Contacts of the strand formed by residues 169 - 176 (chain A) in PDB entry 1M1U
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 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ASP* 4.6 1.2 + - - -
133A SER* 3.2 20.3 - - - +
135A ILE* 3.9 19.5 - - + -
164A LEU 3.8 6.5 - - - +
165A LYS* 5.5 0.2 - - - -
166A LYS* 2.8 49.8 + - + +
167A SER 3.4 1.5 + - - -
168A LYS* 1.3 79.0 + - - +
170A LEU* 1.3 68.3 + - - +
171A PHE* 3.7 29.8 - - + -
189A PHE* 3.9 12.1 - - - -
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Residues in contact with LEU 170 (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 SER 3.0 6.4 + - - +
134A ASP* 4.1 1.8 - - - +
135A ILE* 2.8 28.1 + - - +
167A SER 5.6 4.0 - - - +
168A LYS 5.8 0.2 - - - -
169A THR* 1.3 79.1 - - - +
171A PHE* 1.3 63.7 + - - +
186A PHE* 3.6 38.1 - - + +
189A PHE* 3.9 14.8 - - + -
190A GLN* 3.5 42.4 - - + +
228A GLY 4.1 8.1 - - - +
230A ARG* 3.3 32.5 - - - +
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Residues in contact with PHE 171 (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 ILE* 3.1 35.7 - - + +
137A PHE* 3.7 24.0 - + + -
160A VAL* 4.3 6.5 - - + -
161A MET* 3.7 54.7 - - + -
164A LEU* 3.7 26.7 - - + -
165A LYS* 4.4 3.8 - - - -
169A THR* 3.7 18.8 - - + -
170A LEU* 1.3 74.9 - - - +
172A SER* 1.3 61.1 - - - +
184A PHE* 3.4 6.9 - - + -
185A THR 3.6 2.4 - - - +
186A PHE* 3.7 4.7 - - - -
189A PHE* 3.1 54.8 - + + +
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Residues in contact with SER 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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135A ILE 2.9 5.6 + - - -
136A ALA* 3.3 2.7 - - - -
137A PHE* 2.9 30.5 + - - -
171A PHE* 1.3 75.6 - - - +
173A LEU* 1.3 61.0 + - - +
184A PHE* 2.8 24.7 + - - -
185A THR* 3.6 4.7 - - - -
186A PHE* 3.6 34.7 - - - -
222A LEU* 3.6 25.8 - - - +
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Residues in contact with LEU 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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137A PHE* 3.5 17.7 - - + +
139A ILE* 3.9 23.1 - - + -
154A LYS* 6.5 0.2 - - - -
157A VAL* 3.6 33.4 - - + -
172A SER* 1.3 82.2 + - - +
174A MET* 1.3 70.3 + - - +
182A ILE* 3.6 3.8 - - - +
183A HIS* 2.9 55.7 + - + +
184A PHE* 3.0 34.5 + - + +
199A VAL* 4.5 0.4 - - + -
202A ILE* 4.0 13.5 - - + -
222A LEU* 4.6 1.8 - - - -
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Residues in contact with MET 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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137A PHE 3.0 10.0 + - - +
138A LEU* 3.5 13.7 - - + -
139A ILE* 3.1 24.4 + - - +
173A LEU* 1.3 78.7 - - - +
175A GLN* 1.3 71.4 + - - +
180A PHE* 4.2 19.1 - - + -
181A ARG 3.1 14.8 - - - +
182A ILE* 3.6 23.6 - - + -
214A GLY 4.3 6.1 - - - +
217A LYS* 4.1 24.7 - - + +
218A VAL* 4.0 15.3 - - - +
221A GLU* 4.0 16.4 - - + +
222A LEU* 4.1 24.2 - - + +
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Residues in contact with GLN 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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139A ILE* 3.4 22.0 - - + +
141A GLY* 3.2 18.5 - - - -
150A PHE* 3.3 15.8 - - - -
174A MET* 1.3 78.4 - - - +
176A TYR* 1.3 68.6 + - - +
180A PHE* 3.6 0.7 - - - -
181A ARG 2.7 30.2 + - - +
183A HIS* 2.9 35.5 + - + +
202A ILE* 3.8 4.8 - - - +
203A THR 3.0 19.2 + - - -
205A LEU* 2.9 43.0 + - + +
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Residues in contact with TYR 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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138A LEU* 3.5 40.2 - - + -
139A ILE 3.0 18.1 + - - -
140A ASP* 3.3 37.8 + - - +
141A GLY* 2.7 33.1 + - - -
142A SER 3.6 0.3 + - - -
175A GLN* 1.3 80.3 - - - +
177A SER* 1.3 67.0 + - - +
179A GLU 3.5 6.1 - - - -
180A PHE* 3.5 22.2 - + + -
205A LEU* 4.2 3.6 - - - -
209A THR* 3.7 13.5 - - + -
210A HIS 3.6 15.3 - - - -
211A THR* 2.9 43.2 + - + +
214A GLY* 5.0 0.2 - - - -
239A VAL* 4.9 0.8 - - + +
241A THR* 3.4 14.1 - - - +
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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