Contacts of the strand formed by residues 161 - 173 (chain A) in PDB entry 1MWT
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 GLU 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A LYS* 3.7 28.7 - - + +
155A LEU* 3.4 21.2 - - + +
159A ASN 4.0 5.8 - - - +
160A VAL* 1.3 78.3 - - - +
162A LEU* 1.3 64.4 + - - +
163A ALA 5.1 0.4 - - - +
164A ASN* 3.0 33.2 + - + +
244A PRO* 3.4 23.4 - - + +
245A LEU* 4.8 0.2 - - - +
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Residues in contact with LEU 162 (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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154A ILE* 2.8 16.1 + - + +
155A LEU 4.0 1.1 - - - -
156A ASP* 3.8 28.3 - - + +
160A VAL* 3.7 13.0 - - + +
161A GLU* 1.3 81.0 - - - +
163A ALA* 1.3 61.7 + - - +
243A TYR* 3.4 16.8 - - - +
244A PRO* 3.3 17.8 - - - +
245A LEU* 3.8 34.1 + - + -
249A THR* 4.9 7.2 + - + -
252A LEU* 6.2 0.7 - - + -
253A LEU* 3.8 16.0 - - + +
326A LEU* 4.0 25.6 - - + -
328A ILE* 4.6 11.4 - - + -
330A ALA* 4.5 7.6 - - + -
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Residues in contact with ALA 163 (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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153A LYS* 3.2 9.9 - - - +
154A ILE* 3.0 47.3 + - + +
161A GLU* 5.4 0.2 - - - +
162A LEU* 1.3 79.2 - - - +
164A ASN* 1.3 60.8 + - - +
241A ARG* 3.5 24.0 - - - +
242A ASN 3.4 6.7 - - - -
243A TYR* 3.7 18.4 - - + -
253A LEU* 4.8 0.7 - - + -
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Residues in contact with ASN 164 (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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153A LYS* 3.9 16.6 - - + -
161A GLU* 3.0 36.8 + - + +
163A ALA* 1.3 75.8 - - - +
165A THR* 1.3 71.0 + - - +
166A GLY* 3.7 0.7 + - - -
241A ARG* 3.5 19.4 - - - +
242A ASN* 3.0 51.6 + - - +
244A PRO* 4.1 13.4 - - - +
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Residues in contact with THR 165 (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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150A GLU* 3.7 41.0 + - + +
151A ARG* 4.7 6.9 + - - +
153A LYS* 5.2 1.5 - - - +
164A ASN* 1.3 82.1 - - - +
166A GLY* 1.3 67.3 + - - +
239A GLU* 4.0 27.6 - - + +
240A SER 4.0 7.9 - - - +
241A ARG* 5.0 2.7 + - - +
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Residues in contact with GLY 166 (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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164A ASN* 4.2 1.1 - - - -
165A THR* 1.3 79.3 - - - +
167A THR* 1.3 61.3 + - - -
239A GLU* 3.5 9.5 - - - +
240A SER 2.9 27.6 + - - -
242A ASN* 3.4 24.0 - - - +
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Residues in contact with THR 167 (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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166A GLY* 1.3 75.5 - - - -
168A ALA* 1.3 60.1 + - - +
169A TYR* 4.7 14.8 - - + +
218A LYS* 3.2 30.6 + - - +
237A GLU* 3.3 28.5 + - + +
238A THR 3.1 15.8 + - - -
239A GLU* 5.1 0.2 - - - -
240A SER* 4.1 2.4 + - - +
242A ASN* 5.0 0.2 - - - -
317B LYS* 4.8 4.9 + - - -
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Residues in contact with ALA 168 (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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167A THR* 1.3 75.4 + - - +
169A TYR* 1.3 71.2 + - - +
216A THR* 3.7 15.0 - - + -
217A VAL 3.8 4.3 - - - +
218A LYS* 3.7 11.9 - - + -
237A GLU* 3.5 4.5 - - - -
238A THR* 2.7 33.3 + - + +
240A SER* 3.7 11.2 - - - -
373A TYR* 3.5 25.6 - - + +
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Residues in contact with TYR 169 (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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167A THR* 4.7 14.6 - - + +
168A ALA* 1.3 81.3 - - - +
170A GLU* 1.3 64.5 + - - +
171A ILE 3.8 0.3 + - - -
216A THR* 3.3 5.0 - - - -
217A VAL* 2.7 56.7 + - + +
218A LYS 3.5 16.8 - - - -
219A LYS* 4.3 10.5 - - - -
220A MET* 4.5 26.0 - - + -
235A THR* 5.1 6.7 - - - -
236A ASN 3.6 6.1 - - - +
237A GLU* 3.8 40.8 + - + -
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Residues in contact with GLU 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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168A ALA 4.3 0.4 - - - -
169A TYR* 1.3 72.0 - - - +
171A ILE* 1.3 61.3 + - - +
211A PHE* 3.7 18.1 - - + -
213A PRO* 3.5 27.1 - - + +
215A LYS 3.7 4.0 - - - +
216A THR* 3.7 19.4 + - - +
234A THR 3.7 0.9 - - - +
235A THR* 3.2 5.0 - - - -
236A ASN* 2.7 63.2 + - - +
238A THR* 4.1 20.2 + - + +
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Residues in contact with ILE 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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169A TYR 4.5 0.4 - - - +
170A GLU* 1.3 77.7 - - - +
172A GLY* 1.3 61.1 + - - +
190A LEU* 4.6 19.5 - - + +
211A PHE* 4.3 0.7 - - - -
214A LEU* 2.9 27.8 + - + +
215A LYS 2.9 17.6 + - - +
217A VAL* 3.8 26.5 - - + -
220A MET* 3.5 39.0 - - + -
224A LEU* 4.1 12.1 - - + +
227A PHE* 5.0 4.9 - - + -
228A ALA* 5.1 3.8 - - + -
233A LEU* 4.2 27.8 - - + -
234A THR 3.5 6.3 - - - +
235A THR* 4.3 7.4 - - + -
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Residues in contact with GLY 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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171A ILE* 1.3 75.6 - - - +
173A ILE* 1.3 64.6 + - - -
211A PHE* 3.4 14.1 - - - -
212A VAL 3.0 16.2 - - - -
214A LEU* 3.7 8.3 - - - -
233A LEU* 3.5 9.6 - - - +
234A THR 2.8 37.8 + - - -
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Residues in contact with ILE 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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172A GLY* 1.3 78.4 - - - -
174A VAL* 1.3 71.9 + - - +
175A PRO* 3.7 5.2 - - + +
178A VAL* 3.2 37.0 - - + +
183A TYR* 3.9 28.3 - - + +
186A ILE* 4.2 9.4 - - + -
197A ILE* 4.4 7.0 - - + -
201A MET* 3.4 24.4 - - + +
210A THR 3.4 2.1 - - - +
212A VAL* 2.8 39.4 + - - +
214A LEU* 3.5 24.9 - - + -
233A LEU* 3.6 11.2 - - + -
234A THR 4.8 0.4 - - - +
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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