Contacts of the strand formed by residues 213 - 219 (chain D) in PDB entry 3CII
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 ILE 213 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A GLN* 4.1 14.6 + - - -
185D PRO* 4.4 6.5 - - + -
205D ALA* 4.7 5.6 - - + -
208D PHE* 3.8 39.0 - - + -
211D ALA 3.1 3.9 + - - +
212D GLU* 1.3 82.0 + - - +
214D THR* 1.3 80.4 + - - +
215D LEU* 5.0 3.8 - - + +
233D THR* 4.5 4.2 + - + +
243D LYS* 3.7 29.7 + - + +
261D VAL* 4.1 16.8 - - + -
262D GLN 3.4 16.2 - - - +
263D HIS* 3.5 27.4 - - + -
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Residues in contact with THR 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLN* 3.9 19.6 + - + +
144A GLU* 5.8 3.6 - - - +
212D GLU* 3.5 10.6 + - - -
213D ILE* 1.3 84.6 + - - +
215D LEU* 1.3 66.4 + - - +
216D THR* 4.0 13.0 + - + +
243D LYS* 5.8 0.2 - - - -
260D HIS 4.2 0.7 - - - +
262D GLN* 3.1 41.2 + - + +
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Residues in contact with LEU 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLN* 4.4 8.5 + - - +
145A GLN* 4.3 3.8 - - - +
203D CYS* 4.3 6.7 - - + +
204D TRP 5.4 1.6 - - - +
205D ALA* 4.2 12.6 - - + -
213D ILE* 5.1 6.2 - - + +
214D THR* 1.3 76.5 - - - +
216D THR* 1.3 65.5 + - - +
230D LEU* 4.5 12.8 - - + +
243D LYS* 3.6 46.6 - - + +
244D TRP* 4.2 0.7 - - - -
245D ALA* 3.9 29.4 - - + +
259D CYS* 4.6 10.5 - - - -
260D HIS 3.8 5.6 - - - +
261D VAL* 3.8 38.1 - - + -
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Residues in contact with THR 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLN* 3.4 33.7 - - + +
214D THR* 4.6 14.8 + - + +
215D LEU* 1.3 81.2 - - - +
217D TRP* 1.3 66.5 + - - +
218D GLN* 4.8 6.5 + - - -
245D ALA* 5.6 1.1 - - - -
259D CYS* 3.7 9.7 - - - -
260D HIS* 3.1 54.2 + - - +
262D GLN* 6.0 1.2 - - - +
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Residues in contact with TRP 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLN* 4.6 5.1 + - - -
189D VAL* 4.3 11.4 - - + -
201D LEU* 3.2 35.0 - - + -
203D CYS* 3.7 22.7 - - + -
216D THR* 1.3 75.5 - - - +
218D GLN* 1.3 62.1 + - - +
223D GLY 4.3 1.2 - - - +
224D HIS 3.1 20.5 - - - +
225D THR* 4.1 10.2 - - + +
228D THR* 3.7 22.0 - - + +
245D ALA* 3.1 30.6 + - + +
246D ALA 3.4 23.2 - - - -
247D VAL* 3.6 20.0 - - + -
257D TYR* 4.3 17.5 - - + -
258D THR* 3.4 33.2 - - - -
259D CYS* 3.6 24.2 - - + -
272D LEU 5.2 0.4 - - - -
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Residues in contact with GLN 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D THR* 4.8 6.8 + - - +
217D TRP* 1.3 76.2 - - - +
219D GLN* 1.3 57.5 + - - +
221D GLY* 3.0 23.6 + - - +
222D GLU 4.5 2.9 - - - +
223D GLY* 3.3 21.3 - - - +
224D HIS 4.4 0.2 - - - -
257D TYR* 4.7 3.1 - - - -
258D THR* 2.7 51.5 + - - +
260D HIS* 3.2 55.7 + - + +
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Residues in contact with GLN 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D GLN* 1.3 71.9 - - - +
220D ASP* 1.3 69.0 + - - +
221D GLY 2.5 30.3 + - - -
222D GLU* 3.7 12.4 + - - +
223D GLY* 3.3 8.1 + - - +
224D HIS* 3.9 41.3 + - + +
256D ARG* 3.3 11.0 - - + +
257D TYR* 3.6 37.2 + - + +
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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