Contacts of the helix formed by residues 346 - 364 (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 GLN 346 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341E HIS* 4.5 3.8 - - - -
344E GLY 5.5 0.2 - - - +
345E LEU* 1.3 75.2 - - - +
347E VAL* 1.3 58.5 + - - +
348E GLU* 2.8 41.3 - - + +
349E PHE* 2.8 23.7 + - - +
350E ILE* 2.9 16.1 + - - +
437E GLU* 4.0 5.0 + - - +
438E GLN* 2.9 54.2 + - - +
441E ALA* 3.7 20.4 - - + +
445E GLN* 5.6 4.0 - - - +
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Residues in contact with VAL 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E HIS* 4.2 20.6 - - + +
346E GLN* 1.3 73.4 - - - +
348E GLU* 1.3 81.7 + - + +
350E ILE* 4.1 11.4 - - + +
351E ASN* 3.0 50.1 + - - +
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Residues in contact with GLU 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346E GLN* 2.8 37.1 + - + +
347E VAL* 1.3 104.5 - - + +
349E PHE* 1.3 56.2 + - - +
352E PRO* 3.1 22.5 - - - +
434E VAL* 3.4 11.0 - - + +
437E GLU* 6.5 0.9 - - + -
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Residues in contact with PHE 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E ILE* 4.6 4.7 - - + -
313E LEU* 4.9 7.4 - - + -
345E LEU* 4.3 11.4 - - + -
346E GLN* 2.8 6.7 + - - +
348E GLU* 1.3 78.7 - - - +
350E ILE* 1.3 65.1 + - - +
351E ASN 3.4 1.3 - - - -
352E PRO* 3.3 5.3 - - + +
353E ILE* 3.3 48.3 + - + +
431E LEU* 4.7 6.1 - - + -
434E VAL* 3.8 17.5 - - + +
435E HIS* 3.8 39.7 - + + -
438E GLN* 3.3 47.6 - - + +
501E 67S 3.9 25.8 - + + -
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Residues in contact with ILE 350 (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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337E LYS* 3.9 34.3 - - + +
340E PHE* 3.7 15.5 - - + -
341E HIS* 3.4 42.6 - - + +
345E LEU* 3.8 20.0 - - + +
346E GLN 2.9 21.4 + - - +
347E VAL* 4.1 9.0 - - + +
349E PHE* 1.3 76.3 - - - +
351E ASN* 1.3 67.8 + - - +
353E ILE* 3.1 12.3 + - - +
354E PHE* 3.1 29.8 + - + -
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Residues in contact with ASN 351 (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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337E LYS* 3.0 33.9 + - - +
347E VAL* 3.0 32.2 + - - +
348E GLU* 5.5 0.2 - - - -
350E ILE* 1.3 80.5 - - - +
352E PRO* 1.3 64.1 - - + +
354E PHE* 3.4 2.3 + - - +
355E GLU* 2.9 30.7 + - - +
358E ARG* 5.1 1.4 + - - -
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Residues in contact with PRO 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348E GLU* 3.1 28.7 - - - +
349E PHE 3.3 7.4 - - - +
351E ASN* 1.3 91.7 - - + +
353E ILE* 1.3 59.5 + - - +
355E GLU* 3.6 17.0 - - - +
356E PHE* 2.8 32.7 + - - +
431E LEU* 3.5 24.0 - - + +
434E VAL* 4.2 13.9 - - + -
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Residues in contact with ILE 353 (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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313E LEU* 3.8 21.1 - - + -
316E THR* 4.0 26.5 - - + -
327E ILE* 4.4 5.4 - - + -
340E PHE* 4.7 11.9 - - + -
345E LEU* 5.1 0.7 - - + -
349E PHE* 3.3 52.0 + - + +
350E ILE* 3.1 11.6 + - - +
352E PRO* 1.3 77.9 - - - +
354E PHE* 1.3 66.5 + - + +
356E PHE* 3.4 6.7 + - - +
357E SER* 2.8 34.8 + - - -
431E LEU* 4.9 4.0 - - + -
501E 67S 3.9 14.4 - - + -
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Residues in contact with PHE 354 (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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320E TYR* 4.0 21.2 - + - -
325E GLU* 3.6 25.1 - - + -
326E CYS* 4.9 0.4 - - - -
327E ILE* 3.7 28.3 - - + -
335E TYR 4.5 1.3 - - - -
336E SER 4.0 4.5 - - - -
337E LYS* 3.6 51.6 - - + -
340E PHE* 4.1 19.1 - + - -
350E ILE* 3.1 26.4 + - + +
351E ASN 3.9 2.9 - - - +
353E ILE* 1.3 81.9 - - + +
355E GLU* 1.3 66.1 + - - +
357E SER* 3.3 6.7 + - - -
358E ARG* 3.0 43.0 + - - +
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Residues in contact with GLU 355 (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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351E ASN 2.9 16.1 + - - +
352E PRO* 3.3 20.3 + - - +
354E PHE* 1.3 76.5 - - - +
356E PHE* 1.3 59.8 + - - +
358E ARG* 3.4 27.0 + - - +
359E ALA* 3.0 27.5 + - + +
362E ARG* 5.3 0.9 + - - -
450F ASP* 3.5 28.4 - - - +
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Residues in contact with PHE 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313E LEU* 3.8 30.3 - - + -
314E LEU* 4.1 9.2 - - + -
317E ALA* 4.1 8.5 - - + -
352E PRO 2.8 19.1 + - - +
353E ILE* 3.6 6.3 - - - +
355E GLU* 1.3 76.7 - - - +
357E SER* 1.3 60.0 + - - +
359E ALA* 3.4 6.3 + - + +
360E MET* 3.0 62.9 + - + +
424E LYS* 4.5 7.4 - - + -
427E SER* 4.2 19.3 - - - -
428E LEU* 3.5 33.4 - - + -
431E LEU* 3.6 23.1 - - + -
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Residues in contact with SER 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313E LEU 5.4 0.2 + - - -
316E THR* 4.6 0.2 - - - +
317E ALA* 3.5 29.7 + - - +
320E TYR* 3.7 37.0 - - - +
327E ILE* 4.5 5.0 - - - +
353E ILE* 2.8 27.9 + - - +
354E PHE* 3.6 7.4 - - - -
355E GLU 3.3 0.2 - - - -
356E PHE* 1.3 74.4 - - - +
358E ARG* 1.3 59.6 + - - +
360E MET* 3.2 3.1 + - - +
361E ARG* 2.9 29.1 + - - +
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Residues in contact with ARG 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E TYR* 3.7 31.9 + - + +
322E HIS* 6.1 1.1 - - + -
325E GLU* 6.0 2.2 - - - -
337E LYS* 4.1 15.6 - - - +
351E ASN 5.1 1.2 + - - -
354E PHE* 3.0 35.9 + - - +
355E GLU* 3.5 32.9 - - - +
357E SER* 1.3 76.3 - - - +
359E ALA* 1.3 61.4 + - - +
361E ARG* 3.1 15.8 + - + +
362E ARG* 3.2 30.3 + - - +
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Residues in contact with ALA 359 (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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355E GLU* 3.0 16.7 + - + +
356E PHE* 3.5 13.5 - - + +
357E SER 3.2 0.2 - - - -
358E ARG* 1.3 75.6 - - - +
360E MET* 1.3 63.4 + - + +
362E ARG* 3.5 36.3 + - - +
363E LEU* 3.5 17.3 + - - +
424E LYS* 3.6 23.1 + - - +
450F ASP* 6.1 1.3 - - - +
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Residues in contact with MET 360 (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* 4.3 10.8 - - + -
317E ALA* 3.9 17.0 - - + +
356E PHE* 3.0 63.3 + - + +
357E SER 3.2 4.9 + - - +
359E ALA* 1.3 74.4 - - - +
361E ARG* 1.3 66.8 + - - +
363E LEU* 3.1 26.0 + - - +
364E GLY* 3.5 4.3 + - - -
365E LEU* 4.6 11.1 + - + +
370E TYR* 3.3 34.2 + - + +
373E LEU* 5.4 1.3 - - - -
424E LYS* 3.5 34.8 - - + +
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Residues in contact with ARG 361 (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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317E ALA 4.9 4.8 + - - +
318E ARG 4.9 5.3 + - - -
320E TYR* 2.7 36.2 + - + -
321E ASN* 4.5 1.4 - - - +
322E HIS* 3.4 50.4 + - + +
357E SER 2.9 13.6 + - - +
358E ARG* 3.1 12.8 + - + +
360E MET* 1.3 77.4 - - - +
362E ARG* 1.3 64.8 + - + +
364E GLY* 3.1 15.6 + - - +
370E TYR* 5.8 0.2 - - - -
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Residues in contact with ARG 362 (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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355E GLU 5.3 0.6 + - - -
358E ARG* 3.2 18.6 + - - +
359E ALA* 3.6 43.6 + - - +
361E ARG* 1.3 82.4 - - + +
363E LEU* 1.3 64.0 + - + +
364E GLY* 3.5 0.7 + - - -
424E LYS* 5.7 0.6 - - - +
461F GLU* 4.8 16.5 + - - -
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Residues in contact with LEU 363 (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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359E ALA 3.5 10.7 + - - +
360E MET* 3.1 16.6 + - - +
362E ARG* 1.3 82.7 - - + +
364E GLY* 1.3 59.7 + - - +
365E LEU* 3.6 25.9 + - + -
417E ARG* 3.0 31.5 + - + +
420E ARG* 4.2 29.4 - - + +
421E MET* 3.9 28.0 - - + +
424E LYS* 4.0 28.3 - - + +
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Residues in contact with GLY 364 (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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446A ASP* 5.1 2.4 - - - +
360E MET 3.5 2.2 + - - -
361E ARG* 3.1 15.5 + - - -
362E ARG 3.3 0.9 - - - -
363E LEU* 1.3 79.1 - - - +
365E LEU* 1.3 64.4 + - - +
366E ASP 3.8 0.7 + - - -
410E LYS* 4.7 1.9 - - - -
411E ARG* 4.5 9.1 + - - -
417E ARG* 2.9 15.9 + - - -
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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
------------------------------------------------------------
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