Contacts of the strand formed by residues 189 - 194 (chain B) in PDB entry 3MEV
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 LYS 189 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SO4 5.2 4.0 + - - -
183B TYR* 3.4 8.0 - - - -
184B SER* 2.9 35.0 + - - -
187B THR* 3.6 34.4 + - + +
188B ASN* 1.3 81.2 - - - +
190B TYR* 1.3 63.0 + - - +
204B THR* 3.8 24.2 - - + -
205B LEU* 3.4 17.5 - - - +
206B SER* 4.0 13.9 - - - +
207B ARG 4.6 0.7 - - - +
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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
----------------------------------------------------------
154B TYR* 3.9 6.4 + - - -
155B VAL* 3.3 25.9 - - + -
156B ALA* 2.9 37.4 + - + +
180B VAL* 3.9 18.4 - - + -
182B SER 3.3 15.9 - - - -
183B TYR* 3.9 13.2 - + + -
189B LYS* 1.3 74.3 - - - +
191B GLU* 1.3 60.1 + - - +
192B VAL* 4.1 7.2 - - + -
203B HIS 3.7 0.3 - - - +
204B THR* 3.3 7.4 - - - +
205B LEU* 2.9 45.6 + - + -
207B ARG* 3.7 35.0 - - + +
210B VAL* 3.6 36.3 - - + +
212B PRO* 5.6 1.6 - - - +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B VAL* 3.7 0.9 - - - +
181B VAL* 2.7 44.1 + - + +
182B SER* 2.6 43.3 + - - +
190B TYR* 1.3 73.1 - - - +
192B VAL* 1.3 59.9 + - - +
202B ARG* 4.0 24.9 + - + +
203B HIS 3.4 4.3 - - - +
204B THR* 3.9 21.7 + - + +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B VAL* 4.3 15.3 - - + -
164B ALA* 4.0 12.6 - - + -
166B VAL* 5.7 0.9 - - + -
176B ILE* 6.2 0.2 - - + -
178B ALA* 3.9 19.7 - - + -
179B GLU 3.3 9.0 - - - +
180B VAL* 4.2 13.2 - - + -
181B VAL* 4.1 1.6 - - - +
190B TYR* 4.1 8.3 - - + -
191B GLU* 1.3 80.5 - - - +
193B ASP* 1.3 64.8 + - - +
201B GLU 3.6 0.9 - - - +
202B ARG* 3.3 2.9 - - - +
203B HIS* 2.7 58.2 + - + +
205B LEU* 4.0 20.9 - - + -
210B VAL* 4.3 3.1 - - + -
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Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ALA* 3.1 5.6 - - - -
179B GLU* 2.8 47.1 + - + +
181B VAL* 3.4 13.0 - - + +
192B VAL* 1.3 71.8 - - - +
194B ASP* 1.3 66.5 + - - +
195B ILE* 3.2 1.6 + - - -
201B GLU* 3.3 22.2 - - + +
202B ARG* 2.8 53.5 + - - +
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Residues in contact with ASP 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ILE* 3.6 24.4 - - + +
177B LEU 4.1 8.9 - - - +
178B ALA* 4.2 0.8 - - - +
192B VAL 4.1 0.8 + - - -
193B ASP* 1.3 69.6 - - - +
195B ILE* 1.3 63.1 + - - +
196B ASP* 3.1 19.0 + - - +
197B GLU* 2.9 26.0 + - - +
198B GLU 6.0 0.7 - - - +
201B GLU* 2.7 31.0 + - + +
203B HIS* 4.4 9.4 + - - +
242B THR* 4.6 0.2 + - - -
1D ALA* 2.6 36.9 + - - +
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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
------------------------------------------------------------
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