Contacts of the strand formed by residues 187 - 190 (chain B) in PDB entry 2VUU
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 LEU 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B ILE* 3.6 24.2 - - + -
177B TRP* 4.8 0.2 - - + -
181B PHE* 3.7 50.0 - - + -
182B ASP 5.8 0.2 - - - +
185B ILE* 4.4 11.4 - - + +
186B PRO* 1.3 78.4 - - - +
188B PRO* 1.3 70.8 - - + +
189B TRP* 2.9 39.5 - - + +
222B THR* 3.3 4.8 - - - -
223B LEU 2.7 20.5 + - - +
225B PRO* 4.3 9.6 - - + -
269B PHE* 4.2 18.6 - - + -
276B TYR* 4.8 2.2 - - + +
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Residues in contact with PRO 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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151B GLY* 3.2 1.0 - - - -
152B ILE* 2.8 28.4 + - + +
186B PRO 4.5 2.5 - - - +
187B LEU* 1.3 84.9 - - + +
189B TRP* 1.3 61.8 + - - +
219B THR* 3.3 24.2 - - + +
221B GLU 4.1 0.2 - - - +
222B THR* 4.0 15.2 - - + -
276B TYR* 3.6 45.8 - - + -
277B PHE* 3.7 15.9 - - + -
317B VAL* 5.6 2.0 - - + -
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Residues in contact with TRP 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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152B ILE* 3.3 46.4 - - + -
153B TYR 3.9 7.9 - - - -
154B ASN* 3.6 13.2 - - - +
157B PHE* 3.4 36.6 - + - -
165B PHE* 4.1 8.7 - + - -
177B TRP* 4.2 6.7 - + - -
187B LEU* 2.9 46.1 + - + +
188B PRO* 1.3 73.2 - - - +
190B LEU* 1.3 61.2 + - - +
219B THR* 3.3 7.0 - - - -
220B PHE* 3.3 23.2 + - - +
221B GLU* 2.9 26.5 + - + +
223B LEU* 3.2 38.2 + - + -
225B PRO* 5.7 0.2 - - + -
228B VAL* 3.5 22.3 - - + +
331B MET* 3.4 16.6 - - + -
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Residues in contact with LEU 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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150B ALA* 3.4 28.7 - - + -
151B GLY 3.6 13.7 - - - +
152B ILE 2.8 7.9 + - - -
153B TYR* 3.0 16.6 - - + -
154B ASN* 2.8 28.6 + - - -
189B TRP* 1.3 77.5 - - - +
191B ASP* 1.3 73.5 + - - +
192B ALA* 3.4 7.5 + - - +
195B ASP* 4.4 2.9 - - + -
196B VAL* 4.3 19.1 - - + +
218B LEU* 3.0 35.0 - - + +
220B PHE* 3.5 31.9 - - + +
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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