Contacts of the strand formed by residues 251 - 256 (chain E) in PDB entry 3EXF
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 251 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E LEU* 4.3 11.4 - - + -
189E CYS 3.5 2.4 + - - +
190E ILE* 3.9 10.8 - - + -
191E PHE* 3.2 23.0 + - - +
220E ILE* 3.5 9.0 - - - -
221E PRO* 3.6 14.4 - - + +
223E LEU* 4.2 12.8 - - + -
239E PHE* 4.2 21.5 - - + -
240E ALA* 3.6 28.9 - - + +
243E TYR* 3.8 26.9 - - + -
244E CYS* 3.9 13.9 - - - -
250E PRO* 1.3 75.3 - - - +
252E LEU* 1.3 73.2 + - - +
253E MET 4.1 0.2 + - - -
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Residues in contact with LEU 252 (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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165E TYR* 3.2 23.1 - - - +
179E TYR* 3.8 22.2 - - + +
191E PHE* 3.5 32.8 - - + +
193E CYS* 5.4 4.3 - - + -
213E TYR 3.5 23.1 - - - +
214E TYR* 3.9 20.0 - - - +
217E GLY* 4.3 7.6 - - - +
220E ILE* 4.1 14.6 - - + +
221E PRO 2.7 17.5 + - - +
222E GLY* 3.3 0.6 - - - -
223E LEU* 2.7 39.5 + - - +
251E ILE* 1.3 72.2 - - - +
253E MET* 1.3 57.2 + - - +
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Residues in contact with MET 253 (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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75E LEU* 3.9 12.8 - - + -
162E LEU* 6.1 0.7 - - + -
190E ILE* 4.7 7.9 - - + -
191E PHE 2.9 12.8 + - - +
192E ILE* 3.0 21.6 - - + +
193E CYS* 2.9 24.2 + - - -
223E LEU* 3.3 19.7 - - + -
225E VAL* 3.8 15.0 - - + -
233E VAL* 4.4 2.9 - - + +
236E ALA* 4.0 24.7 - - + +
237E THR* 3.5 31.9 - - + +
240E ALA* 4.1 11.0 - - - -
252E LEU* 1.3 76.1 - - - +
254E GLU* 1.3 57.4 + - - +
255E LEU* 3.8 20.4 - - + -
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Residues in contact with GLU 254 (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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193E CYS* 3.5 10.8 - - + +
195E ASN* 3.4 32.9 + - + -
211E THR 4.3 2.1 - - - +
212E ASP 3.8 0.2 - - - -
213E TYR* 2.8 43.8 + - + -
214E TYR* 2.9 29.3 + - + +
223E LEU 3.1 7.5 + - - +
224E ARG* 3.2 30.7 + - + +
225E VAL* 2.7 33.4 + - - +
252E LEU* 4.2 0.8 - - + -
253E MET* 1.3 70.5 - - - +
255E LEU* 1.3 59.6 + - - +
256E GLN* 3.5 4.6 + - + -
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Residues in contact with LEU 255 (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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71E CYS* 3.4 45.1 - - + -
75E LEU* 4.2 21.5 - - + -
192E ILE* 4.3 15.9 - - + -
193E CYS 3.0 11.0 + - - +
194E GLU* 4.0 8.6 - - + -
195E ASN* 3.1 28.1 + - - +
225E VAL* 3.8 11.9 - - + -
227E GLY* 4.3 2.0 - - - -
233E VAL* 4.4 14.4 - - + -
253E MET* 3.8 33.4 - - + -
254E GLU* 1.3 76.3 - - - +
256E GLN* 1.3 60.8 + - - +
257E THR* 3.6 1.5 + - + +
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Residues in contact with GLN 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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195E ASN* 3.6 14.2 - - - +
224E ARG* 2.8 47.2 + - + +
225E VAL 3.1 20.1 + - - +
226E ASP* 4.4 4.2 - - - +
227E GLY* 2.7 28.3 + - - +
228E MET* 3.9 4.6 + - - +
254E GLU* 3.5 17.1 + - - +
255E LEU* 1.3 71.3 - - - +
257E THR* 1.3 59.0 + - - +
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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