Contacts of the strand formed by residues 213 - 219 (chain C) in PDB entry 2CNW
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 GLU 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C PRO* 4.5 9.1 - - - +
94C VAL 4.9 6.6 + - - +
96C LYS* 4.8 7.8 + - - +
100C LEU 3.4 2.8 + - - -
101C TRP* 3.2 42.0 - - + +
102C PHE 2.9 23.3 + - - -
211C PRO* 3.5 2.6 - - - +
212C ASP* 1.3 85.2 - - + +
214C VAL* 1.3 66.2 + - - +
215C LEU* 4.0 10.3 - - + -
240C THR* 2.5 32.6 + - - +
268C TYR* 3.0 37.6 + - - -
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Residues in contact with VAL 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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102C PHE* 3.7 8.7 - - + -
104C VAL* 3.9 32.5 - - + -
206C LYS* 4.8 7.4 - - + -
211C PRO* 3.7 24.5 - - + +
213C GLU* 1.3 78.1 - - - +
215C LEU* 1.3 61.3 + - - +
237C VAL* 4.0 19.7 - - + -
238C GLY 3.4 24.9 - - - +
239C VAL* 3.5 10.1 - - + +
240C THR* 2.9 28.8 + - + +
241C GLY 3.6 2.4 + - - -
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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
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101C TRP* 3.9 29.4 - - + -
102C PHE 2.8 18.5 + - - +
103C LEU* 3.6 9.0 - - + -
104C VAL* 2.9 30.8 + - - +
118C LEU* 4.1 13.0 - - + -
213C GLU* 4.1 15.7 - - + +
214C VAL* 1.3 74.9 - - - +
216C LEU* 1.3 59.3 + - - +
217C VAL* 3.3 3.2 + - - +
241C GLY* 3.5 15.0 - - - +
242C LEU* 4.3 0.7 - - - +
243C VAL* 4.1 26.2 - - + -
268C TYR* 3.8 35.4 - - + -
269C PHE* 5.4 3.6 - - + -
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Residues in contact with LEU 216 (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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104C VAL* 3.6 5.6 - - + +
105C GLY* 3.8 26.5 - - - -
214C VAL 3.7 2.2 + - - -
215C LEU* 1.3 68.6 - - - +
217C VAL* 1.3 62.5 + - - +
218C LEU* 3.3 16.4 + - + -
229C VAL* 4.9 4.9 - - + -
230C ALA* 3.7 37.0 - - + +
233C PHE* 4.0 21.8 - - + -
239C VAL* 3.8 27.4 - - + -
241C GLY 2.9 11.5 + - - +
242C LEU* 3.4 24.0 - - + +
243C VAL 3.0 21.0 + - - +
259C ALA* 5.0 0.9 - - + -
263C THR* 5.6 1.3 - - + -
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Residues in contact with VAL 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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103C LEU* 3.9 24.2 - - + -
104C VAL 2.8 12.3 + - - +
105C GLY* 4.2 5.7 - - - -
106C LEU 4.6 0.9 + - - -
109C SER* 2.9 32.9 + - - +
110C GLY 3.9 16.4 - - - -
111C LYS* 3.6 21.3 - - + -
114C THR* 4.2 3.6 - - + +
215C LEU 3.7 12.1 - - - +
216C LEU* 1.3 71.9 - - - +
218C LEU* 1.3 58.0 + - - +
243C VAL* 3.4 18.8 - - + +
245C THR* 3.6 29.4 - - + -
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Residues in contact with LEU 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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106C LEU* 5.5 5.2 - - + -
109C SER* 4.7 0.4 - - - -
216C LEU* 3.3 19.2 + - + +
217C VAL* 1.3 74.7 - - - +
219C ASP* 1.3 68.4 + - - +
222C THR* 4.0 24.2 - - + +
226C ALA* 4.7 9.9 - - + +
229C VAL* 5.2 11.2 - - + -
230C ALA* 6.2 0.2 - - + -
242C LEU* 4.5 8.3 - - + -
243C VAL 2.7 14.1 + - - +
244C LEU* 3.4 11.2 - - + +
245C THR* 2.9 27.8 + - - -
255C ALA* 3.6 35.0 - - + +
256C ALA* 4.4 4.3 - - - +
259C ALA* 3.7 19.1 - - + -
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Residues in contact with ASP 219 (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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108C GLY 4.4 1.7 - - - +
109C SER* 4.3 14.5 - - - +
217C VAL 4.2 1.0 + - - -
218C LEU* 1.3 76.2 - - - +
220C ALA* 1.3 67.6 + - - +
221C MET* 3.1 36.0 + - - +
222C THR* 2.6 36.8 + - - +
244C LEU* 4.5 1.5 - - - +
245C THR* 3.3 9.0 - - - +
246C LYS* 2.8 44.1 + - - +
255C ALA* 4.7 1.2 - - - +
229F ASP* 5.3 2.3 - - - +
231F VAL* 6.0 4.2 - - + +
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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