Contacts of the strand formed by residues 213 - 217 (chain C) in PDB entry 5DO7
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 VAL 213 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 3.5 31.9 - - + -
115C VAL* 6.1 3.1 - - + -
128C CYS* 2.8 35.9 - - - +
129C PHE* 3.6 16.3 - - + -
130C SER* 2.8 32.7 + - - -
211C PRO* 3.5 2.2 - - + +
212C LYS* 1.3 83.2 - - - +
214C MET* 1.3 62.1 + - - +
215C LEU* 5.2 1.8 - - + -
244C ILE* 3.6 16.8 - - + -
356C PHE 4.4 10.8 - - - +
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Residues in contact with MET 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C SER* 3.5 8.7 - - - +
132C VAL* 5.8 1.3 - - + -
203C ILE* 4.8 1.6 - - + -
206C GLN* 4.0 8.5 - - - +
207C LEU* 3.5 34.8 - - + -
211C PRO* 3.9 18.4 - - + -
213C VAL* 1.3 85.9 - - - +
215C LEU* 1.3 62.0 + - - +
216C PHE* 3.5 36.5 - - + -
238C LEU* 3.9 21.3 - - + -
243C ARG* 4.1 18.2 - - + -
244C ILE 2.8 17.4 + - - +
245C VAL* 3.4 2.5 - - + -
246C VAL* 2.8 31.4 + - - +
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Residues in contact with LEU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 5.6 0.7 - - + -
96C LEU* 3.7 19.7 - - + -
99C MET* 3.8 21.8 - - + -
100C SER* 3.9 28.7 - - - +
129C PHE* 3.7 36.3 - - + -
130C SER 2.8 14.1 + - - +
131C TYR* 3.5 9.1 - - + -
132C VAL* 2.8 33.3 + - - +
213C VAL* 5.2 2.0 - - + -
214C MET* 1.3 77.0 - - - +
216C PHE* 1.3 57.0 + - - +
246C VAL* 3.6 33.0 - - + -
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Residues in contact with PHE 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LEU* 3.6 6.1 - - - +
132C VAL* 3.4 42.0 - - + -
203C ILE* 3.9 26.2 - - + -
214C MET* 3.5 48.7 - - + -
215C LEU* 1.3 77.7 - - - +
217C ASP* 1.3 60.2 + - - +
219C PRO* 3.8 13.4 - - + +
235C LEU* 3.4 31.2 - - + -
238C LEU* 4.7 1.1 - - + -
245C VAL* 4.6 7.4 - - + -
246C VAL 2.8 22.4 + - - +
247C LEU* 3.5 15.4 - - + -
248C THR 3.4 17.3 + - - -
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Residues in contact with ASP 217 (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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93C THR* 4.4 10.6 - - - +
96C LEU* 4.0 11.0 - - + +
97C ASP* 3.7 17.9 - - - +
131C TYR* 3.8 12.5 + - + +
132C VAL 2.8 17.5 + - - +
133C LEU* 4.2 0.9 - - - -
134C GLN* 3.2 52.2 - - + +
199C ARG* 3.6 3.1 + - - -
215C LEU 4.3 0.2 - - - -
216C PHE* 1.3 69.9 - - - +
218C GLU* 1.3 76.1 + - - +
219C PRO* 2.9 14.0 - - - +
248C THR* 2.7 26.0 + - - +
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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
------------------------------------------------------------
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