Contacts of the helix formed by residues 352 - 365 (chain A) in PDB entry 5AVL
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 ASN 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A GLN 3.7 1.4 + - - -
351A LEU* 1.3 75.9 - - - +
353A ASP* 1.3 68.9 + - - +
354A ALA* 3.1 7.3 + - - +
355A GLU* 2.8 36.5 + - - +
356A PHE* 2.9 24.3 + - - -
392A TYR* 3.3 18.1 + - - -
396A HIS* 3.1 33.9 + - + -
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Residues in contact with ASP 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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218A VAL* 3.9 22.7 - - + +
221A GLN* 4.6 1.9 - - - +
222A GLN* 4.1 13.7 - - - +
304A ARG* 3.2 31.6 + - - +
352A ASN* 1.3 79.0 - - - +
354A ALA* 1.3 51.6 + - - +
356A PHE* 3.1 2.9 + - - +
357A ALA* 2.8 35.9 + - - +
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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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214A ILE* 3.8 16.7 - - + +
218A VAL* 3.7 15.6 - - + +
352A ASN* 3.1 2.2 + - - -
353A ASP* 1.3 77.3 - - - +
355A GLU* 1.3 62.3 + - - +
357A ALA* 3.6 1.4 + - - +
358A LEU* 3.2 31.2 + - + +
392A TYR* 3.2 43.3 - - + +
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Residues in contact with GLU 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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350A GLN 4.3 0.2 - - - +
351A LEU* 3.4 19.7 - - + -
352A ASN* 2.8 40.9 + - - +
354A ALA* 1.3 74.3 - - - +
356A PHE* 1.3 63.8 + - - +
358A LEU* 3.4 2.9 + - - +
359A LEU* 3.0 27.5 + - - +
389A LEU* 4.3 7.6 - - + +
392A TYR* 3.7 17.4 - - + -
393A VAL* 4.1 5.5 - - + +
396A HIS* 2.4 37.5 + - - +
397A HIS* 3.9 1.7 + - - -
407A MET* 3.6 38.9 - - - +
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Residues in contact with PHE 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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300A LEU* 3.6 39.5 - - + -
303A SER* 3.9 11.0 - - - -
304A ARG* 3.6 60.8 - - + +
346A MET* 4.4 10.5 - - + -
351A LEU* 3.5 45.3 - - + -
352A ASN 2.9 23.6 + - - -
353A ASP 3.5 6.5 - - - +
355A GLU* 1.3 73.6 - - - +
357A ALA* 1.3 65.9 + - - +
359A LEU* 3.2 6.1 + - + +
360A ILE* 3.0 30.5 + - + +
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Residues in contact with ALA 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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214A ILE* 6.4 0.2 - - + -
217A LEU* 3.8 37.2 - - + +
218A VAL* 4.4 6.3 - - + +
221A GLN* 4.2 17.0 + - - +
271A PHE* 4.1 10.4 - - + -
353A ASP 2.8 18.1 + - - +
354A ALA 4.0 3.8 - - - +
356A PHE* 1.3 73.7 - - - +
358A LEU* 1.3 59.3 + - + +
360A ILE* 3.3 4.8 + - - +
361A ALA* 2.9 27.7 + - - +
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Residues in contact with LEU 358 (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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213A MET* 4.6 0.9 - - - -
214A ILE* 3.9 33.4 - - + -
217A LEU* 4.1 11.4 - - + -
354A ALA 3.2 20.6 + - - +
355A GLU 3.8 0.2 - - - +
356A PHE 3.2 0.2 - - - -
357A ALA* 1.3 76.9 - - + +
359A LEU* 1.3 57.5 + - - +
361A ALA* 3.0 4.5 + - - +
362A ILE* 2.8 34.8 + - + +
385A TYR* 4.0 38.6 - - + +
388A ALA* 4.3 4.9 - - + -
389A LEU* 3.7 46.9 - - + +
392A TYR* 4.7 4.0 - - + -
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Residues in contact with LEU 359 (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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300A LEU* 4.1 25.4 - - + -
346A MET* 4.8 5.4 - - + -
351A LEU* 3.6 31.0 - - + -
355A GLU 3.0 16.5 + - - +
356A PHE* 3.2 5.3 + - - +
358A LEU* 1.3 74.6 - - - +
360A ILE* 1.3 53.5 + - - +
362A ILE* 3.3 6.7 + - + +
363A SER* 2.8 35.7 + - - -
389A LEU* 4.2 22.4 - - + -
407A MET* 3.8 29.6 - - + +
408A LEU* 4.7 0.4 - - - +
410A LYS* 5.2 0.4 - - + -
411A LEU* 3.8 33.0 - - + +
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Residues in contact with ILE 360 (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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221A GLN* 3.7 16.2 - - - +
271A PHE* 3.6 23.1 - - + -
297A VAL* 3.8 26.0 - - + -
300A LEU* 3.8 26.5 - - + -
301A GLU* 3.6 28.9 - - + +
304A ARG* 4.6 4.0 - - - +
356A PHE* 3.0 16.9 + - + +
357A ALA 3.4 7.4 - - - +
359A LEU* 1.3 72.5 - - - +
361A ALA* 1.3 66.7 + - - +
363A SER* 3.2 3.9 + - - -
364A ILE* 2.9 36.6 + - + +
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Residues in contact with ALA 361 (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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217A LEU* 4.1 3.6 - - + -
271A PHE* 4.5 0.4 - - - -
275A LEU* 3.7 36.1 - - + -
357A ALA 2.9 14.1 + - - +
358A LEU 3.4 7.9 - - - +
360A ILE* 1.3 78.0 - - - +
362A ILE* 1.3 62.4 + - - +
364A ILE* 3.2 2.8 + - - +
365A PHE* 3.0 28.3 + - - -
385A TYR* 3.9 25.8 - - + -
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Residues in contact with ILE 362 (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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358A LEU 2.8 28.3 + - - +
359A LEU* 3.7 11.2 - - + +
361A ALA* 1.3 71.2 - - - +
363A SER* 1.3 63.0 + - - +
365A PHE* 3.2 7.0 + - - -
382A GLN* 2.6 48.8 + - + +
385A TYR* 3.9 23.1 - - + +
386A VAL* 3.8 28.0 - - + -
389A LEU* 3.9 26.9 - - + -
408A LEU* 4.4 4.5 - - + -
411A LEU* 3.6 23.8 - - + -
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Residues in contact with SER 363 (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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293A SER* 4.2 3.5 + - - -
296A GLU* 3.0 34.9 + - - +
297A VAL* 4.8 3.3 - - - +
300A LEU* 4.6 8.1 - - - -
359A LEU 2.8 21.1 + - - -
360A ILE* 3.5 7.9 - - - -
362A ILE* 1.3 75.3 - - - +
364A ILE* 1.3 57.2 + - - +
366A SER* 2.5 26.4 + - - -
369A ARG* 2.9 15.1 + - - -
411A LEU* 4.5 13.9 - - - +
414A LEU* 4.9 0.9 - - - -
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Residues in contact with ILE 364 (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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268A ILE* 4.9 7.4 - - + -
271A PHE* 4.2 8.1 - - + -
272A ALA* 4.6 8.5 - - + -
275A LEU* 3.8 26.7 - - + -
278A PHE* 3.8 31.4 - - + -
289A LEU* 3.6 25.9 - - + +
290A LEU* 4.7 4.9 - - + -
293A SER* 3.6 21.5 - - - +
297A VAL* 4.1 10.3 - - + -
360A ILE* 2.9 39.4 + - + +
361A ALA 3.5 6.5 - - - +
363A SER* 1.3 73.2 - - - +
365A PHE* 1.3 60.4 + - + +
366A SER* 3.0 7.3 + - - -
369A ARG* 4.9 1.0 + - - -
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Residues in contact with PHE 365 (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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275A LEU* 3.8 17.9 - - + -
276A PRO 3.9 8.3 - - - -
278A PHE* 3.6 45.1 - + + -
281A LEU* 4.0 9.0 - - + -
289A LEU* 3.8 12.6 - - + -
361A ALA 3.0 24.1 + - - +
362A ILE 3.2 0.8 + - - +
364A ILE* 1.3 74.3 - - + +
366A SER* 1.3 59.6 + - - +
367A ALA 3.7 0.5 + - - -
378A VAL* 3.6 21.9 - - + +
381A LEU* 3.7 28.3 - - + -
382A GLN* 2.9 35.2 + - + +
385A TYR* 3.4 37.5 - + - -
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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