Contacts of the strand formed by residues 350 - 359 (chain C) in PDB entry 5AEW
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 350 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215C VAL* 3.5 8.5 - - - +
216C ILE* 2.9 49.5 + - + +
218C CYS* 3.5 20.9 - - - +
220C TRP* 3.4 40.4 - - + +
223C ALA* 4.2 10.8 - - + -
342C TRP* 3.8 31.4 - - + -
343C HIS 3.2 15.7 - - - +
344C PRO* 4.3 1.6 - - + -
345C ARG* 4.3 1.6 - - - +
349C GLU* 1.3 81.6 - - - +
351C GLU* 1.3 65.3 + - - +
352C VAL* 4.2 9.0 - - + -
392C TRP* 4.8 0.2 - - + -
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Residues in contact with GLU 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C TYR* 5.5 0.7 - - - -
214C TRP 3.3 5.8 - - - +
215C VAL* 4.1 16.5 - - + +
341C THR 3.6 2.1 - - - +
342C TRP* 3.7 1.9 - - - -
343C HIS* 2.9 40.8 + - + +
345C ARG* 3.0 37.0 + - + +
349C GLU* 5.0 1.4 - - - +
350C ILE* 1.3 78.6 - - - +
352C VAL* 1.3 62.9 + - - +
353C TRP* 3.0 32.6 + - + +
178D THR* 4.0 19.2 + - + +
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Residues in contact with VAL 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C GLN 3.3 2.1 - - - +
213C LYS* 3.2 6.8 - - - -
214C TRP* 2.7 65.5 + - + +
216C ILE* 3.5 36.8 - - + -
340C ARG* 4.1 18.4 - - + +
341C THR 3.9 2.7 - - - -
342C TRP* 3.7 35.4 - - + -
350C ILE* 4.2 2.9 - - + -
351C GLU* 1.3 74.3 - - - +
353C TRP* 1.3 62.8 + - - +
354C ALA* 4.4 1.8 - - + -
385C GLU* 5.5 0.2 - - - +
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Residues in contact with TRP 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LEU 6.0 0.2 - - - -
74C LEU* 5.6 2.7 - - + -
75C ALA 3.4 21.8 - - - -
76C THR* 3.3 34.1 - - - -
77C TYR* 3.9 24.5 - + - -
211C MET* 3.8 24.7 - - + +
212C GLN 3.4 4.3 - - - -
213C LYS* 3.5 50.0 - - + +
340C ARG* 3.2 3.8 - - - -
341C THR* 3.1 34.2 + - - +
343C HIS* 3.5 26.8 - + - +
351C GLU* 3.0 30.1 + - + -
352C VAL* 1.3 79.1 - - - +
354C ALA* 1.3 59.9 + - - +
355C PHE* 4.6 2.6 - - - -
178D THR* 5.3 1.6 - - - -
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Residues in contact with ALA 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C MET* 3.5 4.6 - - - +
212C GLN* 2.8 63.6 + - + +
214C TRP* 4.2 8.7 - - + -
338C THR* 4.5 1.8 - - - +
339C ILE 3.3 9.9 - - - +
340C ARG* 3.7 24.9 - - + +
352C VAL* 4.4 0.9 - - + -
353C TRP* 1.3 73.9 - - - +
355C PHE* 1.3 63.2 + - - +
79D LEU* 4.3 0.2 - - - +
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Residues in contact with PHE 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU* 4.3 15.3 - - + -
61C LEU 5.5 0.4 - - - -
62C GLY* 3.9 27.4 - - - -
63C HIS* 4.0 6.1 - - + -
66C HIS* 3.7 21.3 - + - +
171C LEU* 4.7 1.6 - - + -
207C ALA* 4.0 5.4 - - + -
208C ILE 5.0 1.8 - - - +
210C GLY 3.8 15.5 - - - +
211C MET* 3.5 29.8 - - + -
212C GLN* 5.7 0.7 - - - -
338C THR* 3.6 4.0 + - - -
339C ILE* 2.8 69.1 + - + -
341C THR* 5.5 1.1 - - - -
353C TRP 4.6 3.4 - - - -
354C ALA* 1.3 75.4 - - - +
356C THR* 1.3 67.4 + - - +
357C LEU* 3.7 22.0 - - + -
79D LEU* 3.9 7.4 - - - -
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Residues in contact with THR 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C ALA* 3.4 5.7 - - - +
208C ILE* 2.8 55.2 + - + -
212C GLN* 5.3 1.7 + - - -
336C ILE 4.6 0.9 - - - +
337C ASN* 3.4 9.0 - - + +
338C THR* 4.3 0.9 + - - -
355C PHE* 1.3 78.9 + - - +
357C LEU* 1.3 72.9 + - - +
370C TYR* 4.4 4.3 - - + +
374C ASN* 2.9 46.6 + - + +
79D LEU* 3.8 18.2 - - - +
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Residues in contact with LEU 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C HIS* 3.5 26.7 - - + +
171C LEU* 4.2 11.9 - - + -
197C MET* 3.8 18.4 - - + -
198C LEU* 3.8 29.4 - - + -
205C THR* 4.2 14.4 - - + +
206C VAL 3.5 3.6 - - - +
207C ALA* 3.9 13.9 - - - -
337C ASN* 3.0 39.5 + - + +
339C ILE* 3.9 13.0 - - + -
355C PHE* 3.7 18.2 - - + -
356C THR* 1.3 76.7 - - - +
358C VAL* 1.3 68.8 + - - +
370C TYR* 4.3 0.5 - - - -
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Residues in contact with VAL 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C THR* 3.3 6.7 - - - -
206C VAL* 2.9 53.2 + - + +
208C ILE* 3.8 23.6 - - + -
337C ASN* 4.5 4.3 - - - +
357C LEU* 1.3 80.8 - - - +
359C ASP* 1.3 65.3 + - - +
362C ALA* 5.2 2.2 - - + -
367C LYS* 3.9 31.9 - - + -
370C TYR* 3.6 36.6 - - + -
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Residues in contact with ASP 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C MET 4.4 2.1 - - - +
200C ARG* 4.0 28.6 + - - +
201C THR* 4.0 15.7 + - - +
204C GLY 3.8 6.8 - - - +
205C THR* 4.0 13.7 - - - +
295C TYR* 2.5 40.8 + - - +
296C TRP* 5.8 0.2 - - - -
337C ASN* 5.2 5.1 + - - +
358C VAL* 1.3 72.0 - - - +
360C ALA* 1.3 66.5 + - - +
361C ASP* 3.1 13.8 + - - +
362C ALA* 3.1 15.4 + - + +
367C LYS* 3.4 10.7 - - - -
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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