Contacts of the helix formed by residues 366 - 379 (chain A) in PDB entry 5I4V
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 366 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A GLY 3.8 0.4 + - - -
365A LEU* 1.3 73.9 - - - +
367A ASP* 1.3 66.2 + - - +
368A ALA* 2.9 16.2 + - - +
369A GLU* 2.8 28.3 + - - +
370A TYR* 3.1 22.2 + - - -
406A TYR* 2.4 28.5 + - - -
410A LYS* 2.9 27.1 + - - +
417A ARG* 4.6 0.2 - - - +
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Residues in contact with ASP 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A VAL* 4.1 19.8 - - + +
235A GLN* 4.1 0.2 - - - +
236A LEU* 5.6 7.9 - - - +
318A ARG* 3.3 35.0 + - - +
366A ASP* 1.3 76.6 - - - +
368A ALA* 1.3 58.0 + - - +
370A TYR* 3.5 1.8 + - - -
371A ALA* 3.0 28.9 + - - +
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Residues in contact with ALA 368 (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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228A ILE* 3.6 25.5 - - + +
232A VAL* 3.6 16.5 - - + +
366A ASP* 2.9 9.2 + - - +
367A ASP* 1.3 77.2 - - - +
369A GLU* 1.3 64.1 + - - +
371A ALA* 3.5 1.7 + - - +
372A LEU* 3.0 30.2 + - - +
406A TYR* 3.6 23.8 - - + +
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Residues in contact with GLU 369 (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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365A LEU* 3.4 10.2 - - + -
366A ASP* 2.8 43.1 + - - +
368A ALA* 1.3 75.8 - - - +
370A TYR* 1.3 63.4 + - - +
372A LEU* 3.3 3.0 + - - +
373A LEU* 3.0 24.6 + - - +
403A LEU* 4.2 7.0 - - + -
406A TYR* 3.7 15.5 - - + -
407A THR* 3.2 21.8 - - + +
410A LYS* 3.5 15.9 - - - +
417A ARG* 2.7 42.1 + - - -
421A MET* 3.7 19.3 - - + +
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Residues in contact with TYR 370 (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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314A LEU* 3.8 38.8 - - + -
317A ALA 4.3 1.2 + - - -
318A ARG* 3.6 57.6 + - + +
360A MET* 3.3 38.4 + - + +
361A ARG* 5.7 0.2 - - - -
365A LEU* 3.4 37.7 - - + +
366A ASP 3.1 21.4 + - - -
367A ASP* 3.7 6.7 - - - +
369A GLU* 1.3 77.4 - - - +
371A ALA* 1.3 63.5 + - - +
373A LEU* 3.1 7.5 + - + +
374A ILE* 3.0 29.9 + - + +
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Residues in contact with ALA 371 (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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228A ILE* 6.2 0.2 - - + -
231A LEU* 3.9 33.7 - - + +
232A VAL* 4.3 5.6 - - + +
235A GLN* 3.5 27.3 + - + +
285A PHE* 4.4 4.3 - - + -
367A ASP 3.0 16.6 + - - +
368A ALA 3.8 4.3 - - - +
370A TYR* 1.3 75.3 - - - +
372A LEU* 1.3 63.1 + - - +
374A ILE* 3.2 7.5 + - - +
375A ALA* 3.0 21.7 + - - +
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Residues in contact with LEU 372 (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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227A MET* 4.4 1.1 - - + -
228A ILE* 3.9 31.9 - - + -
231A LEU* 3.9 20.2 - - + -
368A ALA 3.0 21.9 + - - +
369A GLU 3.6 4.5 - - - +
371A ALA* 1.3 75.9 - - - +
373A LEU* 1.3 58.8 + - - +
375A ALA* 3.2 3.6 + - - +
376A ILE* 3.0 34.3 + - - +
399A TYR* 3.8 30.7 - - + +
402A ALA* 4.2 9.9 - - + +
403A LEU* 3.7 41.3 - - + +
406A TYR* 4.4 4.9 - - + -
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Residues in contact with LEU 373 (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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314A LEU* 4.5 17.3 - - + -
360A MET* 4.3 24.5 - - + -
365A LEU* 4.3 5.2 - - + -
369A GLU 3.0 15.0 + - - +
370A TYR* 3.1 5.8 + - + +
372A LEU* 1.3 74.5 - - - +
374A ILE* 1.3 66.6 + - - +
376A ILE* 3.4 8.6 + - + +
377A ASN* 3.0 25.0 + - - +
403A LEU* 4.4 15.5 - - + -
421A MET* 4.0 39.7 - - + +
422A LEU* 4.9 1.8 - - + -
424A LYS* 4.9 2.9 - - + -
425A LEU* 3.8 32.1 - - + -
428A LEU* 6.1 0.4 - - + -
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Residues in contact with ILE 374 (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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235A GLN* 3.6 13.5 - - - +
285A PHE* 3.6 27.6 - - + -
311A ILE* 4.1 33.3 - - + +
314A LEU* 3.9 23.6 - - + -
315A GLU* 3.2 30.1 - - + +
318A ARG* 4.2 2.9 - - - +
370A TYR* 3.0 24.9 + - + +
371A ALA 3.4 6.3 - - - +
373A LEU* 1.3 76.9 - - - +
375A ALA* 1.3 62.4 + - - +
377A ASN* 3.3 7.8 + - - +
378A ILE* 3.1 23.5 + - + +
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Residues in contact with ALA 375 (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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231A LEU* 4.2 11.0 - - + -
285A PHE* 4.8 2.0 - - + -
289A VAL* 4.3 16.8 - - + -
371A ALA 3.0 11.8 + - - +
372A LEU 3.2 8.5 + - - +
374A ILE* 1.3 77.4 - - - +
376A ILE* 1.3 62.6 + - - +
378A ILE* 3.2 13.6 + - - +
379A PHE* 3.2 29.5 + - - -
399A TYR* 4.0 26.5 - - + -
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Residues in contact with ILE 376 (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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372A LEU 3.0 22.2 + - - +
373A LEU* 3.6 9.2 - - + +
374A ILE 3.3 0.2 - - - -
375A ALA* 1.3 75.4 - - - +
377A ASN* 1.3 62.9 + - - +
379A PHE* 3.1 11.5 + - - -
380A SER* 3.7 0.9 + - - -
396A GLN* 3.0 44.4 - - - +
399A TYR* 3.6 38.8 - - + +
400A VAL* 4.0 16.8 - - + -
403A LEU* 3.7 27.1 - - + -
422A LEU* 5.0 4.7 - - + -
425A LEU* 3.9 23.8 - - + -
491B LEU* 4.8 2.2 - - + -
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Residues in contact with ASN 377 (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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307A SER* 3.4 15.4 - - - +
310A GLU* 2.7 36.2 + - - +
311A ILE* 4.1 6.3 - - + +
314A LEU* 5.1 3.4 - - + -
373A LEU 3.0 17.3 + - - +
374A ILE* 3.4 9.2 - - - +
376A ILE* 1.3 76.4 - - - +
378A ILE* 1.3 58.9 + - - +
380A SER* 2.5 23.7 + - - -
383A ARG* 3.2 14.0 + - - +
425A LEU* 3.6 27.3 - - + +
428A LEU* 3.7 15.3 - - - +
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Residues in contact with ILE 378 (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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282A ILE* 5.7 2.0 - - + -
285A PHE* 4.5 13.9 - - + -
286A ALA* 4.6 16.2 - - + -
289A VAL* 4.8 5.2 - - + -
292A PHE* 4.1 26.9 - - + -
303A LEU* 3.4 29.1 - - + +
304A LEU* 4.7 5.6 - - + -
307A SER* 4.1 10.5 - - - +
311A ILE* 3.7 25.6 - - + -
374A ILE* 3.1 26.2 + - + +
375A ALA* 3.4 11.4 - - - +
376A ILE 3.2 0.2 - - - -
377A ASN* 1.3 78.0 - - - +
379A PHE* 1.3 71.4 + - + +
380A SER* 2.9 7.3 + - - +
383A ARG* 5.1 1.2 + - - -
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Residues in contact with PHE 379 (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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289A VAL* 3.8 23.6 - - + -
290A PRO 4.4 2.7 - - - -
292A PHE* 4.0 39.9 - + + -
295A LEU* 4.3 2.5 - - + -
303A LEU* 4.4 4.7 - - + -
375A ALA 3.2 18.1 + - - +
376A ILE 3.1 7.5 + - - -
378A ILE* 1.3 81.5 - - + +
380A SER* 1.3 58.4 + - - +
381A ALA 3.8 1.0 + - - -
392A VAL* 3.4 23.8 - - + +
393A GLU* 5.0 0.5 - - - -
395A LEU* 3.9 35.0 - - + -
396A GLN* 2.9 38.9 - - + +
399A TYR* 3.6 37.0 - + - -
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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