Contacts of the strand formed by residues 184 - 191 (chain B) in PDB entry 2GTP
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 ILE 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B THR 4.2 0.2 + - - -
183B GLY* 1.3 80.8 - - - +
185B VAL* 1.3 65.1 + - - +
186B GLU 4.4 0.3 + - - -
199B PHE* 3.9 29.4 - - + -
200B ASP 3.5 4.5 - - - +
201B VAL* 3.7 25.8 - - + -
210B LYS* 3.3 33.4 - - + +
211B TRP* 5.4 0.9 - - + -
213B HIS* 4.2 8.3 - - + -
214B CYS* 4.4 14.1 - - + -
92C SER 4.4 2.4 - - - +
93C GLU* 2.7 33.2 + - - +
94C PHE* 3.8 31.7 - - + -
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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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181B THR* 4.4 13.5 - - + -
182B THR 4.7 1.6 - - - +
184B ILE* 1.3 82.1 - - - +
186B GLU* 1.3 66.8 + - - +
187B THR* 4.9 6.1 + - - +
198B MET 3.6 1.4 - - - +
199B PHE* 3.4 2.7 - - - -
200B ASP* 2.9 45.0 + - + +
93C GLU* 3.6 26.7 - - - +
176C ARG* 3.8 37.5 - - + +
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Residues in contact with GLU 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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184B ILE 4.3 1.0 + - - -
185B VAL* 1.3 78.7 - - - +
187B THR* 1.3 63.7 + - - +
188B HIS* 2.7 34.8 + - + +
197B LYS* 4.2 5.5 - - - +
198B MET 3.2 7.6 - - - +
199B PHE* 3.6 40.5 - - + -
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Residues in contact with THR 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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50B VAL* 4.3 19.5 - - + +
53B MET* 6.0 1.8 - - + -
58B GLU* 6.5 0.7 - - + -
185B VAL* 4.9 7.6 + - - +
186B GLU* 1.3 75.1 + - - +
188B HIS* 1.3 79.8 + - - +
189B PHE* 4.3 12.6 - - + -
196B PHE 3.7 0.3 - - - +
198B MET* 2.7 49.9 + - - +
200B ASP* 5.9 1.4 - - - +
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Residues in contact with HIS 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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58B GLU* 4.2 7.8 - - - +
186B GLU* 2.7 35.2 + - + -
187B THR* 1.3 90.5 - - - +
189B PHE* 1.3 67.8 + - - +
196B PHE 3.4 3.8 - - - +
197B LYS* 3.3 39.7 + - + +
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Residues in contact with PHE 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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53B MET* 3.9 29.8 - - + +
57B HIS* 3.8 33.9 - + + -
58B GLU* 3.4 26.5 - - + +
187B THR* 4.3 10.8 - - + -
188B HIS* 1.3 80.0 - - - +
190B THR* 1.3 65.4 + - - +
191B PHE* 4.6 0.2 - - + -
195B HIS* 3.8 1.1 - - - -
196B PHE* 2.8 74.2 + + + +
198B MET* 3.5 37.0 - - + -
336B PHE* 4.1 5.6 - + - -
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Residues in contact with THR 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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57B HIS* 4.3 12.3 - - - +
58B GLU* 3.9 7.2 + - - +
189B PHE* 1.3 79.0 - - - +
191B PHE* 1.3 71.3 + - - +
193B ASP* 4.3 18.6 - - - +
194B LEU 3.2 9.6 - - - +
195B HIS* 3.3 29.5 + - + +
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Residues in contact with PHE 191 (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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56B ILE* 6.0 1.1 - - + -
57B HIS* 3.5 37.9 - + + -
189B PHE* 4.5 2.0 - - + -
190B THR* 1.3 78.9 - - - +
192B LYS* 1.3 109.9 + - + +
193B ASP 3.1 0.7 - - - -
194B LEU* 2.9 27.1 + - - +
196B PHE* 3.9 14.6 - + + -
333B GLN* 5.9 1.1 - - + -
336B PHE* 3.8 13.9 - + - -
337B ASP* 4.1 16.2 - - + -
340B THR* 3.5 28.0 - - + -
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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