Contacts of the helix formed by residues 316 - 328 (chain E) in PDB entry 4E2I
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 TYR 316 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276E TYR* 3.6 32.5 - + + -
279E GLU* 3.5 51.6 + - + +
280E THR* 4.6 5.7 - - + +
295E PHE* 4.6 4.3 - - + -
311E PRO 3.3 24.5 - - - -
312E SER* 3.9 17.3 - - - +
313E HIS 3.1 4.0 + - - +
315E LYS* 1.3 102.3 + - + +
317E HIS* 1.3 63.1 + - - +
318E GLU 3.5 2.2 - - - -
319E LYS* 3.3 24.1 + - + -
320E HIS* 3.0 29.1 + - + +
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Residues in contact with HIS 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294E GLU 3.7 16.8 - - - -
295E PHE* 3.3 40.3 + + + -
298E SER 3.6 8.9 - - - -
299E PHE* 3.4 29.4 + + + +
302E CYS* 3.9 4.7 - - - -
305E CYS* 5.4 0.7 - - - -
313E HIS* 2.9 16.8 + - - +
314E TYR* 4.5 3.7 - - - -
315E LYS 3.9 0.2 - - - -
316E TYR* 1.3 77.6 - - - +
318E GLU* 1.3 55.7 + - + +
319E LYS 3.0 0.2 - - - -
320E HIS 3.1 0.9 + - - -
321E TYR* 2.6 62.4 + + + +
700E ZN 2.5 28.8 - - - -
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Residues in contact with GLU 318 (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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299E PHE* 3.6 51.0 - - + -
305E CYS* 5.1 7.1 - - - -
314E TYR 4.8 10.7 + - - +
315E LYS 5.6 0.4 - - - -
316E TYR 5.0 0.2 - - - +
317E HIS* 1.3 77.6 - - + +
319E LYS* 1.3 59.4 + - - +
321E TYR* 4.1 6.3 + - - +
322E ALA 5.3 0.5 + - - -
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Residues in contact with LYS 319 (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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272E LEU* 4.9 8.8 - - + +
275E GLU* 3.2 37.3 + - - -
279E GLU* 5.5 5.4 - - - -
315E LYS 4.8 4.0 - - - +
316E TYR* 3.5 32.0 - - + +
317E HIS 3.0 0.4 - - - -
318E GLU* 1.3 81.9 - - - +
320E HIS* 1.3 79.0 + - + +
321E TYR 3.6 0.2 - - - -
322E ALA* 5.3 2.5 + - - +
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Residues in contact with HIS 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E LEU* 3.2 36.9 + - + +
275E GLU* 3.9 17.3 - - - -
276E TYR* 3.2 40.7 - + + +
292E TYR* 3.4 26.9 + + + +
295E PHE* 4.6 6.3 - + + -
316E TYR* 3.0 27.5 + - + +
317E HIS 3.4 1.3 - - - -
319E LYS* 1.3 102.1 + - + +
321E TYR* 1.3 59.2 + - - +
322E ALA* 3.3 2.7 - - - -
323E ASN* 3.6 4.6 + - - +
324E ALA* 3.0 31.6 + - - +
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Residues in contact with TYR 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E PHE 3.2 21.5 - - - +
296E GLN* 4.6 2.0 - - - -
297E TYR 2.9 36.7 + - - -
298E SER* 3.8 11.2 - - - -
299E PHE* 3.6 28.5 - + + -
300E GLU* 4.3 8.9 + - - +
317E HIS* 2.6 34.1 + - + +
318E GLU* 4.1 5.3 - - - +
319E LYS 3.6 1.2 - - - -
320E HIS* 1.3 74.1 - - - +
322E ALA* 1.3 64.6 + - - +
325E ALA* 3.2 29.6 + - + +
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Residues in contact with ALA 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E LEU* 5.8 3.8 - - + -
318E GLU 5.3 0.4 + - - -
319E LYS 5.3 2.2 + - - +
320E HIS* 4.3 1.1 - - - +
321E TYR* 1.3 85.6 - - - +
323E ASN* 1.3 59.5 + - - +
325E ALA* 3.5 14.0 - - - +
326E ILE* 3.9 13.6 - - - +
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Residues in contact with ASN 323 (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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267E GLN 4.8 0.5 - - - +
268E VAL* 3.5 9.3 - - - +
269E SER* 2.6 50.7 + - - -
272E LEU* 3.5 23.2 - - + +
273E VAL* 3.2 12.3 - - - +
292E TYR* 2.8 29.2 + - - +
320E HIS 3.6 4.8 + - - +
322E ALA* 1.3 74.6 - - - +
324E ALA* 1.3 53.7 - - - +
325E ALA 3.0 2.0 - - - -
326E ILE* 2.9 9.7 + - - +
327E PHE* 2.7 34.0 + - - +
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Residues in contact with ALA 324 (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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292E TYR* 3.9 20.3 + - + +
295E PHE* 3.1 36.1 - - + +
296E GLN* 3.2 19.3 - - + +
320E HIS 3.0 19.8 + - - +
323E ASN* 1.3 77.6 - - - +
325E ALA* 1.3 59.9 + - - +
327E PHE* 3.2 19.5 + - - +
328E ALA 3.3 5.4 + - - -
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Residues in contact with ALA 325 (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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295E PHE 4.2 0.2 + - - -
296E GLN* 4.3 12.6 - - - +
321E TYR* 3.2 29.2 + - + +
322E ALA* 3.5 10.1 - - - +
323E ASN 3.0 0.6 - - - -
324E ALA* 1.3 79.8 - - - +
326E ILE* 1.3 61.7 + - + +
328E ALA* 4.0 6.1 - - - +
329E ASP* 4.0 13.0 - - - +
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Residues in contact with ILE 326 (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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266E LYS* 4.1 20.0 - - - +
267E GLN* 3.7 27.6 - - - +
268E VAL* 3.5 24.4 - - + +
322E ALA 3.9 15.0 - - - +
323E ASN* 2.9 7.7 + - - +
325E ALA* 1.3 76.9 - - + +
327E PHE* 1.3 65.8 + - - +
328E ALA 3.1 2.5 - - - -
329E ASP* 3.0 22.2 + - + +
330E SER 3.5 4.2 + - - -
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Residues in contact with PHE 327 (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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268E VAL* 3.9 8.9 - - + +
273E VAL* 4.8 2.0 - - + -
289E LEU* 3.7 10.1 - - + -
292E TYR* 3.7 30.5 - + + -
293E LEU* 3.5 33.0 - - + -
296E GLN* 5.1 0.2 - - - -
323E ASN* 2.7 16.4 + - - +
324E ALA* 3.2 15.9 + - - +
326E ILE* 1.3 78.8 - - - +
328E ALA* 1.3 60.7 + - - +
330E SER* 3.1 18.0 + - - -
333E GLN* 3.3 40.3 - - + +
336E ILE* 3.5 42.6 - - + -
337E CYS* 3.5 16.2 - - - -
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Residues in contact with ALA 328 (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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270D TRP* 5.3 1.0 - - - +
271D LYS* 4.0 27.3 + - + +
274D THR* 5.6 0.2 + - - -
339D GLN* 5.4 0.2 - - - +
296E GLN* 3.2 48.0 + - + +
324E ALA 3.3 2.8 + - - -
325E ALA 4.0 5.6 - - - +
326E ILE 3.1 0.8 - - - -
327E PHE* 1.3 78.5 - - - +
329E ASP* 1.3 67.2 + - - +
330E SER 3.3 3.5 + - - +
333E GLN* 3.0 19.1 - - - +
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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