130A GLY* 2.8 59.4 + - - +
131A PHE* 4.6 0.4 - - - -
132A ILE* 3.4 32.5 - - + -
146A ASN* 2.6 27.2 + - - -
176A ALA* 1.3 78.4 - - - +
178A ASP* 1.3 67.7 + - - +
179A SER* 4.0 20.9 - - - -
182A PRO* 3.9 25.4 - - + -
184A GLU 3.5 18.2 - - - +
185A TRP* 3.7 15.0 - + + -
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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