Contacts of the strand formed by residues 235 - 241 (chain B) in PDB entry 5E0T
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 LEU 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B ILE* 4.4 8.1 - - + -
205B LEU* 6.4 0.2 - - - -
207B PHE* 3.4 47.7 - - + -
212B LEU* 3.9 26.0 - - + -
227B LEU* 4.5 10.1 - - + -
228B ILE 3.7 20.9 - - - +
229B MET* 4.2 21.1 - - + +
230B SER 5.6 0.2 - - - +
233B VAL 3.6 2.2 + - - -
234B PRO* 1.3 73.9 - - - +
236B VAL* 1.3 72.8 + - - +
237B VAL* 4.1 14.6 - - + -
249B TYR 3.4 0.9 - - - +
250B TYR* 3.2 7.3 - - - -
251B LEU* 2.9 34.8 + - + +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLN* 4.4 19.3 - - + +
226B THR 3.4 3.5 - - - +
227B LEU* 3.5 3.1 - - - -
228B ILE* 2.9 57.1 + - + +
233B VAL* 5.6 1.3 - - + -
234B PRO 4.0 6.5 - - - +
235B LEU* 1.3 78.5 - - - +
237B VAL* 1.3 74.2 + - - +
238B GLU* 4.4 4.0 - - + -
248B LYS* 4.2 26.5 - - + -
249B TYR 3.3 7.2 - - - +
250B TYR* 3.6 27.6 - - + -
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE* 4.1 11.7 - - + -
212B LEU* 4.3 6.3 - - + -
215B PHE* 4.0 28.7 - - + -
225B VAL* 3.5 26.9 - - + -
226B THR 3.6 1.8 - - - -
227B LEU* 3.9 18.4 - - + -
235B LEU* 4.1 20.2 - - + -
236B VAL* 1.3 77.7 - - - +
238B GLU* 1.3 57.9 + - - +
239B TYR* 3.8 13.7 - - + +
248B LYS* 3.5 1.2 - - - -
249B TYR* 2.7 48.0 + - + +
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Residues in contact with GLU 238 (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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131B GLN* 5.2 0.7 + - - -
224B THR 4.4 0.2 - - - +
225B VAL* 3.5 8.0 - - - +
226B THR* 3.0 47.2 + - + +
228B ILE* 4.1 18.9 - - + +
236B VAL* 4.4 5.6 - - + -
237B VAL* 1.3 76.4 - - - +
239B TYR* 1.3 66.4 + - - +
240B LYS* 3.5 40.1 + - + +
246B HIS* 3.9 2.7 - - + +
247B LEU 3.6 2.5 - - - +
248B LYS* 3.6 37.8 - - + +
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Residues in contact with TYR 239 (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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141B SER* 4.2 8.0 + - - -
144B PHE* 4.0 4.7 - - - -
215B PHE 3.5 18.1 + - - -
216B THR* 3.4 31.7 - - - +
218B ALA* 3.5 31.0 - - + +
219B THR* 4.0 19.9 + - - -
221B LEU* 4.8 5.8 - - + -
222B SER* 4.6 9.2 - - - -
224B THR 4.3 9.0 - - - -
225B VAL* 3.6 31.4 - - + +
237B VAL* 3.8 16.9 - - + +
238B GLU* 1.3 75.3 - - - +
240B LYS* 1.3 66.3 + - - +
241B ILE* 3.5 1.4 + - - +
246B HIS* 3.3 2.3 - - - +
247B LEU* 2.9 39.7 + - + +
249B TYR* 3.8 16.2 - + - -
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Residues in contact with LYS 240 (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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53B ARG* 4.6 10.3 - - - +
138B LYS* 6.2 2.2 - - - +
221B LEU 3.5 5.5 - - - +
222B SER* 3.4 29.3 + - - +
224B THR* 4.8 2.5 + - - +
238B GLU* 3.5 26.1 + - + +
239B TYR* 1.3 72.4 - - - +
241B ILE* 1.3 61.0 - - - +
242B ALA 3.7 6.9 + - - +
245B GLY 3.8 8.4 + - - +
246B HIS* 3.2 34.4 + - + +
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Residues in contact with ILE 241 (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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11B ILE* 3.8 28.3 - - + -
15B VAL* 4.3 9.0 - - + -
50B LEU* 3.8 19.7 - - + -
52B LEU* 4.0 15.3 - - + -
221B LEU* 4.0 26.0 - - + -
239B TYR 3.5 2.9 + - - +
240B LYS* 1.3 73.2 - - - +
242B ALA* 1.3 75.0 + - + +
244B MET* 2.9 22.4 + - + -
245B GLY* 2.7 20.3 + - - +
246B HIS* 3.5 31.2 - - - +
247B LEU* 3.8 5.8 - - + +
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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