Contacts of the strand formed by residues 176 - 184 (chain M) in PDB entry 1MCW
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 TYR 176 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M GLU* 5.4 2.3 + - - -
141M SER* 3.6 12.0 - - - -
142M ASP 4.0 0.2 + - - -
143M PHE* 2.9 37.1 + - + +
144M TYR* 3.0 41.0 + + - -
146M GLY* 4.1 14.4 - - - -
168M PRO* 3.9 8.7 - - + -
169M SER* 2.8 45.1 - - - +
170M LYS* 3.2 35.6 + - + +
171M GLN* 3.5 11.4 + - - -
175M LYS* 1.3 78.7 - - - +
177M ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M LEU* 5.9 2.0 - - + -
140M ILE 3.1 10.3 - - - +
141M SER* 4.4 1.6 - - - -
168M PRO* 2.5 28.2 - - - +
169M SER 3.4 6.8 + - - +
171M GLN* 2.5 32.6 - - + +
176M TYR* 1.3 72.2 - - - +
178M ALA* 1.3 53.7 + - - +
165W THR 5.0 4.7 - - - +
166W THR* 2.6 31.2 + - - +
181W TYR* 4.2 13.2 - - + -
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Residues in contact with ALA 178 (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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139M LEU* 3.4 5.5 - - - +
140M ILE* 2.7 49.2 + - + -
143M PHE* 4.0 6.5 - - + -
148M VAL* 4.9 9.6 - - + -
150M VAL* 5.9 0.9 - - + -
165M THR* 5.8 5.6 - - + -
166M THR 4.6 7.4 - - - +
168M PRO* 3.7 16.8 - - + -
177M ALA* 1.3 77.1 - - - +
179M SER* 1.3 66.0 - - - +
166W THR* 4.0 4.4 - - - -
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Residues in contact with SER 179 (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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137M VAL* 4.6 7.6 - - - -
138M CYS 2.6 16.4 - - - -
139M LEU* 3.8 14.9 - - - +
140M ILE* 3.6 1.1 - - - +
164M GLU 4.1 0.3 - - - +
165M THR* 3.3 18.2 + - - -
166M THR* 4.2 6.8 + - - +
178M ALA* 1.3 81.2 - - - +
180M SER* 1.3 62.3 + - - +
181M TYR* 4.9 5.0 - - - -
166W THR* 3.7 8.7 + - - +
179W SER* 3.3 29.4 + - - -
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Residues in contact with SER 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137M VAL* 3.0 9.0 - - - +
138M CYS* 2.7 29.9 + - - -
140M ILE* 4.5 2.0 - - - +
150M VAL* 3.8 22.2 + - - +
152M TRP* 2.0 45.2 + - - -
163M VAL 4.7 0.3 + - - -
164M GLU 3.4 3.1 + - - -
165M THR* 2.3 29.5 + - - -
179M SER* 1.3 68.8 - - - +
181M TYR* 1.3 59.4 + - - +
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Residues in contact with TYR 181 (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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135M THR* 3.4 25.6 - - + -
136M LEU 2.7 15.7 - - - +
137M VAL* 3.5 12.6 - - + -
152M TRP* 3.9 3.1 - - - -
163M VAL* 3.0 3.1 - - - -
164M GLU* 2.6 70.6 + - + +
165M THR 4.8 0.2 - - - -
179M SER 4.9 4.7 - - - -
180M SER* 1.3 75.2 - - - +
182M LEU* 1.3 59.1 + - - +
183M SER* 3.8 21.8 - - - -
139W LEU* 3.6 17.5 - - + -
141W SER* 2.5 32.0 + - - -
142W ASP* 4.3 3.1 + - - -
171W GLN* 3.2 12.6 + - - +
177W ALA* 3.9 19.7 - - + -
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Residues in contact with LEU 182 (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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135M THR* 3.6 0.2 - - - -
136M LEU* 2.8 45.0 + - + +
152M TRP* 3.5 22.3 - - + -
159M VAL* 4.1 16.2 - - + -
162M GLY* 3.6 10.3 - - - +
163M VAL* 3.0 29.2 - - + -
181M TYR* 1.3 71.7 - - - +
183M SER* 1.3 68.5 + - - +
184M LEU* 3.5 29.6 + - + +
195M TYR* 3.7 28.0 - - + +
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Residues in contact with SER 183 (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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133M LYS* 4.0 6.5 - - - -
135M THR* 3.8 14.6 - - - +
162M GLY* 2.6 28.7 + - - +
163M VAL* 4.1 1.0 + - - -
164M GLU* 4.6 4.3 + - - +
181M TYR* 3.7 26.1 + - - -
182M LEU* 1.3 70.3 - - - +
184M LEU* 1.3 65.7 - - - +
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Residues in contact with LEU 184 (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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133M LYS* 2.9 19.0 + - - +
134M ALA* 2.8 62.2 + - + +
136M LEU* 4.4 7.6 - - + -
182M LEU* 3.5 36.6 - - + +
183M SER* 1.3 76.2 - - - +
185M THR* 1.3 81.1 + - - +
186M PRO 3.6 0.2 - - - -
188M GLN* 3.7 23.3 - - + +
189M TRP* 3.7 21.3 - - + +
195M TYR* 3.9 14.4 - - + +
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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