Contacts of the strand formed by residues 131 - 138 (chain A) in PDB entry 1N3Y
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A GLN* 3.7 12.3 - - - +
130A GLU* 1.3 80.9 - - - +
132A ASP* 1.3 59.1 + - - +
133A ILE* 3.8 7.0 - - + -
162A PHE* 3.9 7.4 - - - -
166A SER 2.9 7.1 + - - -
167A THR* 3.3 22.1 + - + +
168A GLN 3.0 18.5 + - - +
228A ARG* 2.9 16.0 + - - -
232A ALA* 3.5 9.6 - - + -
234A ILE* 4.1 15.1 - - + +
314A ILE* 2.8 45.9 + - - +
315A PHE* 4.6 3.9 + - - +
317A ILE* 3.8 20.9 - - - +
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Residues in contact with ASP 132 (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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131A GLN* 1.3 69.6 - - - +
133A ILE* 1.3 61.4 + - - +
168A GLN* 3.6 10.6 - - - +
184A PHE* 3.5 22.3 - - + -
188A ARG* 4.8 0.7 + - - -
221A PHE* 3.5 6.3 - - + -
226A GLY 5.0 0.2 - - - +
227A ALA* 3.4 12.0 - - - +
228A ARG* 2.7 61.5 + - - +
231A ALA* 3.5 13.0 - - - +
232A ALA 2.9 11.5 + - - +
233A LYS* 3.8 11.0 - - + -
234A ILE 3.0 23.7 + - - -
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Residues in contact with ILE 133 (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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131A GLN* 4.1 8.1 - - + +
132A ASP* 1.3 75.5 - - - +
134A VAL* 1.3 64.0 - - - +
135A PHE* 4.9 0.2 - - + -
162A PHE* 4.5 0.9 - - + -
167A THR* 3.7 22.0 - - + -
168A GLN 2.9 10.2 + - - +
169A PHE* 3.2 36.1 - - + -
170A SER 3.0 23.6 + - - +
184A PHE* 3.4 4.0 - - - -
234A ILE* 3.4 28.3 - - + +
236A ILE* 3.7 25.4 - - + -
314A ILE* 3.6 34.5 - - + -
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Residues in contact with VAL 134 (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 ILE* 1.3 74.0 - - - +
135A PHE* 1.3 75.6 + - - +
136A LEU 4.3 0.2 - - - +
170A SER* 3.3 7.6 - - - +
172A MET 4.8 0.2 - - - +
184A PHE* 3.6 20.4 - - + -
216A VAL* 3.8 14.8 - - + -
220A LEU* 3.7 35.2 - - + -
221A PHE* 3.5 26.5 - - + -
234A ILE 2.8 13.1 + - - +
235A LEU* 3.4 11.7 - - + +
236A ILE* 2.8 28.9 + - - +
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Residues in contact with PHE 135 (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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134A VAL* 1.3 77.5 - - - +
136A LEU* 1.3 59.0 + - - +
137A ILE* 3.9 3.1 - - + -
154A PHE* 4.6 6.1 - + - -
155A VAL* 4.0 34.3 - - + -
158A VAL* 3.8 25.6 - - + -
159A ILE* 3.9 14.1 - - + -
169A PHE* 3.7 36.6 - + - -
170A SER 2.9 9.7 + - - +
171A LEU* 3.5 20.6 - - + +
172A MET 3.0 26.3 + - - +
236A ILE* 3.5 41.7 - - + -
238A ILE* 4.2 13.5 - - + -
310A LEU* 5.0 0.7 - - + -
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Residues in contact with LEU 136 (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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134A VAL 3.9 0.4 + - - -
135A PHE* 1.3 74.6 - - - +
137A ILE* 1.3 58.3 + - - +
172A MET* 3.3 26.9 - - + +
174A PHE* 3.6 27.7 - - + -
209A THR* 4.9 0.7 - - + +
212A ALA* 3.9 22.0 - - + -
213A ILE* 3.9 26.9 - - + +
216A VAL* 3.8 24.0 - - + -
235A LEU* 3.7 17.5 - - + -
236A ILE 2.8 10.1 + - - +
237A VAL* 3.4 14.3 - - + +
238A ILE 3.0 25.1 + - - +
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Residues in contact with ILE 137 (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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135A PHE* 4.7 2.2 - - + -
136A LEU* 1.3 79.3 - - - +
138A ASP* 1.3 61.2 + - - +
148A PHE* 4.4 10.5 - - + -
151A MET* 4.0 20.9 - - + -
152A MET* 3.5 32.1 - - - -
155A VAL* 4.2 13.0 - - + -
171A LEU* 4.0 21.1 - - + -
172A MET 2.9 13.4 + - - +
173A GLN* 3.2 13.6 - - + +
174A PHE* 2.9 28.6 + - - -
200A VAL* 4.8 1.6 - - + -
238A ILE* 3.8 28.0 - - + -
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Residues in contact with ASP 138 (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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137A ILE* 1.3 72.2 - - - +
139A GLY* 1.3 59.5 + - - +
140A SER* 2.7 39.3 + - - -
143A ILE* 3.2 16.2 - - + +
148A PHE* 4.1 0.2 - - - -
151A MET* 3.2 25.8 - - - +
173A GLN* 4.6 0.2 - - - -
174A PHE* 3.4 25.1 - - + +
206A PHE 4.2 0.5 - - - +
207A THR* 3.5 15.5 + - - +
238A ILE 3.0 20.3 + - - +
239A THR* 3.9 13.0 - - - -
240A ASP* 2.9 19.2 + - - +
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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