Contacts of the strand formed by residues 173 - 184 (chain B) in PDB entry 3MEU
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 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B ARG* 3.5 43.2 + - - +
166B VAL 3.6 1.3 - - - +
167B LYS* 3.4 31.0 + - - +
171B GLY 3.8 6.2 - - - +
172B ASP* 1.3 83.2 + - - +
174B GLN* 1.3 64.9 + - - +
209B ARG* 2.8 40.3 + - - -
289B GLU* 4.3 9.2 - - - +
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Residues in contact with GLN 174 (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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164B ALA 3.4 1.0 - - - +
165B ARG* 4.3 1.8 - - - -
166B VAL* 2.9 38.4 + - + +
172B ASP* 4.6 10.0 - - - +
173B GLU* 1.3 77.0 + - - +
175B TRP* 1.3 81.8 + - - +
176B ILE* 3.6 11.1 + - + +
243B CYS* 3.6 27.8 - - - +
244B PHE 2.9 27.9 + - - -
245B TYR* 3.5 25.8 + - - -
3D THR* 5.1 6.9 - - + +
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Residues in contact with TRP 175 (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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163B ALA* 3.4 23.8 - - + -
164B ALA 3.3 9.0 - - - -
165B ARG* 3.4 38.1 - - + +
174B GLN* 1.3 84.6 + - - +
176B ILE* 1.3 59.8 + - - +
208B ARG 3.8 20.6 - - - -
209B ARG 3.3 19.5 - - - -
211B ILE* 3.6 24.5 - - + -
235B LEU* 3.8 22.3 - - + +
243B CYS* 3.5 1.7 - - - -
244B PHE* 2.9 48.3 + - + +
288B LYS* 3.7 22.9 - - + -
289B GLU* 2.8 41.8 + - + +
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Residues in contact with ILE 176 (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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163B ALA* 3.4 4.2 - - - -
164B ALA* 2.8 44.2 + - + +
166B VAL* 3.9 23.6 - - + -
174B GLN* 3.8 22.9 - - + +
175B TRP* 1.3 79.4 - - - +
177B LEU* 1.3 64.0 + - - +
178B ALA* 3.6 3.1 + - + -
192B VAL* 6.0 0.2 - - + -
194B ASP* 3.6 44.2 - - + +
203B HIS* 4.7 5.4 - - + +
242B THR 3.6 8.3 - - - +
243B CYS* 4.0 1.6 - - - -
244B PHE* 3.8 6.7 - - - -
1D ALA* 3.7 21.3 - - + -
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Residues in contact with LEU 177 (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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123B LEU* 3.6 42.2 - - + -
161B LYS* 4.6 7.2 - - + -
162B VAL 3.7 6.1 - - - +
176B ILE* 1.3 72.7 - - - +
178B ALA* 1.3 68.0 + - - +
194B ASP* 4.0 6.1 - - - +
195B ILE* 3.0 35.9 + - + +
213B LEU* 3.6 31.4 - - + -
237B LEU* 4.3 7.4 - - + -
242B THR* 2.8 19.9 + - - +
244B PHE* 3.7 13.4 - - + -
283B TYR* 3.9 20.6 - - + +
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Residues in contact with ALA 178 (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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161B LYS* 3.5 7.4 - - - +
162B VAL* 2.9 32.4 + - + -
164B ALA* 4.0 16.2 - - + -
176B ILE* 4.4 3.6 - - + +
177B LEU* 1.3 78.0 - - - +
179B GLU* 1.3 61.4 + - - +
192B VAL* 3.9 22.4 - - + -
193B ASP 3.2 20.9 - - - +
194B ASP* 4.3 2.7 - - - +
195B ILE* 4.0 6.7 - - - +
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Residues in contact with GLU 179 (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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159B GLY* 3.4 39.6 + - - +
160B ASP 3.4 4.9 - - - +
161B LYS* 2.9 25.8 + - + +
178B ALA* 1.3 75.8 - - - +
180B VAL* 1.3 69.0 + - - +
181B VAL* 3.4 2.1 + - + +
192B VAL* 3.3 3.4 - - - -
193B ASP* 2.8 39.0 + - + +
195B ILE* 4.3 12.0 - - + +
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Residues in contact with VAL 180 (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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156B ALA* 3.8 20.9 - - + +
157B ARG 3.4 27.4 - - - +
158B PRO* 3.5 2.1 - - + +
159B GLY* 2.8 26.7 + - - -
160B ASP 2.9 12.3 + - - +
162B VAL* 3.6 32.1 - - + -
179B GLU* 1.3 75.1 - - - +
181B VAL* 1.3 62.1 + - - +
182B SER 3.8 22.9 - - - +
190B TYR* 4.0 15.3 - - + -
191B GLU 3.8 4.3 - - - +
192B VAL* 4.2 7.2 - - + -
210B VAL* 4.9 0.4 - - + -
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Residues in contact with VAL 181 (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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158B PRO* 3.5 18.7 - - - +
179B GLU 4.0 0.9 - - - +
180B VAL* 1.3 79.0 - - - +
182B SER* 1.3 63.7 + - - +
191B GLU* 2.8 30.1 + - + +
192B VAL 4.1 0.9 - - - -
193B ASP* 3.3 46.4 - - + +
202B ARG* 3.6 28.5 - - - +
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Residues in contact with SER 182 (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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158B PRO* 4.5 7.6 - - - -
180B VAL* 3.8 7.9 - - - +
181B VAL* 1.3 85.6 - - - +
183B TYR* 1.3 66.4 + - - +
184B SER* 5.0 1.6 + - - -
190B TYR* 3.3 8.8 - - - -
191B GLU* 2.8 54.4 + - - +
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Residues in contact with TYR 183 (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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155B VAL* 3.6 41.2 - - + +
156B ALA 4.8 2.7 - - - +
158B PRO* 5.4 2.9 - - + +
182B SER* 1.3 81.2 - - - +
184B SER* 1.3 68.4 + - - +
185B HIS* 3.5 36.7 + - + -
188B ASN* 2.6 40.2 + - - -
189B LYS 3.6 17.0 - - - -
190B TYR* 4.2 14.6 - + + -
207B ARG* 4.2 10.7 + - + -
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Residues in contact with SER 184 (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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182B SER* 5.0 2.0 + - - -
183B TYR* 1.3 76.8 - - - +
185B HIS* 1.3 54.3 + - - +
186B ALA* 3.1 25.8 + - - +
187B THR* 3.3 17.5 + - - +
188B ASN* 2.7 36.9 + - - -
189B LYS 3.0 11.1 + - - -
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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