Contacts of the strand formed by residues 184 - 190 (chain B) in PDB entry 1MHP
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 GLN 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B LEU 3.0 6.9 + - - +
148B ASP* 3.5 11.2 - - - +
149B ILE* 2.9 26.3 + - - +
178B ILE* 4.8 2.7 - - + -
179B GLY 3.8 12.8 - - - +
180B PRO* 4.1 17.2 - - - +
183B THR* 1.3 73.1 - - - +
185B VAL* 1.3 68.5 + - - +
200B LEU* 3.3 26.8 + - + +
201B ASN* 3.5 19.0 - - - +
203B TYR 5.2 4.9 + - - +
243B GLY 2.7 25.5 - - - +
245B ARG* 3.4 35.5 + - - +
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Residues in contact with VAL 185 (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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149B ILE* 3.1 16.4 - - + +
151B ILE* 4.2 11.9 - - + -
173B LEU* 3.8 33.0 - - + -
176B MET* 4.4 5.4 - - + -
178B ILE* 4.2 19.3 - - + +
183B THR* 4.3 10.1 + - + -
184B GLN* 1.3 82.4 - - - +
186B GLY* 1.3 68.6 + - - +
187B ILE* 4.3 2.9 - - + -
198B PHE* 3.0 27.1 - - + -
199B ASN 3.4 10.9 - - - +
200B LEU* 3.7 9.1 + - - +
203B TYR* 5.6 0.9 + - - -
209B VAL* 4.5 12.5 - - + +
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Residues in contact with GLY 186 (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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149B ILE 2.9 7.9 + - - +
150B VAL* 3.2 9.7 - - - -
151B ILE 2.7 25.5 + - - -
185B VAL* 1.3 75.8 - - - +
187B ILE* 1.3 65.5 + - - +
188B VAL* 5.6 0.2 - - - -
198B PHE* 3.2 15.5 - - - -
199B ASN* 4.7 0.2 - - - -
200B LEU* 3.6 15.3 - - - +
237B ALA* 6.3 0.9 - - - -
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Residues in contact with ILE 187 (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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151B ILE* 3.4 30.5 - - + +
153B LEU* 3.8 18.4 - - + -
169B LEU* 3.6 27.4 - - + -
173B LEU* 4.8 2.7 - - + -
185B VAL* 4.3 2.7 - - + -
186B GLY* 1.3 78.8 - - - +
188B VAL* 1.3 68.4 + - - +
196B HIS* 3.8 1.4 - - - -
197B GLU* 2.9 38.5 + - + +
198B PHE* 3.1 38.8 + - + +
213B ALA* 4.5 6.1 - - + -
216B ILE* 3.8 18.6 - - + -
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Residues in contact with VAL 188 (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 VAL* 4.2 16.2 - - + -
151B ILE 2.7 12.3 + - - +
152B VAL* 3.3 10.6 - - + +
153B LEU* 2.7 34.7 + - - +
187B ILE* 1.3 80.0 - - - +
189B GLN* 1.3 58.4 - - - +
194B VAL* 3.4 28.9 - - + -
195B THR 3.6 5.8 - - - +
196B HIS* 4.0 24.2 - - + +
229B GLY* 4.2 15.3 - - - +
232B THR* 4.9 1.6 - - + -
233B ALA* 4.4 9.0 - - + -
237B ALA* 4.3 9.6 - - + -
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Residues in contact with GLN 189 (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 LEU* 3.2 16.4 - - + +
155B GLY* 3.6 16.4 - - - +
162B TRP* 3.9 12.0 - - + -
187B ILE* 4.3 0.6 + - + -
188B VAL* 1.3 76.3 - - - +
190B TYR* 1.3 69.5 + - - +
194B VAL* 3.4 3.8 - - - +
195B THR* 2.9 36.8 + - - +
197B GLU* 3.1 26.6 + - + +
216B ILE* 3.7 10.9 - - + +
217B VAL 3.1 21.8 + - - -
218B GLN* 3.6 2.1 - - - -
219B ARG* 2.8 39.7 + - + +
220B GLY 5.2 0.2 - - - +
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Residues in contact with TYR 190 (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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152B VAL* 3.7 30.1 - - + -
153B LEU 2.9 31.6 + - - -
154B ASP* 3.6 17.0 - - + -
155B GLY* 2.9 27.7 + - - -
156B SER 3.6 1.0 + - - -
188B VAL* 5.3 0.2 - - + -
189B GLN* 1.3 76.6 - - - +
191B GLY* 1.3 60.8 + - - +
193B ASN 3.3 10.5 - - - +
194B VAL* 4.1 6.1 - - + -
220B GLY 4.9 1.3 - - - -
224B THR* 3.7 13.7 - - + -
225B MET* 3.5 21.8 - - + +
226B THR* 2.9 44.9 + - + +
229B GLY* 4.0 17.7 - - - +
254B ILE* 4.6 2.3 - - + +
256B THR* 3.2 26.3 + - - +
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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