Contacts of the strand formed by residues 189 - 193 (chain G) in PDB entry 3MQ6
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 189 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G SER* 3.4 37.2 - - - +
110G MET* 4.0 21.8 - - + -
147G VAL* 3.9 17.0 - - + -
148G LEU 3.4 12.8 - - - +
149G ASN* 4.8 0.4 - - - -
150G LEU* 4.2 3.6 - - - -
187G PRO* 3.2 6.6 - - - +
188G ASP* 1.3 83.3 - - - +
190G ALA* 1.3 79.7 + - - +
191G VAL* 3.8 17.5 - - + +
238G ALA* 3.3 5.0 - - - -
239G VAL* 3.0 38.2 + - + +
241G PHE* 4.1 14.1 - - + -
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Residues in contact with ALA 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G ALA 3.6 1.6 - - - +
148G LEU* 2.9 37.3 + - + +
150G LEU* 4.0 17.9 - - + +
159G LEU* 4.4 16.8 - - + -
187G PRO* 4.9 4.5 - - + -
189G LEU* 1.3 82.1 - - - +
191G VAL* 1.3 60.4 + - - +
192G VAL* 3.9 8.5 - - + -
235G ILE* 4.8 9.9 - - + -
237G LEU 3.3 7.4 - - - +
238G ALA* 5.1 1.1 - - + -
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Residues in contact with VAL 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G MET* 3.9 7.0 - - + -
145G VAL* 3.9 34.5 - - + -
146G ALA 3.4 5.4 - - - +
147G VAL* 4.5 6.5 - - + -
189G LEU* 3.8 16.4 - - + -
190G ALA* 1.3 74.4 - - - +
192G VAL* 1.3 65.4 + - - +
235G ILE* 3.8 1.4 - - - +
236G SER* 2.9 32.6 + - - -
237G LEU* 2.7 29.2 + - + +
326G PHE* 3.7 31.4 - - + -
329G PHE* 5.8 0.7 - - + -
330G LEU* 4.6 4.7 - - + -
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Residues in contact with VAL 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G VAL* 3.3 5.4 - - - -
146G ALA* 2.8 42.5 + - + +
148G LEU* 4.2 18.4 - - + -
159G LEU* 4.7 4.5 - - + -
190G ALA* 4.5 10.1 - - + -
191G VAL* 1.3 80.1 - - - +
193G VAL* 1.3 66.1 + - - +
226G LEU* 3.2 35.0 - - + -
230G VAL* 4.2 22.2 - - + -
234G GLU 3.2 11.9 - - - +
235G ILE* 4.4 10.8 - - + -
236G SER* 4.4 1.3 - - - -
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Residues in contact with VAL 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G ARG 3.8 18.4 - - - +
144G GLN 3.6 11.9 - - - +
145G VAL* 4.3 1.8 - - + +
192G VAL* 1.3 78.6 - - - +
194G LEU* 1.3 74.8 + - - +
195G PRO* 3.4 8.7 - - - +
199G GLN* 4.9 1.1 - - - +
230G VAL* 5.1 2.1 - - - +
233G GLY 5.4 0.7 - - - +
234G GLU* 2.9 50.8 + - + +
236G SER* 3.6 18.3 + - - +
334G MET* 3.7 20.9 - - + -
337G VAL* 4.5 14.4 - - + -
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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
------------------------------------------------------------
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