Contacts of the helix formed by residues 278 - 294 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F MSE 3.1 44.6 - - + -
273F ASN* 3.8 28.6 + - + -
274F TYR 5.3 0.2 - - - +
275F GLU* 3.0 23.7 + - + +
277F ALA* 1.3 76.5 - - - +
279F GLN* 1.3 63.2 + - - +
280F TYR 3.4 1.6 - - - -
281F PHE* 3.2 12.6 + - + +
282F ALA* 3.1 20.8 + - - +
330F LEU* 4.3 24.7 - - + +
332F VAL* 4.2 24.5 - - + -
386F ILE* 4.7 4.9 - - + -
389F LEU* 4.4 8.7 - - + -
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Residues in contact with GLN 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E GLN* 3.7 24.5 - - - +
280E TYR* 4.6 12.9 + - - -
94F GLU* 5.4 3.1 - - - +
273F ASN* 4.1 2.1 - - - +
276F PRO* 3.1 20.6 + - - +
277F ALA 3.2 1.0 - - - -
278F LEU* 1.3 76.0 - - - +
280F TYR* 1.3 83.9 + - + +
282F ALA* 3.2 15.5 + - - +
283F GLU* 3.3 18.3 + - + +
306F ASN* 4.1 32.6 + - - +
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Residues in contact with TYR 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E GLN* 4.8 10.2 + - - -
86F TYR* 3.3 19.2 + + - -
87F LEU* 4.1 26.2 - - + +
90F ARG* 3.5 51.1 + - + +
91F ALA* 3.7 26.6 - - - +
94F GLU* 3.4 27.0 + - + +
277F ALA 4.5 2.6 + - - -
278F LEU 3.4 0.2 - - - -
279F GLN* 1.3 95.8 - - + +
281F PHE* 1.3 66.0 + - - +
282F ALA 3.1 1.8 - - - -
283F GLU* 3.0 16.5 + - + +
284F TRP 3.0 18.7 + - - -
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Residues in contact with PHE 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ALA* 3.6 16.3 + - + +
95F MSE 3.5 31.4 - - + -
271F LEU* 4.6 2.2 - - + -
277F ALA 5.1 0.2 + - - -
278F LEU* 3.2 13.6 + - + +
280F TYR* 1.3 77.0 - - - +
282F ALA* 1.3 57.1 + - - +
284F TRP* 3.2 28.5 + + - +
285F TRP* 2.9 29.8 + - + +
330F LEU* 3.9 22.2 - - + -
394F PHE* 4.1 13.0 - + - -
397F LEU* 3.6 31.9 - - + -
398F VAL* 4.3 17.0 - - + -
401F PHE* 3.7 30.7 - + - -
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Residues in contact with ALA 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271F LEU* 3.9 22.4 - - + +
273F ASN* 5.0 7.4 - - - +
278F LEU 3.1 10.8 + - - +
279F GLN* 3.3 12.8 - - - +
280F TYR 3.1 0.8 - - - -
281F PHE* 1.3 78.0 - - - +
283F GLU* 1.3 56.5 - - + +
285F TRP* 3.2 3.1 + - - +
286F LYS* 2.9 35.4 + - - +
304F SER* 3.8 27.4 - - - +
306F ASN* 5.5 1.3 - - - +
330F LEU* 5.9 0.9 - - + +
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Residues in contact with GLU 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E ASN* 5.8 3.8 + - - -
310E ASP* 4.4 18.5 - - - +
313E SER* 5.0 4.7 + - - -
87F LEU* 3.6 28.7 - - + +
279F GLN* 3.3 15.9 + - + +
280F TYR* 3.0 27.4 + - + +
282F ALA* 1.3 76.4 - - - +
284F TRP* 1.3 63.1 + - - +
286F LYS* 3.1 36.7 + - - +
287F GLN* 3.1 18.4 + - - +
304F SER* 4.5 3.1 + - - -
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Residues in contact with TRP 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F GLY* 6.5 1.1 - - - -
87F LEU* 4.1 16.5 - - + +
88F GLY* 3.6 27.8 - - - -
91F ALA* 4.3 11.9 - - + -
208F ARG* 3.8 18.7 + - - -
211F VAL* 4.2 15.1 - - + +
280F TYR 3.0 12.1 + - - +
281F PHE* 3.4 41.3 - + - +
283F GLU* 1.3 75.4 - - - +
285F TRP* 1.3 73.1 + - - +
287F GLN* 3.3 7.2 + - + +
288F LEU* 3.0 57.5 + - + +
394F PHE* 6.2 2.0 - + - -
398F VAL* 3.8 42.6 - - + -
401F PHE* 4.0 9.6 - + + -
402F GLU* 4.1 10.5 - - + -
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Residues in contact with TRP 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254F TYR* 3.4 15.3 + - - -
258F ARG* 4.7 2.2 - - - -
269F GLU* 3.4 52.9 - - + -
271F LEU* 3.5 37.8 - - + +
281F PHE* 2.9 15.1 + - + +
282F ALA 3.5 5.8 - - - +
284F TRP* 1.3 84.7 - - + +
286F LYS* 1.3 80.9 + - + +
288F LEU* 3.3 4.7 + - - +
289F PHE* 2.9 52.7 + + - +
302F PRO* 3.5 24.2 - - + -
303F SER 3.3 20.6 - - - -
401F PHE* 3.6 33.0 - + + -
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Residues in contact with LYS 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304E SER 5.1 7.9 + - - -
313E SER* 5.9 0.9 - - - -
314E LEU* 3.9 24.0 - - + +
282F ALA 2.9 16.0 + - - +
283F GLU* 3.1 44.0 + - - +
285F TRP* 1.3 95.9 - - + +
287F GLN* 1.3 57.6 + - - +
290F GLY* 2.8 30.8 + - - -
302F PRO* 3.5 31.2 - - + +
303F SER* 4.1 4.6 - - - +
304F SER* 3.3 25.9 + - - +
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Residues in contact with GLN 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E HIS 3.1 16.7 + - - +
313E SER* 3.6 28.6 - - - -
83F GLY 3.5 12.8 - - - +
84F GLY* 3.5 17.1 + - - +
87F LEU* 3.4 20.6 - - + +
207F GLY* 4.6 0.6 - - - -
208F ARG* 3.6 22.9 - - + +
283F GLU 3.1 10.5 + - - +
284F TRP* 3.3 10.6 + - + +
286F LYS* 1.3 75.5 - - - +
288F LEU* 1.3 66.2 + - - +
291F GLU* 2.9 50.2 + - - +
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Residues in contact with LEU 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F ARG* 3.8 26.5 - - + +
209F PHE* 3.8 37.5 - - + -
284F TRP* 3.0 41.9 + - + +
285F TRP* 3.3 9.4 + - - +
287F GLN* 1.3 78.7 - - - +
289F PHE* 1.3 64.8 + - + +
292F SER* 2.7 30.7 + - - -
401F PHE* 3.7 33.4 - - + +
402F GLU* 3.9 2.7 - - + +
405F CYS* 3.5 9.3 - - + -
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Residues in contact with PHE 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254F TYR* 3.8 18.6 - + - -
258F ARG* 3.5 48.9 - - - +
285F TRP* 2.9 53.2 + + + +
286F LYS 4.7 0.2 - - - +
288F LEU* 1.3 83.7 - - + +
290F GLY* 1.3 60.0 + - - +
293F GLU* 2.9 40.8 + - - +
300F ILE 5.4 2.3 - - - +
302F PRO* 4.7 10.8 - - + -
401F PHE* 3.8 19.1 - + - -
404F ALA 4.4 0.9 - - - -
405F CYS* 3.6 36.3 - - + -
408F SER* 4.4 3.4 - - - -
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Residues in contact with GLY 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E SER 4.5 2.2 - - - -
314E LEU* 4.3 6.5 - - - -
317E TYR* 3.8 16.0 + - - +
286F LYS 2.8 23.0 + - - -
289F PHE* 1.3 73.2 - - - +
291F GLU* 1.3 56.4 + - - +
294F GLY* 3.0 28.6 + - - -
300F ILE 5.5 0.4 - - - -
302F PRO* 3.7 20.9 - - - +
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Residues in contact with GLU 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E LEU 4.9 0.2 - - - +
312E HIS* 3.4 17.7 - - - +
313E SER 3.3 19.8 + - - +
316E GLN* 3.6 20.0 + - + +
208F ARG* 3.0 30.7 + - - +
287F GLN* 2.9 43.2 + - - +
290F GLY* 1.3 75.0 - - - +
292F SER* 1.3 59.9 + - - +
295F LYS* 3.0 26.0 + - - -
418F ASP 3.7 3.8 - - - +
419F GLN* 4.4 9.5 - - + +
422F VAL* 4.3 16.6 - - - +
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Residues in contact with SER 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F ARG* 2.8 18.2 + - - +
209F PHE* 4.1 4.2 - - - -
288F LEU 2.7 22.9 + - - -
289F PHE 4.0 0.7 - - - -
291F GLU* 1.3 78.8 - - - +
293F GLU* 1.3 63.8 + - - +
295F LYS* 3.0 17.5 + - - -
405F CYS* 3.2 25.2 - - - -
414F VAL* 3.7 5.7 - - - +
415F ASN 3.5 7.4 - - - +
416F PRO* 3.0 29.3 + - - +
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Residues in contact with GLU 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E TYR* 5.0 0.4 - - + -
258F ARG* 2.8 26.4 + - - -
289F PHE* 2.9 23.4 + - + +
292F SER* 1.3 87.8 - - - +
294F GLY* 1.3 57.9 + - - +
295F LYS* 2.9 12.2 + - - +
298F LYS 3.2 10.8 - - - +
299F GLY* 4.5 5.8 - - - -
300F ILE* 4.7 11.8 + - - +
405F CYS 5.1 0.9 - - - +
408F SER* 2.5 38.2 + - - +
409F GLY* 3.1 20.4 + - - +
412F LEU* 3.8 25.1 - - + +
414F VAL* 4.3 5.8 - - - +
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Residues in contact with GLY 294 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E GLN* 2.9 34.1 + - - +
317E TYR* 3.5 23.7 - - - -
320E GLU 3.7 1.7 - - - -
321E GLY* 3.9 7.9 - - - -
290F GLY 3.0 20.2 + - - -
291F GLU 4.4 0.6 - - - -
292F SER 3.8 1.0 - - - -
293F GLU* 1.3 72.5 - - - +
295F LYS* 1.3 59.4 + - - -
298F LYS 3.6 5.4 - - - -
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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