Contacts of the strand formed by residues 189 - 195 (chain B) in PDB entry 4RG1
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 PHE 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B MET* 3.6 1.2 - - - +
187B SER* 2.4 25.8 + - - -
188B GLU* 1.3 113.2 - - + +
190B ARG* 1.3 66.2 + - - +
228B THR* 4.4 3.8 - - + -
229B VAL 3.2 7.6 - - - +
230B ARG* 3.9 37.0 - - + -
231B LEU* 4.1 1.1 - - - -
247B VAL* 4.1 18.2 - - + -
251B ASP* 4.3 14.1 - - + -
252B PRO* 3.8 31.9 - - + -
255B LYS* 5.3 5.2 - - + -
256B ALA* 4.0 10.3 - - + -
258B LEU* 3.9 15.7 - - + +
260B TRP* 3.4 24.7 - - + -
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Residues in contact with ARG 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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154B TYR* 4.0 9.8 - - - +
181B MET* 3.5 31.9 + - + +
182B ARG 3.0 26.5 + - - -
183B GLN* 3.5 11.3 + - - +
185B GLU 3.1 22.0 + - - -
187B SER* 4.5 5.6 + - - +
189B PHE* 1.3 80.3 - - - +
191B GLU* 1.3 72.7 + - - +
209B CYS* 3.0 31.5 + - + -
210B GLY 4.0 11.5 + - - -
211B MET* 3.5 35.4 - - - +
228B THR* 4.7 0.2 - - - -
229B VAL* 2.8 36.2 + - - +
231B LEU* 3.8 13.8 - - + +
260B TRP* 4.2 4.9 - - - -
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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
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152B PRO* 4.0 13.0 - - + -
154B TYR* 2.6 34.0 + - - +
155B LEU* 4.0 8.7 - - + -
179B HIS* 4.2 13.4 + - + +
181B MET* 5.3 1.0 - - - +
190B ARG* 1.3 74.0 - - - +
192B GLY* 1.3 57.8 + - - +
209B CYS* 3.4 8.5 - - - -
226B ARG* 2.8 46.5 + - - +
227B VAL 3.4 4.7 - - - +
228B THR* 2.6 33.7 + - - +
249B SER* 5.7 0.3 - - - -
260B TRP* 2.7 30.8 + - + +
403B 15P 5.1 4.4 + - - -
404B 15P 5.2 0.5 - - - -
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Residues in contact with GLY 192 (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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155B LEU* 4.0 9.2 - - - +
190B ARG 3.9 0.4 + - - -
191B GLU* 1.3 76.7 - - - +
193B ILE* 1.3 61.0 + - - -
207B VAL* 3.6 17.5 - - - -
208B ASN 3.1 14.4 - - - -
209B CYS* 4.1 1.1 - - - -
226B ARG* 3.2 8.7 - - - +
227B VAL 2.9 31.3 + - - -
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Residues in contact with ILE 193 (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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155B LEU* 3.6 21.1 - - + -
158B ALA* 3.7 27.8 - - + +
159B PHE* 3.6 26.0 - - + -
192B GLY* 1.3 73.4 - - - +
194B VAL* 1.3 73.1 + - - +
195B VAL* 3.3 8.9 + - + +
207B VAL* 3.8 2.7 - - - -
208B ASN* 2.8 46.2 + - + +
224B GLY* 3.7 30.3 - - - +
225B LEU 3.3 3.8 - - - +
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Residues in contact with VAL 194 (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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193B ILE* 1.3 76.8 - - - +
195B VAL* 1.3 66.8 + - - +
205B SER* 4.2 11.4 - - - -
206B PHE 3.5 13.7 - - - +
207B VAL* 4.2 11.4 - - + +
217B ILE* 5.2 0.2 - - + -
221B LEU* 3.7 51.6 - - + +
222B GLU 3.5 15.9 - - - +
223B PRO* 3.4 5.8 - - + +
224B GLY 2.8 23.8 + - - +
225B LEU* 3.0 19.9 + - + +
227B VAL* 4.4 6.5 - - + -
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Residues in contact with VAL 195 (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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193B ILE* 3.7 18.6 - - + +
194B VAL* 1.3 79.1 - - - +
196B ASP* 1.3 59.8 + - - +
197B ARG* 3.2 53.4 + - + +
205B SER* 5.8 0.2 - - - -
206B PHE* 3.0 28.1 + - + +
208B ASN* 4.0 20.2 - - + +
214B GLU* 3.9 10.8 - - - +
223B PRO* 4.0 9.4 - - - +
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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
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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