Contacts of the helix formed by residues 344 - 357 (chain A) in PDB entry 5U3Y
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 ASP 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A LYS* 4.9 4.5 - - - -
342A GLU 3.8 1.3 + - - +
343A LEU* 1.3 73.6 - - - +
345A ASP* 1.3 58.7 + - - +
346A SER* 2.7 24.8 + - - -
347A ASP* 2.9 16.9 + - - +
348A LEU* 3.0 32.6 + - - +
388A ASN* 2.7 28.4 + - - +
389A HIS* 4.7 2.7 + - + +
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Residues in contact with ASP 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TYR* 3.8 18.3 - - + +
186A TYR* 2.5 43.9 + - + -
187A LEU* 5.1 1.3 - - + -
193A THR* 3.6 7.6 - - - -
194A LYS* 2.8 23.1 + - - +
195A LYS* 3.0 33.9 + - - +
344A ASP* 1.3 77.1 - - - +
346A SER* 1.3 58.1 + - - +
348A LEU* 3.8 2.9 - - - +
349A ALA* 2.9 30.3 + - - +
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Residues in contact with SER 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TYR* 3.8 37.9 + - - +
344A ASP* 2.7 26.7 + - - -
345A ASP* 1.3 75.5 - - - +
347A ASP* 1.3 65.1 + - - +
349A ALA* 3.9 2.9 - - - +
350A LEU* 3.8 16.5 + - - +
384A HIS* 2.9 37.0 + - - -
388A ASN* 3.5 2.8 + - - -
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Residues in contact with ASP 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A LEU* 3.6 22.4 - - + +
344A ASP* 2.9 32.1 + - - +
346A SER* 1.3 75.6 - - - +
348A LEU* 1.3 63.2 + - - +
350A LEU* 3.2 7.3 + - - +
351A PHE* 3.0 22.0 + - - +
381A LEU* 4.1 6.0 - - + +
384A HIS* 3.1 18.9 - - - -
385A LEU* 3.6 16.4 - - + +
388A ASN* 3.0 15.9 + - - -
389A HIS* 2.5 29.4 + - - -
399A LEU* 5.8 0.4 - - + -
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A TYR* 4.1 21.1 - - + +
194A LYS* 4.1 20.0 - - + -
292A ALA 5.0 6.3 - - - +
293A MET* 5.7 4.9 - - + -
296A SER* 3.5 24.2 - - - +
338A PHE* 3.8 32.5 - - + -
343A LEU* 3.8 16.8 - - + -
344A ASP 3.0 20.2 + - - +
345A ASP 3.4 4.0 + - - +
347A ASP* 1.3 73.5 - - - +
349A ALA* 1.3 61.1 + - - +
351A PHE* 4.0 8.7 - - + -
352A ILE* 2.7 44.8 + - + +
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Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ILE* 3.5 12.5 - - + +
183A TYR* 3.9 18.8 - - + -
186A TYR* 3.7 36.9 - - + -
263A PHE* 3.6 5.3 - - - -
345A ASP 2.9 17.6 + - - +
346A SER 3.9 6.3 - - - +
347A ASP 3.3 0.4 - - - -
348A LEU* 1.3 76.7 - - - +
350A LEU* 1.3 62.8 + - + +
352A ILE* 4.9 0.2 - - - -
353A ALA* 3.1 23.6 + - - +
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Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A SER* 3.6 31.4 - - - +
182A ILE* 3.9 28.3 - - + -
346A SER 3.8 6.5 + - - +
347A ASP 3.2 6.7 + - - +
349A ALA* 1.3 77.2 - - + +
351A PHE* 1.3 68.2 + - - +
353A ALA* 3.2 5.8 + - - +
354A ALA* 3.0 20.1 + - - +
377A ILE* 3.5 14.5 - - + +
380A ALA* 3.9 18.4 - - + +
381A LEU* 3.9 19.5 - - + +
384A HIS* 3.5 43.7 - - + -
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Residues in contact with PHE 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ALA* 3.9 15.0 - - + -
338A PHE* 3.9 27.1 - + - -
343A LEU* 5.0 2.9 - - + -
347A ASP 3.0 17.0 + - - +
348A LEU* 3.1 11.9 + - + +
350A LEU* 1.3 77.2 - - - +
352A ILE* 1.3 70.7 + - + +
354A ALA* 3.2 6.6 + - - +
355A ILE* 3.2 41.4 + - + +
381A LEU* 4.4 10.9 - - + +
399A LEU* 3.5 50.0 - - + -
402A LYS* 4.2 3.4 - - + -
403A MET* 3.6 31.8 - - + +
406A LEU* 3.9 9.6 - - + -
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Residues in contact with ILE 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A TYR* 5.2 3.4 - - + -
190A PHE* 4.9 0.9 - - + -
260A LEU* 3.7 28.7 - - + -
263A PHE* 3.8 15.9 - - + -
289A ALA* 3.7 22.4 - - + +
292A ALA* 3.8 18.4 - - + -
293A MET* 3.7 32.8 - - + -
348A LEU* 2.7 32.0 + - + +
349A ALA* 4.0 3.8 - - - +
351A PHE* 1.3 74.0 - - + +
353A ALA* 1.3 67.0 + - - +
355A ILE* 3.0 14.9 + - + +
356A ILE* 3.1 14.6 + - + +
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ILE* 4.1 17.7 - - + -
263A PHE* 4.1 8.2 - - + -
267A ILE* 4.2 15.5 - - + -
349A ALA 3.1 19.0 + - - +
350A LEU 3.2 5.6 + - - +
352A ILE* 1.3 76.8 - - - +
354A ALA* 1.3 58.6 + - - +
356A ILE* 3.3 3.6 + - - +
357A LEU* 3.0 35.1 + - - +
377A ILE* 3.9 20.4 - - + +
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Residues in contact with ALA 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A LEU 3.0 12.9 + - - +
351A PHE* 3.5 9.0 - - - +
352A ILE 3.2 0.4 - - - -
353A ALA* 1.3 76.0 - - - +
355A ILE* 1.3 62.0 + - - +
357A LEU 3.4 19.4 - - - +
358A CYS* 4.2 0.9 - - - +
374A GLN* 4.1 13.4 + - + +
377A ILE* 3.7 19.5 - - + +
378A LEU* 3.9 15.9 - - + -
381A LEU* 5.3 0.9 - - + -
403A MET* 3.6 24.4 - - + +
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Residues in contact with ILE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A GLY 3.6 13.5 - - - +
288A GLU* 3.6 42.6 - - + +
289A ALA* 3.9 8.7 - - + +
292A ALA* 4.3 4.0 - - + -
351A PHE* 3.2 41.6 + - + +
352A ILE* 3.0 11.1 + - + +
354A ALA* 1.3 77.1 - - - +
356A ILE* 1.3 62.6 + - - +
358A CYS* 3.4 7.7 - - - +
361A ARG* 2.9 26.3 + - - +
403A MET* 4.4 15.7 - - + -
406A LEU* 3.7 19.1 - - + -
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LEU* 4.7 8.5 - - + -
263A PHE* 5.2 6.5 - - + -
264A ALA* 4.3 8.1 - - + -
270A PHE* 4.1 27.6 - - + -
281A LEU* 3.4 30.4 - - + +
282A LEU* 4.3 20.9 - - + -
285A GLY* 3.7 30.3 - - - +
286A VAL* 4.2 4.9 - - + +
289A ALA* 4.0 13.9 - - + -
352A ILE* 3.1 24.1 + - + +
353A ALA* 3.9 4.7 - - - +
355A ILE* 1.3 77.0 - - - +
357A LEU* 1.3 60.5 + - + +
358A CYS* 3.0 7.4 + - - +
361A ARG* 4.9 0.9 + - - -
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ILE* 4.7 14.1 - - + -
269A SER* 4.7 3.8 - - - +
270A PHE* 4.0 30.1 - - + -
273A LEU* 4.2 10.5 - - + -
281A LEU* 3.9 20.0 - - + -
353A ALA* 3.0 15.9 + - - +
354A ALA 3.4 4.8 - - - +
356A ILE* 1.3 75.6 - - + +
358A CYS* 1.3 58.5 + - - +
370A VAL* 3.9 9.9 - - + -
373A ILE* 3.6 29.6 - - + -
374A GLN* 3.0 31.0 - - - +
377A ILE* 3.3 31.2 - - + -
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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