Contacts of the helix formed by residues 278 - 294 (chain E) in PDB entry 3IFS
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 LEU 278 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E MSE 4.0 22.0 - - + -
273E ASN* 3.9 28.0 + - + -
274E TYR 5.4 0.4 - - - +
275E GLU* 2.9 19.5 + - + +
277E ALA* 1.3 80.7 - - + +
279E GLN* 1.3 64.0 + - - +
280E TYR 3.3 2.0 - - - -
281E PHE* 3.1 20.1 + - + +
282E ALA* 3.2 12.6 + - - +
330E LEU* 4.2 26.7 - - + +
332E VAL* 4.1 22.0 - - + -
386E ILE* 4.6 6.3 - - + -
389E LEU* 3.8 30.1 - - + -
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Residues in contact with GLN 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E GLU* 5.4 2.2 - - - +
273E ASN* 4.1 2.1 - - - +
276E PRO* 3.0 20.5 + - - +
277E ALA 3.3 1.0 - - - -
278E LEU* 1.3 76.9 - - - +
280E TYR* 1.3 83.7 + - + +
282E ALA* 3.3 14.6 + - - +
283E GLU* 3.5 16.4 + - + +
306E ASN* 4.0 35.0 + - - +
279F GLN* 3.7 24.7 - - - +
280F TYR* 4.8 11.4 + - - -
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Residues in contact with TYR 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E TYR* 3.8 10.5 + + - -
87E LEU* 4.3 13.8 - - + +
90E ARG* 3.4 57.4 + - + +
91E ALA* 3.8 26.6 - - - +
94E GLU* 3.1 28.2 + - + +
277E ALA 4.5 3.0 + - - -
278E LEU 3.3 0.4 - - - -
279E GLN* 1.3 97.6 - - + +
281E PHE* 1.3 66.0 + - - +
283E GLU* 3.0 35.9 + - + +
284E TRP* 3.0 10.2 + - - +
279F GLN* 4.6 13.2 + - - -
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Residues in contact with PHE 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E ALA* 3.6 14.5 + - + +
95E MSE 3.4 33.2 - - + -
271E LEU* 4.6 2.7 - - + -
277E ALA 5.1 0.4 + - - -
278E LEU* 3.1 13.9 + - + +
280E TYR* 1.3 77.4 - - - +
282E ALA* 1.3 58.0 + - - +
284E TRP* 3.0 36.9 + + - +
285E TRP* 2.9 29.7 + - + +
330E LEU* 4.1 20.6 - - + -
394E PHE* 4.1 11.9 - + - -
397E LEU* 3.7 27.6 - - + -
398E VAL* 4.2 15.9 - - + -
401E PHE* 3.8 28.3 - + - -
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Residues in contact with ALA 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E LEU* 3.7 26.2 - - + +
273E ASN* 5.1 7.2 - - - +
278E LEU 3.2 10.5 + - - +
279E GLN* 3.5 12.1 - - - +
280E TYR 3.1 0.6 - - - -
281E PHE* 1.3 77.8 - - - +
283E GLU* 1.3 56.7 + - - +
285E TRP* 3.3 1.7 + - - +
286E LYS* 2.9 36.1 + - - +
304E SER* 3.8 25.6 - - - +
306E ASN* 5.7 1.1 - - - +
330E LEU* 6.1 0.4 - - + -
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Residues in contact with GLU 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E LEU* 3.5 31.4 - - + +
279E GLN* 3.5 16.8 + - + +
280E TYR* 3.0 26.7 + - + +
282E ALA* 1.3 77.0 - - - +
284E TRP* 1.3 61.6 + - - +
286E LYS* 2.7 39.3 + - - +
287E GLN 3.1 18.4 + - - -
304E SER* 4.2 2.8 + - - -
306F ASN* 5.8 2.7 + - - -
310F ASP* 4.5 16.6 - - - +
313F SER* 4.8 4.7 + - - -
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Residues in contact with TRP 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E GLY* 6.4 1.6 - - - -
87E LEU* 4.2 15.6 - - + +
88E GLY* 3.6 26.6 - - - -
91E ALA* 4.3 11.9 - - + -
208E ARG* 3.9 18.9 + - - -
211E VAL* 4.2 15.9 - - + +
280E TYR 3.0 9.8 + - - +
281E PHE* 3.0 44.5 + + - +
283E GLU* 1.3 77.7 - - - +
285E TRP* 1.3 71.5 - - - +
287E GLN* 3.3 6.2 + - - +
288E LEU* 3.0 48.6 + - + +
394E PHE* 6.2 1.6 - + - -
398E VAL* 3.7 44.2 - - + -
401E PHE* 3.9 14.6 - + + -
402E GLU* 4.1 12.6 - - + -
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Residues in contact with TRP 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254E TYR* 3.5 10.4 + - - -
258E ARG* 4.8 1.1 - - - -
269E GLU* 3.4 51.6 - - + -
271E LEU* 3.6 34.6 - - + +
281E PHE* 2.9 14.8 + - + +
282E ALA* 3.5 7.2 - - - +
283E GLU 3.3 0.2 - - - -
284E TRP* 1.3 85.4 - - + +
286E LYS* 1.3 84.1 + - + +
288E LEU* 3.3 3.3 + - - +
289E PHE* 3.0 61.0 + + - +
302E PRO* 3.6 24.2 - - + -
303E SER 3.3 22.0 - - - -
401E PHE* 3.6 28.2 - + + -
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Residues in contact with LYS 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E ALA 2.9 17.8 + - - +
283E GLU* 2.7 45.1 + - - +
284E TRP 3.3 0.2 - - - -
285E TRP* 1.3 92.9 - - + +
287E GLN* 1.3 60.0 + - - +
290E GLY* 2.8 30.1 + - - -
302E PRO* 3.7 27.2 - - + +
303E SER* 4.0 7.7 - - - +
304E SER* 3.2 25.7 + - - +
304F SER 5.3 6.9 + - - -
313F SER* 4.1 4.1 - - - +
314F LEU* 4.2 20.1 - - + +
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Residues in contact with GLN 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E GLY* 3.3 19.6 - - - +
84E GLY* 3.4 17.9 + - - +
87E LEU* 3.4 14.7 - - + +
207E GLY* 5.4 0.4 - - - -
208E ARG* 3.8 21.9 - - + +
283E GLU 3.1 11.4 + - - +
284E TRP* 3.7 9.5 - - + +
286E LYS* 1.3 77.2 - - - +
288E LEU* 1.3 64.6 + - - +
291E GLU* 2.9 43.6 + - - +
312F HIS 2.9 26.2 + - - +
313F SER* 3.6 24.8 - - - -
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Residues in contact with LEU 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E ARG* 3.8 26.2 - - + +
209E PHE* 3.8 38.6 - - + -
284E TRP* 3.0 46.6 + - + +
285E TRP* 3.6 4.5 - - - +
286E LYS 3.3 0.2 - - - -
287E GLN* 1.3 75.9 - - - +
289E PHE* 1.3 67.2 + - + +
292E SER* 2.6 36.2 + - - -
401E PHE* 3.6 32.8 - - + +
402E GLU* 3.9 3.4 - - + +
405E CYS* 3.4 8.6 - - - -
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Residues in contact with PHE 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254E TYR* 3.9 19.5 - + - -
258E ARG* 3.4 48.7 - - - +
285E TRP* 3.0 50.8 + + + +
288E LEU* 1.3 91.2 - - + +
290E GLY* 1.3 60.7 + - - +
293E GLU* 2.9 40.8 + - - +
300E ILE 5.4 2.9 - - - +
302E PRO* 4.6 9.9 - - + -
401E PHE* 3.9 13.5 - + - -
404E ALA 4.5 0.7 - - - -
405E CYS* 3.7 36.8 - - + -
408E SER* 4.5 3.1 - - - -
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Residues in contact with GLY 290 (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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286E LYS 2.8 23.1 + - - -
289E PHE* 1.3 73.3 - - - +
291E GLU* 1.3 55.9 + - - +
294E GLY* 3.0 28.2 + - - -
300E ILE 5.4 0.4 - - - -
302E PRO* 3.6 21.7 - - - +
313F SER 4.3 6.1 - - - -
314F LEU* 4.7 1.1 - - - -
317F TYR* 3.8 17.9 + - - +
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Residues in contact with GLU 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E ARG* 2.8 37.8 + - - +
287E GLN* 2.9 39.8 + - + +
290E GLY* 1.3 73.4 - - - +
292E SER* 1.3 62.0 + - - +
294E GLY 4.5 0.2 + - - -
295E LYS* 2.9 24.6 + - - -
418E ASP 3.7 0.7 - - - +
419E GLN* 4.3 10.7 - - + +
422E VAL* 4.3 16.8 - - - +
311F LEU 4.8 0.2 - - - +
312F HIS* 3.5 16.5 - - - +
313F SER 3.4 20.1 + - - +
316F GLN* 3.6 22.6 + - + +
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Residues in contact with SER 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E ARG* 2.9 17.4 + - - +
209E PHE* 4.1 4.9 - - - -
288E LEU 2.6 24.5 + - - -
289E PHE 4.0 1.1 - - - -
291E GLU* 1.3 79.9 - - - +
293E GLU* 1.3 60.5 + - - +
295E LYS* 2.5 22.1 + - - +
405E CYS* 3.3 24.2 - - - -
414E VAL* 3.8 3.1 - - - +
415E ASN 3.4 7.1 - - - +
416E PRO* 3.1 27.6 + - - +
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Residues in contact with GLU 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E ARG* 2.8 28.2 + - - -
259E ASN* 4.8 0.3 + - - -
289E PHE* 2.9 20.7 + - + +
292E SER* 1.3 84.7 - - - +
294E GLY* 1.3 57.9 + - - +
295E LYS* 2.7 16.5 + - - +
298E LYS 3.4 8.9 - - - +
299E GLY* 3.8 6.6 - - - -
300E ILE* 4.7 12.2 + - - +
405E CYS* 5.1 1.3 - - - -
408E SER* 2.4 43.5 + - - +
409E GLY* 3.2 14.8 + - - +
412E LEU* 3.8 26.8 - - + +
414E VAL* 4.2 5.4 - - - +
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Residues in contact with GLY 294 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E PHE 4.2 0.2 + - - -
290E GLY 3.0 14.2 + - - -
291E GLU 4.5 0.2 + - - -
292E SER 3.8 0.8 - - - -
293E GLU* 1.3 71.8 - - - +
295E LYS* 1.3 57.9 + - - -
298E LYS 3.5 5.8 - - - -
316F GLN* 3.0 34.9 + - - +
317F TYR* 3.4 30.4 - - - -
320F GLU 3.7 3.3 - - - -
321F GLY* 3.9 7.6 - - - -
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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
------------------------------------------------------------
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