Contacts of the helix formed by residues 366 - 379 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A ARG* 3.7 16.7 - - + +
446A ASP* 4.5 6.1 - - - +
364E GLY 3.8 0.6 + - - -
365E LEU* 1.3 75.2 - - - +
367E ASP* 1.3 67.0 + - - +
368E ALA* 2.9 17.1 + - - +
369E GLU* 2.8 27.7 + - - +
370E TYR* 3.1 22.7 + - - -
406E TYR* 2.4 27.4 + - - -
410E LYS* 2.9 26.2 + - - +
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Residues in contact with ASP 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ARG* 4.2 12.5 - - - +
459A VAL 3.6 5.2 - - - +
460A HIS* 3.5 17.6 + - - +
461A GLU* 3.2 33.9 + - - +
232E VAL* 4.1 15.3 - - + +
235E GLN* 4.1 0.3 - - - +
236E LEU* 5.7 0.8 - - - +
318E ARG* 3.3 31.2 + - - +
366E ASP* 1.3 76.8 - - - +
368E ALA* 1.3 57.6 + - - +
370E TYR* 3.5 1.9 + - - -
371E ALA* 3.0 28.9 + - - +
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Residues in contact with ALA 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A PHE* 5.4 0.4 - - + -
443A ARG* 4.2 8.4 - - - +
228E ILE* 3.6 25.1 - - + +
232E VAL* 3.6 16.9 - - + +
366E ASP* 2.9 9.6 + - - +
367E ASP* 1.3 76.3 - - - +
369E GLU* 1.3 66.6 + - - +
371E ALA* 3.4 1.7 + - - +
372E LEU* 3.0 29.6 + - - +
406E TYR* 3.6 23.6 - - + +
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Residues in contact with GLU 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E LEU* 3.4 10.3 - - + -
366E ASP* 2.8 42.2 + - - +
368E ALA* 1.3 73.0 - - - +
370E TYR* 1.3 64.7 + - - +
372E LEU* 3.3 3.1 + - - +
373E LEU* 3.0 24.3 + - - +
403E LEU* 4.2 15.7 - - + -
406E TYR* 3.7 17.0 - - + -
407E THR* 3.4 10.7 + - - -
410E LYS* 3.5 15.5 - - - +
417E ARG* 2.7 41.7 + - - -
421E MET* 3.7 21.0 - - + +
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Residues in contact with TYR 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314E LEU* 3.8 38.4 - - + -
317E ALA 4.2 1.0 + - - -
318E ARG* 3.6 58.2 + - + +
360E MET* 3.3 35.8 + - + +
365E LEU* 3.4 37.9 - - + +
366E ASP 3.1 22.2 + - - -
367E ASP* 3.7 6.5 - - - +
369E GLU* 1.3 77.5 - - - +
371E ALA* 1.3 63.3 + - - +
373E LEU* 3.1 7.0 + - + +
374E ILE* 3.0 31.6 + - + +
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Residues in contact with ALA 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E ILE* 6.2 0.2 - - + -
231E LEU* 3.9 33.3 - - + +
232E VAL* 4.3 6.3 - - + +
235E GLN* 3.5 26.1 + - + +
285E PHE* 4.4 4.9 - - + -
367E ASP 3.0 16.2 + - - +
368E ALA 3.8 4.3 - - - +
369E GLU 3.4 0.2 - - - -
370E TYR* 1.3 75.1 - - - +
372E LEU* 1.3 63.5 + - - +
374E ILE* 3.2 8.3 + - - +
375E ALA* 3.0 21.5 + - - +
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Residues in contact with LEU 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E MET* 5.8 0.9 - - + -
228E ILE* 3.9 31.9 - - + -
231E LEU* 3.9 21.5 - - + -
368E ALA 3.0 21.9 + - - +
369E GLU 3.7 4.3 - - - +
370E TYR 3.2 0.2 - - - -
371E ALA* 1.3 77.5 - - - +
373E LEU* 1.3 58.9 + - - +
375E ALA* 3.2 3.3 + - - +
376E ILE* 3.0 34.7 + - + +
399E TYR* 3.7 30.5 - - + +
402E ALA* 4.2 9.2 - - + +
403E LEU* 3.7 41.1 - - + +
406E TYR* 4.4 5.2 - - + -
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Residues in contact with LEU 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E LEU* 4.5 24.7 - - + -
360E MET* 5.4 0.9 - - - -
365E LEU* 4.3 14.6 - - + -
369E GLU 3.0 14.9 + - - +
370E TYR* 3.5 5.8 - - + +
372E LEU* 1.3 74.6 - - - +
374E ILE* 1.3 65.9 + - - +
376E ILE* 3.4 9.3 + - + +
377E ASN* 3.0 25.2 + - - +
403E LEU* 4.4 16.2 - - + -
421E MET* 4.0 41.3 - - + +
422E LEU* 4.9 2.5 - - + -
424E LYS* 4.9 8.7 - - + -
425E LEU* 3.8 31.2 - - + -
428E LEU* 6.3 0.2 - - + -
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Residues in contact with ILE 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E GLN* 3.6 17.9 - - - +
285E PHE* 3.6 28.0 - - + -
311E ILE* 4.1 31.9 - - + -
314E LEU* 4.0 23.3 - - + -
315E GLU* 3.5 26.9 - - + +
318E ARG* 4.2 1.6 - - - +
370E TYR* 3.0 26.5 + - + +
371E ALA 3.4 7.0 - - - +
373E LEU* 1.3 77.4 - - - +
375E ALA* 1.3 62.4 + - - +
377E ASN* 3.3 8.1 + - - +
378E ILE* 3.1 24.0 + - + +
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Residues in contact with ALA 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E LEU* 4.2 10.3 - - + -
285E PHE* 4.8 1.8 - - + -
289E VAL* 4.4 14.4 - - + -
371E ALA 3.0 13.7 + - - +
372E LEU 3.2 8.5 + - - +
374E ILE* 1.3 77.6 - - - +
376E ILE* 1.3 62.6 + - - +
378E ILE* 3.2 13.6 + - - +
379E PHE* 3.2 29.5 + - + -
399E TYR* 4.0 28.9 - - + -
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Residues in contact with ILE 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372E LEU 3.0 22.7 + - - +
373E LEU* 3.6 9.0 - - + +
375E ALA* 1.3 75.4 - - - +
377E ASN* 1.3 63.3 + - - +
379E PHE* 3.2 11.4 + - - -
380E SER* 3.7 0.7 + - - -
396E GLN* 3.0 44.8 - - - +
399E TYR* 3.6 38.1 - - + +
400E VAL* 4.0 16.6 - - + -
403E LEU* 3.7 27.4 - - + -
422E LEU* 5.0 4.0 - - + -
425E LEU* 3.9 23.6 - - + -
491F LEU* 4.8 2.5 - - + -
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Residues in contact with ASN 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E SER* 3.4 15.1 - - - +
310E GLU* 2.7 34.6 + - - +
311E ILE* 4.1 8.1 - - + +
314E LEU* 5.1 3.4 - - + -
373E LEU 3.0 19.0 + - - +
374E ILE* 3.4 8.5 - - - +
375E ALA 3.2 0.2 - - - -
376E ILE* 1.3 79.1 - - - +
378E ILE* 1.3 58.2 + - - +
380E SER* 2.5 23.5 + - - -
383E ARG* 3.3 13.1 + - - +
425E LEU* 3.6 25.3 - - + +
428E LEU* 3.7 15.1 - - - +
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Residues in contact with ILE 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282E ILE* 5.7 1.6 - - + +
285E PHE* 4.5 13.9 - - + -
286E ALA* 4.6 16.4 - - + -
289E VAL* 4.8 4.9 - - + -
292E PHE* 4.1 27.1 - - + -
303E LEU* 3.4 29.5 - - + +
304E LEU* 5.3 4.5 - - + -
307E SER* 4.1 11.4 - - - +
311E ILE* 3.7 23.8 - - + -
374E ILE* 3.1 27.7 + - + +
375E ALA* 3.2 11.2 + - - +
377E ASN* 1.3 77.8 - - - +
379E PHE* 1.3 71.4 + - + +
380E SER* 2.9 7.8 + - - -
383E ARG* 5.1 1.0 + - - -
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Residues in contact with PHE 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289E VAL* 3.8 22.9 - - + -
290E PRO 4.5 2.7 - - - -
292E PHE* 4.0 40.2 - + + -
295E LEU* 4.3 2.5 - - + -
303E LEU* 4.4 4.9 - - + -
375E ALA* 3.2 18.3 + - - +
376E ILE 3.2 8.3 + - - -
378E ILE* 1.3 80.2 - - + +
380E SER* 1.3 59.9 + - - +
381E ALA 3.8 1.2 + - - -
392E VAL* 3.4 22.8 - - + +
393E GLU* 5.1 0.5 - - - -
395E LEU* 3.9 32.8 - - + -
396E GLN* 2.9 39.7 - - + +
399E TYR* 3.6 36.3 - + - -
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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