Contacts of the strand formed by residues 209 - 214 (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 LYS 209 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A TYR* 2.7 64.7 + - - +
235B GLU 3.3 29.5 - - - +
236B THR* 3.4 18.6 - - - +
249B GLU* 5.3 15.7 - - - +
278B LEU* 5.4 1.5 - - - +
203C ILE* 3.6 8.4 - - - +
208C GLY* 1.4 78.4 - - - +
210C VAL* 1.4 66.0 + - - +
220C GLU* 3.0 36.6 + - + +
221C VAL 3.0 13.0 - - - +
222C ALA* 3.8 7.6 - - + -
223C VAL* 4.7 0.2 - - - -
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Residues in contact with VAL 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU* 6.4 0.2 - - - -
283B ASP* 6.0 3.1 - - - +
197C LEU* 3.9 25.5 - - + +
198C ASP 3.2 24.7 - - - +
199C VAL* 3.9 14.1 - - + -
200C PRO* 3.7 26.0 - - + -
203C ILE* 3.7 13.5 - - + -
209C LYS* 1.4 79.0 - - - +
211C ARG* 1.3 65.7 + - - +
220C GLU* 4.6 2.0 - - - -
221C VAL* 2.9 36.0 + - - +
223C VAL* 4.3 3.8 - - + -
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Residues in contact with ARG 211 (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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233B PHE* 3.5 44.6 - - + -
278B LEU* 5.5 3.6 - - + +
283B ASP* 3.0 60.0 + - + +
286B MET* 4.9 4.6 - - - +
197C LEU* 4.0 8.4 - - - +
210C VAL* 1.3 75.8 - - - +
212C ALA* 1.3 69.8 + - - +
213C MET* 3.2 29.4 - - - +
218C PRO* 3.6 21.7 - - + +
219C VAL 3.3 13.5 - - - +
220C GLU* 4.3 3.7 - - - +
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Residues in contact with ALA 212 (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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283B ASP* 5.4 0.2 - - - -
186C PHE* 5.7 2.7 - - + -
197C LEU* 3.7 20.4 - - + -
210C VAL 3.6 2.0 + - - -
211C ARG* 1.3 73.5 - - - +
213C MET* 1.3 59.9 + - - +
214C THR* 3.2 2.3 + - - -
219C VAL* 2.9 50.0 + - + +
221C VAL* 4.2 2.2 - - + +
235C LEU* 4.6 0.4 - - + -
249C LEU* 4.7 5.2 - - + -
251C LEU* 3.8 22.7 - - + -
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Residues in contact with MET 213 (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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170B THR* 5.6 11.2 - - + -
171B ALA* 5.1 10.1 - - + -
283B ASP* 5.3 0.9 - - - +
128C GLU* 3.8 26.5 - - + +
183C HIS* 4.1 20.4 - - + -
186C PHE* 3.0 23.2 - - + -
211C ARG* 3.2 33.1 - - - +
212C ALA* 1.3 67.0 - - - +
214C THR* 1.3 74.0 + - - +
217C GLY* 5.0 4.3 - - - +
218C PRO* 4.2 10.1 - - + -
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Residues in contact with THR 214 (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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171B ALA* 4.7 0.9 - - - +
186C PHE* 4.3 7.0 - - + -
193C LEU* 5.2 0.4 - - + -
212C ALA 3.2 1.4 + - - -
213C MET* 1.3 90.8 - - - +
215C LEU* 1.3 77.3 + - + +
216C GLU* 3.3 9.4 - - - +
217C GLY 3.1 27.9 + - - +
219C VAL* 3.2 30.1 + - - +
238C LYS* 3.6 36.9 - - + +
249C LEU* 4.0 17.5 - - + +
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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