Contacts of the strand formed by residues 255 - 260 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E LEU* 4.0 4.2 - - - +
220E VAL* 3.1 14.3 - - - +
221E PRO* 3.6 9.9 - - + +
223E PHE* 3.9 22.2 - - + -
249E ALA* 3.6 30.1 - - - -
252E HIS 3.8 9.9 - - - +
254E PRO* 1.3 76.9 - - - +
256E ILE* 1.3 60.8 + - - +
257E VAL* 4.1 13.9 - - - -
299E GLY 3.1 7.0 + - - +
300E ILE* 4.2 9.9 - - - -
301E ILE 3.2 22.9 + - - -
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Residues in contact with ILE 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E LEU* 3.7 17.3 - - + -
211E ALA 3.8 3.6 - - - +
214E VAL* 3.3 35.4 - - + -
215E ALA* 3.4 26.2 - - + +
220E VAL* 3.8 1.1 - - + +
221E PRO 3.0 8.1 + - - +
222E PHE* 3.5 27.4 - - + -
223E PHE* 3.0 28.1 + - - -
255E CYS* 1.3 74.6 - - - +
257E VAL* 1.3 74.7 - - - +
258E PHE* 4.2 2.5 - - + +
301E ILE* 3.3 15.9 - - + +
303E MET* 4.5 14.4 - - + -
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Residues in contact with VAL 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E PHE* 3.8 11.4 - - + +
225E ILE* 5.6 0.4 - - + -
245E LEU* 3.5 38.1 - - + -
246E PHE* 5.0 6.5 - - + -
249E ALA* 3.8 29.4 - - + -
255E CYS* 4.1 9.2 - - - -
256E ILE* 1.3 77.5 - - - +
258E PHE* 1.3 65.7 + - - +
259E ILE* 4.2 2.7 - - + -
300E ILE* 4.5 10.3 - - + -
301E ILE 3.0 5.3 + - - +
302E VAL* 3.3 21.5 - - + +
303E MET 2.8 26.7 + - - +
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Residues in contact with PHE 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E LEU* 4.7 3.4 - - + -
207E LYS 4.4 3.6 - - - -
208E THR* 3.7 35.7 - - + -
211E ALA* 3.3 25.4 - - + -
222E PHE* 3.3 33.7 - + + -
223E PHE 2.8 11.3 + - - +
224E HIS* 4.1 12.8 - + - -
225E ILE* 2.8 33.0 + - - +
256E ILE* 4.3 1.3 - - + -
257E VAL* 1.3 75.8 - - - +
259E ILE* 1.3 61.0 + - - +
260E ASP* 3.6 24.7 - - + -
303E MET* 3.3 17.5 - - + -
304E ALA 4.5 2.5 - - - -
305E ALA* 3.8 32.3 - - + -
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Residues in contact with ILE 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E ILE* 3.5 22.2 - - + -
227E GLY* 4.8 5.8 - - - +
245E LEU* 4.9 9.2 - - + -
246E PHE* 5.3 5.4 - - + -
257E VAL* 4.8 6.7 - - + -
258E PHE* 1.3 75.5 - - - +
260E ASP* 1.3 68.9 + - - +
262E ILE* 3.8 28.1 + - + -
265E VAL* 5.0 4.9 - - + -
287E LEU* 4.7 17.7 - - + -
302E VAL* 4.1 21.5 - - + -
303E MET 2.8 13.3 + - - +
304E ALA* 3.3 5.7 - - + +
305E ALA 3.1 21.0 + - - -
322E PHE* 4.5 10.1 - - + -
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Residues in contact with ASP 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E LYS* 5.3 1.9 + - - -
208E THR* 4.1 9.2 + - - -
224E HIS* 4.1 11.1 + - - +
225E ILE 2.9 15.7 + - - +
226E SER* 4.3 9.1 + - - -
227E GLY 3.1 15.5 + - - -
258E PHE* 3.6 25.5 - - + -
259E ILE* 1.3 76.8 - - - +
261E GLU* 1.3 99.4 + - + +
262E ILE* 2.8 2.9 + - - -
305E ALA* 3.7 15.0 - - - +
1604E ADP 4.7 3.6 + - - -
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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