Contacts of the strand formed by residues 137 - 147 (chain M) in PDB entry 3INU
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 THR 137 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131M THR* 3.3 1.0 - - - -
132M SER* 2.7 47.7 + - - +
134M GLY* 1.3 85.4 - - - +
138M ALA* 1.3 58.2 + - - +
192M THR* 4.6 13.4 - - - +
193M VAL* 3.1 20.4 - - - +
194M PRO* 4.3 5.2 - - + -
195M SER* 3.4 5.5 + - - -
116N PHE* 4.9 3.1 - - - -
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Residues in contact with ALA 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126M PRO* 5.5 0.4 - - + -
127M SER 4.6 2.7 - - - +
130M SER 2.7 19.5 - - - +
131M THR* 3.7 7.4 - - - +
137M THR* 1.3 71.4 - - - +
139M ALA* 1.3 59.0 + - - +
191M VAL 3.7 0.2 - - - +
192M THR* 3.0 6.8 - - - -
193M VAL* 2.4 50.4 + - - +
195M SER* 4.1 1.1 - - - +
198M LEU* 3.6 40.2 - - + -
116N PHE* 5.2 2.0 - - - -
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Residues in contact with ALA 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126M PRO* 3.6 10.1 - - - +
130M SER* 3.0 17.4 + - - -
138M ALA* 1.3 76.0 - - - +
140M LEU* 1.3 61.1 + - - +
190M VAL* 5.6 0.7 - - + -
191M VAL 3.5 7.0 - - - +
192M THR* 4.5 7.0 - - + -
116N PHE* 3.8 37.2 - - + -
118N PHE* 3.4 18.7 - - + -
135N LEU* 4.1 13.9 - - + -
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Residues in contact with LEU 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124M LEU* 3.6 7.2 - - - -
126M PRO* 3.4 25.6 - - + -
139M ALA* 1.3 73.0 - - - +
141M GLY* 1.3 58.8 + - - +
157M TRP* 4.4 5.6 - - + -
190M VAL* 3.3 6.1 - - - +
191M VAL* 2.8 51.2 + - + +
193M VAL* 3.2 31.4 - - + -
206M TYR* 3.3 42.8 - - + -
225M VAL* 3.4 21.3 - - + +
118N PHE* 4.4 3.6 - - - -
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Residues in contact with GLY 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124M LEU* 2.6 47.8 + - - +
140M LEU* 1.3 78.8 - - - +
142M CYS* 1.3 57.7 + - - -
157M TRP* 3.4 14.7 - - - -
189M SER 3.0 13.7 - - - -
190M VAL* 4.0 1.6 - - - -
225M VAL* 3.1 9.4 - - - +
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Residues in contact with CYS 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M VAL* 3.7 20.4 - - + -
122M PHE 3.6 3.6 - - - -
124M LEU* 3.8 2.9 - - - +
141M GLY* 1.3 76.9 - - - -
143M LEU* 1.3 61.1 + - - +
144M VAL* 3.5 9.2 + - + +
157M TRP* 3.7 2.8 - - + -
188M SER* 3.2 4.5 - - - -
189M SER* 2.7 37.6 + - - +
208M CYS* 2.0 45.8 - - + -
221M LYS* 4.2 9.2 - - - -
225M VAL* 4.1 14.4 - - - -
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Residues in contact with LEU 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120M SER 3.4 4.9 - - - +
122M PHE* 2.8 49.5 + - + +
123M PRO 5.2 0.7 - - - +
124M LEU* 3.9 16.2 - - + +
142M CYS* 1.3 69.8 - - - +
144M VAL* 1.3 60.1 + - - +
145M LYS* 3.5 16.1 + - + -
186M SER* 5.1 9.0 - - - +
187M LEU 4.1 4.5 - - - +
188M SER* 4.2 16.4 - - - -
124N GLN* 4.1 15.9 - - - +
131N SER* 3.8 29.2 - - - +
133N VAL* 4.4 19.5 - - + -
178N THR* 4.5 11.4 - - + +
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Residues in contact with VAL 144 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M PRO* 3.5 26.2 - - + -
120M SER 3.6 3.1 - - - +
121M VAL* 4.5 5.2 - - + +
142M CYS* 4.2 12.6 - - + +
143M LEU* 1.3 73.2 - - - +
145M LYS* 1.3 57.9 + - - +
147M TYR* 4.0 8.5 - - + -
152M VAL* 4.2 12.6 - - + -
154M VAL* 4.5 3.6 - - + -
186M SER* 3.4 3.3 + - - -
187M LEU* 2.8 59.9 + - + +
210M VAL* 3.5 42.8 - - + -
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Residues in contact with LYS 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M PRO* 3.4 1.6 - - - +
120M SER* 2.8 42.4 + - - +
122M PHE* 4.2 17.9 - - + -
143M LEU* 4.3 16.4 - - + +
144M VAL* 1.3 76.6 - - - +
146M ASP* 1.3 91.4 + - - +
147M TYR* 3.6 2.0 - - - -
179M GLN* 2.9 24.0 + - - -
186M SER* 3.0 15.0 - - - +
124N GLN* 4.1 11.9 - - - +
129N THR* 4.7 8.0 - - + +
131N SER* 3.2 28.0 - - - +
178N THR* 5.5 2.0 - - - -
180N THR* 4.0 17.6 - - - +
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Residues in contact with ASP 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M LYS* 3.5 26.7 - - - +
118M GLY 3.8 5.7 - - - +
120M SER* 5.4 3.7 + - - +
145M LYS* 1.3 103.2 + - - +
147M TYR* 1.3 57.7 + - - +
179M GLN* 2.9 19.2 + - - -
182M SER* 4.0 5.5 + - - -
184M LEU* 3.8 28.8 - - + +
185M TYR 2.8 16.1 + - - -
186M SER* 3.5 0.4 + - - -
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Residues in contact with TYR 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M LYS 3.2 12.8 - - - +
119M PRO* 3.6 29.8 - - + -
144M VAL* 4.0 22.9 - - + -
146M ASP* 1.3 77.7 - - - +
148M PHE* 1.3 62.9 + - - +
149M PRO 3.5 19.5 - - - -
150M GLU* 4.3 13.4 + - - -
151M PRO* 5.3 0.2 - - - +
152M VAL* 3.8 22.9 + - + +
176M ALA* 3.3 26.2 - - - +
184M LEU* 3.8 2.4 - - - -
185M TYR* 2.9 57.7 + + + +
186M SER* 4.0 4.9 - - - -
187M LEU* 3.7 15.5 - - + +
212M HIS* 3.8 9.6 - + - +
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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