Contacts of the strand formed by residues 213 - 219 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B PRO* 4.2 10.8 - - + +
94B VAL 4.8 8.2 + - - +
100B LEU 3.3 2.6 + - - -
101B TRP* 3.2 44.9 - - + +
102B PHE 2.9 23.9 + - - -
211B PRO* 3.6 2.3 - - - +
212B ASP* 1.3 85.1 - - + +
214B VAL* 1.3 65.7 + - - +
215B LEU* 4.0 9.4 - - + +
240B THR* 2.5 35.7 + - - +
268B TYR* 3.4 32.7 + - - -
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PHE* 3.6 11.2 - - + -
104B VAL* 4.0 31.2 - - + -
206B LYS* 4.4 11.0 - - + +
211B PRO* 3.6 26.5 - - + +
213B GLU* 1.3 79.2 - - - +
215B LEU* 1.3 61.3 + - - +
216B LEU 3.5 2.1 + - - -
237B VAL* 4.0 14.1 - - + -
238B GLY 3.4 23.8 - - - +
239B VAL* 3.5 8.6 - - + -
240B THR* 2.9 33.2 + - + -
241B GLY 3.7 1.2 - - - +
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TRP* 4.1 25.4 - - + -
102B PHE 2.8 16.4 + - - +
103B LEU* 3.5 7.4 - - + -
104B VAL* 2.8 27.7 + - - -
118B LEU* 4.2 14.1 - - + -
213B GLU* 4.2 17.9 - - + +
214B VAL* 1.3 73.6 - - - +
216B LEU* 1.3 61.3 + - - +
217B VAL* 3.4 3.9 + - + +
241B GLY* 3.5 14.1 - - - +
242B LEU 4.5 0.4 - - - +
243B VAL* 3.7 29.6 - - + -
268B TYR* 3.6 36.3 - - + -
269B PHE* 5.1 4.5 - - + -
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL* 3.4 7.3 - - + +
105B GLY* 3.8 26.2 - - - -
214B VAL 3.5 3.8 + - - -
215B LEU* 1.3 69.2 - - - +
217B VAL* 1.3 65.4 + - - +
218B LEU* 3.7 13.4 + - + -
229B VAL* 4.9 6.5 - - + -
230B ALA* 3.8 35.4 - - + +
233B PHE* 4.2 20.6 - - + -
239B VAL* 4.0 22.4 - - + -
241B GLY 3.1 11.3 + - - +
242B LEU* 3.3 23.9 - - + +
243B VAL 3.0 23.7 + - - +
259B ALA* 5.0 0.2 - - + -
263B THR* 5.7 0.9 - - + -
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 4.1 20.9 - - + -
104B VAL 2.8 12.1 + - - +
105B GLY* 4.4 5.7 - - - -
106B LEU 4.6 0.7 + - - -
109B SER* 2.9 31.4 + - - +
110B GLY 4.0 14.6 - - - -
111B LYS* 3.8 22.4 - - + -
114B THR* 4.0 4.5 - - + +
215B LEU* 3.6 14.8 - - + +
216B LEU* 1.3 73.5 - - - +
218B LEU* 1.3 58.3 + - - +
243B VAL* 3.5 19.1 - - + +
245B THR* 3.5 30.5 - - + -
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 5.9 3.4 - - + -
109B SER* 4.7 0.4 - - - -
216B LEU* 4.6 17.9 - - + +
217B VAL* 1.3 74.9 - - - +
219B ASP* 1.3 69.8 + - - +
222B THR* 3.9 24.7 - - + +
226B ALA* 4.9 8.3 - - + +
229B VAL* 5.2 11.2 - - + -
230B ALA* 6.1 0.4 - - + -
242B LEU* 4.4 9.9 - - + -
243B VAL 2.7 14.1 + - - +
244B LEU* 3.2 14.9 - - + +
245B THR* 2.9 28.4 + - - -
255B ALA* 3.6 34.8 - - + +
256B ALA* 4.4 2.9 - - - +
259B ALA* 3.8 17.9 - - + -
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Residues in contact with ASP 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B GLY 4.5 0.7 - - - +
109B SER* 4.3 15.1 - - - +
217B VAL 4.2 1.4 + - - -
218B LEU* 1.3 75.4 - - - +
220B ALA* 1.3 62.7 + - - +
221B MET* 3.1 38.3 + - - +
222B THR* 2.8 42.1 + - - +
244B LEU* 4.3 0.8 - - - +
245B THR* 3.5 8.9 + - - +
246B LYS* 2.7 45.6 + - - +
255B ALA* 4.7 1.7 - - - +
229E ASP* 5.7 0.2 - - - +
231E VAL* 6.1 2.2 - - + -
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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