Contacts of the strand formed by residues 255 - 260 (chain D) in PDB entry 2CEA
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 CYS 255 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180D LEU* 4.5 2.6 - - - +
220D VAL* 3.3 12.9 - - - +
221D PRO* 3.6 20.2 - - + +
223D PHE* 4.1 20.9 - - + -
249D ALA* 3.6 33.0 - - - -
252D HIS 4.2 3.8 - - - +
253D ALA* 4.3 2.7 - - - -
254D PRO* 1.3 77.8 - - - +
256D ILE* 1.3 67.8 + - - +
257D VAL* 4.2 0.8 + - - -
299D GLY 3.0 7.7 + - - +
300D ILE* 3.6 9.3 - - - +
301D ILE 3.2 22.2 + - - -
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Residues in contact with ILE 256 (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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180D LEU* 3.7 27.6 - - + -
211D ALA 4.2 1.1 - - - +
214D VAL* 3.8 11.2 - - + -
215D ALA* 3.2 44.0 - - + +
220D VAL* 4.2 2.2 - - + -
221D PRO 3.1 5.7 + - - +
222D PHE* 3.6 19.9 - - + -
223D PHE* 2.9 29.0 + - - +
255D CYS* 1.3 79.4 - - - +
257D VAL* 1.3 74.6 + - - +
301D ILE* 3.2 17.3 - - + +
303D MET* 4.0 22.9 - - + -
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Residues in contact with VAL 257 (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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223D PHE* 3.8 15.3 - - + -
225D ILE* 4.6 2.2 - - + -
245D LEU* 4.1 33.9 - - + -
246D PHE* 5.2 3.8 - - + -
249D ALA* 4.0 27.4 - - + -
255D CYS* 4.2 3.5 + - - -
256D ILE* 1.3 76.8 - - - +
258D PHE* 1.3 58.6 + - - +
259D ILE* 4.1 9.9 - - + -
300D ILE* 5.0 4.0 - - + -
301D ILE 3.0 5.9 + - - +
302D VAL* 3.1 29.4 - - + +
303D MET 2.6 33.8 + - - +
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Residues in contact with PHE 258 (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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199D LEU* 4.7 2.7 - - + -
207D LYS 4.4 2.9 - - - -
208D THR* 3.5 39.9 - - + -
211D ALA* 3.7 21.8 - - + -
222D PHE* 3.7 26.7 - + + -
223D PHE 2.8 16.0 + - - +
224D HIS* 3.9 17.7 - + - -
225D ILE* 2.8 34.0 + - - +
256D ILE* 4.0 1.3 + - + -
257D VAL* 1.3 75.5 - - - +
259D ILE* 1.3 59.2 + - - +
260D ASP* 3.8 22.2 - - + -
303D MET 3.1 17.9 - - - -
304D ALA 4.3 2.0 - - - -
305D ALA* 3.7 36.1 - - + -
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Residues in contact with ILE 259 (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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225D ILE* 3.6 13.5 - - + -
226D SER 5.0 1.1 - - - -
227D GLY* 4.4 10.8 - - - +
230D PHE* 6.3 1.3 - - + -
245D LEU* 4.9 10.5 - - + -
246D PHE* 5.2 0.7 - - + -
257D VAL* 4.1 13.2 - - + -
258D PHE* 1.3 77.4 - - - +
260D ASP* 1.3 68.4 + - - +
262D ILE* 3.8 29.9 - - + +
265D VAL* 5.1 4.0 - - + -
287D LEU* 4.2 30.1 - - + -
302D VAL* 4.1 18.6 - - + -
303D MET 2.7 12.4 + - - +
304D ALA* 3.3 4.0 - - + +
305D ALA 3.1 23.5 + - - +
322D PHE* 5.3 0.4 - - + -
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Residues in contact with ASP 260 (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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207D LYS* 5.4 3.8 + - - -
208D THR* 4.2 8.8 + - - -
224D HIS* 4.3 9.8 + - - +
225D ILE 2.9 18.3 + - - +
226D SER* 4.2 10.4 + - - -
227D GLY* 2.6 29.2 + - - -
258D PHE* 3.8 22.6 + - + -
259D ILE* 1.3 72.8 - - - +
261D GLU* 1.3 74.7 + - + +
262D ILE 3.1 1.7 + - - -
305D ALA* 3.8 16.5 - - - +
1608D ADP 5.0 2.4 + - - -
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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