Contacts of the strand formed by residues 217 - 222 (chain C) in PDB entry 6PSI
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 GLY 217 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B ARG* 5.6 1.1 - - - -
171B ALA* 5.4 0.2 - - - -
231B LYS* 3.5 8.9 - - - +
213C MET* 5.0 1.1 - - - -
214C THR* 3.1 36.4 + - - -
216C GLU* 1.3 88.7 + - - +
218C PRO* 1.4 72.4 - - - +
219C VAL 3.4 0.5 + - - -
238C LYS* 3.7 3.6 + - - -
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Residues in contact with PRO 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B LYS* 4.0 30.3 - - + +
232B THR 5.7 0.4 - - - +
233B PHE* 3.5 38.4 - - + +
211C ARG* 3.6 25.8 - - + +
212C ALA 3.8 7.2 - - - +
213C MET* 4.2 10.5 - - + -
214C THR 4.1 3.6 - - - +
217C GLY* 1.4 80.0 - - - +
219C VAL* 1.4 62.8 + - - +
220C GLU 3.9 0.2 + - - -
238C LYS* 4.9 0.9 - - - -
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Residues in contact with VAL 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B THR* 3.5 42.4 - - + +
239B ALA* 4.1 9.2 - - - +
211C ARG* 3.3 5.6 - - - +
212C ALA* 2.9 52.3 + - + +
214C THR* 3.2 11.7 - - - +
217C GLY 3.4 4.0 + - - -
218C PRO* 1.4 71.5 - - - +
220C GLU* 1.3 64.2 + - - +
221C VAL* 4.5 1.1 - - + -
235C LEU* 3.6 27.1 - - + -
238C LYS* 3.7 22.7 - - + +
249C LEU* 5.0 0.2 - - + -
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Residues in contact with GLU 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A TYR* 3.0 21.8 + - - -
233B PHE* 4.2 25.9 - - + +
234B ALA* 3.6 7.1 - - - +
235B GLU* 3.1 37.3 + - + +
238B THR* 3.8 15.0 + - - +
239B ALA 3.7 13.9 + - - -
278B LEU* 3.3 22.0 - - + +
209C LYS* 3.0 31.7 + - + +
210C VAL 4.1 7.0 - - - +
211C ARG* 4.3 1.8 - - - +
218C PRO 3.9 1.4 + - - -
219C VAL* 1.3 74.0 - - - +
221C VAL* 1.3 63.0 + - - +
222C ALA 3.5 2.8 + - - -
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Residues in contact with VAL 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ALA* 3.7 7.2 - - + -
242B TRP* 4.1 7.4 - - + +
197C LEU* 3.8 21.8 - - + -
209C LYS* 3.0 25.9 - - - -
210C VAL 2.9 25.9 + - - +
212C ALA* 4.2 9.4 - - + +
219C VAL* 4.5 1.3 - - + -
220C GLU* 1.3 70.3 - - - +
222C ALA* 1.3 71.8 - - - +
223C VAL* 3.5 5.2 + - + +
233C LEU* 3.4 22.9 - - + -
235C LEU* 3.8 29.6 - - + -
251C LEU* 4.0 5.4 - - + -
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Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B THR 3.9 9.9 - - - +
237B ALA* 3.7 30.1 - - + -
239B ALA* 3.4 12.7 - - + +
242B TRP* 3.1 20.6 + - - -
245B LYS* 3.7 30.5 - - + +
208C GLY 3.7 6.3 - - - -
209C LYS* 3.8 4.5 - - + +
220C GLU 3.5 2.8 + - - -
221C VAL* 1.3 69.4 - - - +
223C VAL* 1.3 61.6 + - - +
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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