Contacts of the strand formed by residues 213 - 221 (chain R) in PDB entry 4DOH
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 213 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188R THR* 2.5 59.4 + - + +
212R THR* 1.3 77.7 - - - +
214R TYR* 1.3 60.9 + - - +
215R CYS* 4.7 6.3 - - - -
236R CYS* 3.9 11.9 - - + -
237R ALA* 3.5 33.0 - - - +
238R ARG* 3.7 36.5 - - + +
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Residues in contact with TYR 214 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ASP* 4.3 9.2 + - - -
151B HIS* 5.9 0.7 - - - -
151R ILE* 3.9 25.1 - - + -
185R VAL* 4.0 26.0 - - + -
186R LEU 3.4 4.0 - - - +
187R ASN* 3.5 41.0 + - + -
194R TRP* 5.6 3.4 - + - -
205R LEU* 6.0 1.1 - - + -
208R LEU* 3.5 35.2 - - + +
209R GLU* 3.2 27.9 + - - +
212R THR* 3.7 27.6 - - - -
213R LEU* 1.3 75.2 - - - +
215R CYS* 1.3 62.2 + - - +
216R VAL* 4.0 5.5 + - + +
236R CYS* 3.5 2.4 - - - +
237R ALA* 2.7 37.1 + - - +
239R THR* 4.4 2.7 - - + -
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Residues in contact with CYS 215 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184R SER 3.5 2.4 - - - +
185R VAL* 3.7 0.4 - - - -
186R LEU* 2.7 53.6 + - + +
188R THR* 4.1 18.8 - - + +
213R LEU* 4.3 3.6 + - - -
214R TYR* 1.3 72.8 - - - +
216R VAL* 1.3 61.9 + - - +
217R HIS* 4.2 9.6 + - + -
235R GLN 4.3 0.2 - - - +
236R CYS* 2.0 44.2 - - - -
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Residues in contact with VAL 216 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142R VAL* 4.9 3.6 - - + +
144R LEU* 3.8 29.8 - - + -
151R ILE* 5.4 2.7 - - + -
153R VAL* 4.6 14.1 - - + -
183R VAL* 3.9 22.7 - - + -
184R SER 3.2 10.8 - - - +
185R VAL* 4.8 8.1 - - + -
205R LEU* 4.5 17.7 - - + -
214R TYR* 4.8 6.5 - - + +
215R CYS* 1.3 76.2 - - - +
217R HIS* 1.3 67.2 + - - +
218R VAL* 4.4 8.7 - - + -
233R GLU 3.6 1.2 - - - +
234R LYS* 3.5 0.5 - - - -
235R GLN* 2.9 40.2 + - + +
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Residues in contact with HIS 217 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182R ASN 3.7 2.1 - - - +
184R SER* 3.0 55.2 + - - -
186R LEU* 5.8 5.3 - - - +
215R CYS* 5.0 10.4 + - + -
216R VAL* 1.3 76.3 - - - +
218R VAL* 1.3 63.2 + - - +
219R GLU* 5.2 3.8 + - - +
232R SER* 3.9 19.0 + - - +
233R GLU 3.0 18.2 - - - +
234R LYS* 3.6 19.5 - - + -
302R NAG 4.9 7.9 - - - -
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Residues in contact with VAL 218 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139R PRO* 4.0 1.6 - - - +
140R PRO* 3.7 20.9 - - + +
142R VAL* 3.6 23.6 - - + -
153R VAL* 5.1 2.2 - - + -
155R LEU* 3.5 30.1 - - + -
181R TYR* 3.6 13.5 - - + -
182R ASN 3.6 6.7 - - - +
183R VAL* 4.2 13.0 - - + -
216R VAL* 4.4 11.0 - - + -
217R HIS* 1.3 80.8 - - - +
219R GLU* 1.3 72.0 + - - +
232R SER* 3.2 16.3 - - - -
233R GLU 3.2 16.5 + - - -
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Residues in contact with GLU 219 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139R PRO* 5.4 0.9 - - - -
140R PRO* 4.6 0.4 - - - -
181R TYR* 3.4 5.0 - - - -
182R ASN* 2.9 59.1 + - + +
184R SER* 6.0 0.3 - - - -
217R HIS* 5.2 4.7 + - - +
218R VAL* 1.3 78.2 - - - +
220R SER* 1.3 65.4 + - - +
221R PHE* 6.2 0.7 - - + -
229R ALA* 5.4 7.6 - - - +
230R GLN 5.0 7.8 - - - +
232R SER* 3.4 26.7 + - - +
302R NAG 3.7 29.8 - - - +
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Residues in contact with SER 220 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137R ILE* 3.6 26.7 + - - +
138R GLY 3.0 29.0 + - - -
139R PRO* 4.7 2.2 - - - +
140R PRO* 3.3 7.1 - - - +
158R PRO* 3.7 2.4 - - - +
179R LEU* 4.4 3.4 - - - -
180R LYS 3.8 3.8 - - - -
181R TYR* 3.2 28.5 - - - -
218R VAL 4.3 0.2 + - - -
219R GLU* 1.3 76.1 - - - +
221R PHE* 1.3 64.2 + - - +
230R GLN 5.7 0.6 + - - -
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Residues in contact with PHE 221 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ARG* 6.5 0.7 - - + -
137R ILE* 5.6 1.3 - - - -
179R LEU* 3.8 2.4 - - - -
180R LYS* 2.9 75.7 + - + +
182R ASN* 4.7 7.0 - - + -
197R CYS* 3.6 28.5 - - - -
219R GLU* 4.1 1.1 + - + -
220R SER* 1.3 76.6 - - - +
222R VAL* 1.3 72.3 + - - +
223R PRO* 4.0 25.1 - - + +
302R NAG 3.7 32.3 - - + +
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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