Contacts of the strand formed by residues 161 - 173 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A LYS* 5.2 8.7 - - - +
153B LYS* 2.8 31.6 + - - +
155B LEU* 3.8 20.8 - - + +
159B ASN 3.2 6.9 + - - +
160B VAL* 1.3 77.5 - - - +
162B LEU* 1.3 63.9 + - - +
163B ALA 3.5 1.8 - - - +
164B ASN* 2.7 47.2 + - + +
244B PRO* 3.3 23.5 - - + +
245B LEU* 5.5 0.2 - - - +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ILE* 2.9 12.5 + - + +
155B LEU 4.2 0.9 - - - -
156B ASP* 3.9 30.5 - - + +
160B VAL* 3.7 21.8 - - + +
161B GLU* 1.3 77.2 - - - +
163B ALA* 1.3 58.4 + - - +
243B TYR* 3.4 9.0 - - - +
244B PRO* 3.6 13.2 - - - +
245B LEU* 4.0 32.0 + - + +
249B THR* 4.9 6.0 + - + +
252B LEU* 5.5 1.3 - - + -
253B LEU* 3.2 35.6 - - + +
326B LEU* 4.1 24.2 - - + -
328B ILE* 4.4 12.3 - - + -
330B ALA* 4.4 3.1 - - + -
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LYS* 3.3 11.8 - - - +
154B ILE* 3.2 52.5 + - + +
161B GLU* 3.5 1.5 - - - +
162B LEU* 1.3 81.5 + - - +
164B ASN* 1.3 62.6 + - - +
241B ARG* 3.6 16.8 - - - +
242B ASN 3.4 7.6 - - - -
243B TYR* 3.8 13.2 - - + -
244B PRO* 4.2 0.2 - - - +
253B LEU* 4.8 0.7 - - + -
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Residues in contact with ASN 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LYS* 4.5 14.4 - - + -
161B GLU* 2.7 40.4 + - - +
163B ALA* 1.3 74.8 - - - +
165B THR* 1.3 64.1 + - - +
166B GLY* 4.5 0.2 - - - -
241B ARG* 3.6 17.5 - - - +
242B ASN* 2.7 63.1 + - - +
244B PRO* 3.9 13.2 - - - +
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Residues in contact with THR 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLU* 3.9 31.0 + - + +
151B ARG 5.2 4.0 + - - -
153B LYS* 5.9 0.2 - - - +
164B ASN* 1.3 82.2 - - - +
166B GLY* 1.3 59.7 + - - +
239B GLU* 3.3 42.2 - - + +
240B SER* 3.9 8.3 - - - +
241B ARG* 4.9 2.5 + - - +
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Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LYS* 6.0 0.4 - - - -
165B THR* 1.3 74.6 - - - +
167B THR* 1.3 64.0 + - - -
218B LYS* 4.4 0.2 - - - -
239B GLU* 3.2 9.4 - - - +
240B SER 2.8 34.1 + - - -
242B ASN* 3.4 25.5 - - - +
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Residues in contact with THR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A LYS* 4.3 14.4 + - - -
166B GLY* 1.3 76.6 + - - -
168B ALA* 1.3 69.0 + - - +
169B TYR* 4.4 14.7 - - + +
218B LYS* 2.8 33.2 + - - +
237B GLU* 3.2 45.3 + - + +
238B THR 3.3 6.4 + - - +
240B SER* 4.9 0.4 - - - -
242B ASN* 5.1 0.2 - - - -
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLY 4.4 0.4 + - - -
167B THR* 1.3 77.5 - - - +
169B TYR* 1.3 68.4 + - - +
216B THR* 3.8 11.9 - - + -
217B VAL 3.7 9.6 - - - +
218B LYS* 4.0 8.5 - - + -
238B THR* 2.9 34.3 + - + +
240B SER* 3.7 13.2 - - - -
373B TYR* 3.3 27.1 - - + +
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Residues in contact with TYR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B THR* 4.4 15.1 - - + +
168B ALA* 1.3 77.7 - - - +
170B GLU* 1.3 64.2 + - - +
171B ILE 3.9 0.2 + - - -
216B THR* 3.2 7.0 - - - -
217B VAL* 2.6 53.0 + - + +
218B LYS 3.6 20.6 - - - -
219B LYS* 4.9 0.4 - - - -
220B MET* 3.7 42.4 - - + -
235B THR* 5.2 7.9 - - - -
236B ASN 3.7 3.1 - - - +
237B GLU* 4.1 38.3 + - + -
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B TYR* 1.3 72.7 - - - +
171B ILE* 1.3 61.1 + - - +
211B PHE* 3.3 29.3 - - + -
213B PRO* 3.7 23.1 - - + +
215B LYS 3.8 4.0 - - - +
216B THR* 4.0 16.3 + - - +
234B THR 3.5 1.2 - - - +
235B THR* 3.0 8.3 - - - -
236B ASN* 2.8 52.1 + - - +
238B THR* 4.1 21.6 + - + -
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Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B GLU* 1.3 75.5 - - - +
172B GLY* 1.3 61.2 + - - +
190B LEU* 3.7 35.0 - - + -
211B PHE* 4.4 1.1 - - - -
214B LEU* 2.9 25.2 + - - +
215B LYS* 2.9 21.0 + - + +
217B VAL* 4.0 24.7 - - + -
220B MET* 4.1 8.5 - - + -
224B LEU* 3.7 28.7 - - + -
227B PHE* 5.9 0.2 - - + -
228B ALA* 5.4 2.9 - - + -
233B LEU* 3.8 32.8 - - + -
234B THR 3.7 2.9 - - - +
235B THR* 4.6 8.5 - - + +
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Residues in contact with GLY 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ILE* 1.3 77.8 - - - +
173B ILE* 1.3 63.5 + - - -
211B PHE* 3.4 12.0 - - - -
212B VAL 3.0 15.3 - - - -
214B LEU* 4.1 6.3 - - - -
233B LEU* 3.6 7.4 - - - +
234B THR 2.7 44.2 + - - -
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLY* 1.3 74.7 - - - -
174B VAL* 1.3 69.6 + - - +
175B PRO* 3.5 3.4 - - + +
178B VAL* 3.4 41.3 - - + +
183B TYR* 4.2 16.8 - - + +
186B ILE* 4.2 8.3 - - + -
197B ILE* 4.3 11.0 - - + -
201B MET* 3.3 36.1 - - + +
212B VAL* 3.0 27.2 + - - +
214B LEU* 3.9 20.1 - - + +
233B LEU* 3.4 25.6 - - + -
234B THR 4.9 0.2 - - - +
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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