Contacts of the strand formed by residues 130 - 137 (chain A) in PDB entry 3HI6
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLY 3.7 2.2 - - - +
129A ASN* 1.3 80.5 - - - +
131A ASP* 1.3 64.5 + - - +
132A LEU* 3.9 2.4 + - + -
165A SER 2.9 7.5 + - - +
166A TYR* 3.5 28.4 - - + -
167A GLN 3.0 17.2 + - - +
227A ARG* 2.9 16.5 + - - -
231A THR* 3.4 9.0 - - - +
233A VAL* 3.5 35.7 - - + -
302A LEU 4.5 1.6 - - - +
303A GLN* 3.7 42.8 - - + +
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Residues in contact with ASP 131 (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 VAL* 1.3 69.4 - - - +
132A LEU* 1.3 59.8 + - - +
167A GLN* 3.1 14.4 - - - +
183A PHE* 3.7 17.7 - - + -
220A PHE* 3.4 15.7 - - + -
226A ALA* 3.5 7.2 - - - +
227A ARG* 2.7 66.9 + - - +
230A ALA* 3.8 9.7 - - + +
231A THR 2.9 10.8 + - - +
232A LYS* 4.8 3.9 + - + +
233A VAL 2.9 25.3 + - - -
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Residues in contact with LEU 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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130A VAL* 4.3 7.2 - - + -
131A ASP* 1.3 73.3 - - - +
133A VAL* 1.3 79.1 + - - +
134A PHE* 3.9 20.2 - - + +
157A VAL* 5.5 0.2 - - + -
166A TYR* 4.3 15.7 - - + -
167A GLN 2.8 14.9 + - - +
168A PHE* 3.2 28.5 - - + -
169A ALA 2.9 24.3 + - - +
183A PHE* 3.5 2.8 - - - -
233A VAL* 3.2 27.6 - - + +
235A ILE* 4.0 10.1 - - + -
302A LEU* 3.9 30.1 - - + -
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Residues in contact with VAL 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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132A LEU* 1.3 80.9 - - - +
134A PHE* 1.3 74.3 + - - +
169A ALA* 3.3 8.7 - - + +
171A VAL* 3.9 21.8 - - + -
183A PHE* 3.8 6.7 - - + -
215A VAL* 4.1 11.4 - - + -
219A VAL* 3.8 21.3 - - + -
220A PHE* 3.2 34.5 - - + -
233A VAL 2.8 9.8 + - - +
234A LEU* 3.5 14.8 - - + +
235A ILE 2.8 27.7 + - - -
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Residues in contact with PHE 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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132A LEU* 3.9 13.7 - - + -
133A VAL* 1.3 73.3 - - - +
135A LEU* 1.3 55.7 + - - +
136A PHE* 3.8 1.0 + - + -
153A PHE* 4.7 2.5 - + - -
154A MET* 3.4 62.4 - - + -
157A VAL* 4.0 22.4 - - + -
158A MET* 3.8 19.7 - - + -
168A PHE* 3.7 31.9 - + + -
169A ALA 2.8 20.8 + - - +
170A ALA* 3.3 7.7 - - + -
171A VAL 2.8 32.4 + - - +
181A PHE* 4.8 0.2 - + - -
235A ILE* 3.6 19.7 - - + +
237A ILE* 4.4 7.6 - - + -
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Residues in contact with LEU 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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133A VAL 3.7 1.0 + - - -
134A PHE* 1.3 71.7 - - - +
136A PHE* 1.3 58.0 + - - +
171A VAL* 3.4 31.4 - - + +
173A PHE* 3.5 29.5 - - + -
208A THR* 4.8 0.4 - - + +
211A ALA* 3.9 14.6 - - + +
212A ILE* 3.7 43.1 - - + +
215A VAL* 3.9 10.8 - - + -
234A LEU* 3.7 17.7 - - + -
235A ILE 2.9 10.8 + - - +
236A ILE* 3.4 13.8 - - + -
237A ILE* 2.9 27.8 + - - +
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Residues in contact with PHE 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 PHE 4.1 4.7 - - - -
135A LEU* 1.3 73.9 - - - +
137A ASP* 1.3 63.6 + - - +
138A GLY 3.4 1.0 + - - -
147A PHE* 3.8 29.6 - + - -
150A ILE* 3.6 22.2 - - + -
151A LEU* 4.3 4.3 - - + -
154A MET* 3.4 40.6 - - + -
170A ALA* 4.0 13.9 - - + -
171A VAL 2.9 39.5 + - - -
172A GLN* 3.5 27.9 - - + -
173A PHE* 3.1 25.9 + - - -
180A GLU* 4.0 13.5 - - + -
196A LEU* 4.7 1.1 - - + -
199A VAL* 4.3 9.9 - - + -
237A ILE* 3.7 8.1 - - + -
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Residues in contact with ASP 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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136A PHE* 1.3 69.4 - - - +
138A GLY* 1.3 59.2 + - - +
139A SER* 2.6 41.5 + - - -
142A LEU* 3.3 32.3 - - + +
147A PHE* 3.4 18.8 - - - -
150A ILE* 4.3 2.9 - - + +
173A PHE* 3.5 19.4 - - + +
206A THR* 3.5 12.6 - - - +
237A ILE 3.0 20.3 + - - +
238A THR* 2.6 27.3 + - - -
239A ASP* 3.8 4.5 - - - +
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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