Contacts of the helix formed by residues 278 - 294 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C MSE 2.9 46.4 - - + -
273C ASN* 3.8 30.5 + - + +
274C TYR 5.3 0.2 - - - +
275C GLU* 2.9 20.9 + - + +
277C ALA* 1.3 74.9 - - - +
279C GLN* 1.3 65.7 + - - +
280C TYR 3.4 1.3 - - - -
281C PHE* 3.1 20.7 + - + +
282C ALA* 3.1 10.7 + - - +
330C LEU* 4.0 29.8 - - + +
332C VAL* 4.2 22.4 - - + -
386C ILE* 4.8 5.2 - - + -
389C LEU* 4.5 9.4 - - + -
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Residues in contact with GLN 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLU* 5.5 3.3 - - - +
273C ASN* 3.8 2.9 - - - +
276C PRO* 3.1 17.6 + - + +
277C ALA 3.3 0.8 - - - -
278C LEU* 1.3 74.6 - - - +
280C TYR* 1.3 84.4 + - + +
282C ALA* 3.2 15.5 + - - +
283C GLU* 3.3 20.2 + - + +
306C ASN* 4.0 34.1 + - - +
279D GLN* 3.7 23.8 - - - +
280D TYR* 5.0 9.8 + - - -
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Residues in contact with TYR 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C TYR* 3.5 18.0 + + - -
87C LEU* 4.0 27.5 - - + +
90C ARG* 3.4 52.1 + - + +
91C ALA* 3.6 26.9 - - - +
94C GLU* 3.6 22.3 + - + +
277C ALA 4.6 3.0 + - - -
278C LEU 3.4 0.4 - - - -
279C GLN* 1.3 97.3 - - + +
281C PHE* 1.3 65.5 + - - +
283C GLU* 3.0 18.5 + - + +
284C TRP* 3.0 18.2 + - - +
279D GLN* 4.9 11.8 + - - -
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Residues in contact with PHE 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ALA* 3.5 15.4 + - + +
95C MSE 3.6 31.4 - - + -
271C LEU* 4.7 3.1 - - + -
277C ALA 5.2 0.4 + - - -
278C LEU* 3.1 14.4 + - + +
280C TYR* 1.3 76.7 - - - +
282C ALA* 1.3 58.1 + - - +
284C TRP* 3.2 28.2 + + - +
285C TRP* 2.9 29.3 + - + +
330C LEU* 4.0 22.0 - - + -
394C PHE* 3.9 21.3 - + - -
397C LEU* 3.7 24.5 - - + -
398C VAL* 4.3 8.1 - - + -
401C PHE* 3.7 38.8 - + - -
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Residues in contact with ALA 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C LEU* 3.8 22.2 - - + +
273C ASN* 5.2 7.0 - - - +
278C LEU 3.1 10.1 + - - +
279C GLN* 3.4 12.8 - - - +
280C TYR 3.1 0.4 - - - -
281C PHE* 1.3 78.5 - - - +
283C GLU* 1.3 56.9 + - - +
285C TRP* 3.3 2.4 + - - +
286C LYS* 2.9 35.5 + - - +
304C SER* 3.8 28.5 - - - +
306C ASN* 5.4 1.8 - - - +
330C LEU* 6.1 0.7 - - + -
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Residues in contact with GLU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 3.6 30.4 - - + +
279C GLN* 3.3 19.8 + - + +
280C TYR* 3.0 27.9 + - + +
282C ALA* 1.3 73.8 - - - +
284C TRP* 1.3 65.3 + - - +
286C LYS* 2.8 39.7 + - - +
287C GLN 3.1 19.1 + - - -
304C SER* 4.5 3.8 + - - -
306D ASN* 6.4 0.4 - - - -
310D ASP* 4.4 17.3 - - - +
313D SER* 4.9 5.0 + - - -
314D LEU* 5.7 0.7 - - - +
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Residues in contact with TRP 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLY* 6.5 0.9 - - - -
87C LEU* 4.2 21.0 - - + +
88C GLY* 3.6 26.7 - - - -
91C ALA* 4.2 6.5 - - + -
208C ARG* 3.8 19.3 + - - -
211C VAL* 4.1 16.3 - - + +
280C TYR 3.0 11.2 + - - +
281C PHE* 3.4 41.7 - + - +
283C GLU* 1.3 78.8 - - - +
285C TRP* 1.3 71.2 + - - +
287C GLN* 3.4 5.4 + - - +
288C LEU* 3.0 47.2 + - + +
394C PHE* 6.2 1.1 - + - -
398C VAL* 3.8 43.1 - - + -
401C PHE* 4.0 13.9 - + + -
402C GLU* 4.1 12.6 - - + -
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Residues in contact with TRP 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C TYR* 3.5 10.6 + - - -
258C ARG* 4.8 1.1 - - - -
269C GLU* 3.5 51.6 - - + -
271C LEU* 3.6 38.5 - - + +
281C PHE* 2.9 15.0 + - + +
282C ALA 3.5 6.3 - - - +
283C GLU 3.2 0.2 - - - -
284C TRP* 1.3 86.9 - + + +
286C LYS* 1.3 79.3 + - + +
288C LEU* 3.1 4.4 + - - +
289C PHE* 2.9 66.6 + + - +
302C PRO* 3.6 24.2 - - + -
303C SER 3.4 20.9 - - - -
401C PHE* 3.7 25.6 - + + -
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Residues in contact with LYS 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ALA 2.9 17.5 + - - +
283C GLU* 2.8 46.1 + - - +
285C TRP* 1.3 94.6 - - + +
287C GLN* 1.3 57.7 + - - +
290C GLY* 2.8 30.7 + - - -
302C PRO* 3.7 25.9 - - + +
303C SER* 4.2 7.0 - - - +
304C SER* 3.8 21.6 + - - +
304D SER 5.1 8.1 + - - -
310D ASP* 5.8 1.2 + - - -
313D SER 4.2 1.4 - - - +
314D LEU* 3.9 26.8 - - + +
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Residues in contact with GLN 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLY* 3.4 18.6 - - - +
84C GLY* 3.5 18.9 + - - +
87C LEU* 3.4 14.2 - - + +
207C GLY* 4.7 0.8 - - - -
208C ARG* 3.8 21.7 - - + +
283C GLU 3.1 10.3 + - - +
284C TRP* 3.8 9.7 - - + +
286C LYS* 1.3 75.4 - - - +
288C LEU* 1.3 66.0 + - - +
291C GLU* 3.0 45.5 + - - +
312D HIS 3.0 24.5 + - - +
313D SER* 3.6 24.8 - - - -
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Residues in contact with LEU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ARG* 3.7 27.0 - - + +
209C PHE* 3.7 38.1 - - + -
284C TRP* 3.0 37.8 + - + +
285C TRP* 3.1 8.3 + - - +
287C GLN* 1.3 80.2 - - - +
289C PHE* 1.3 65.9 + - + +
292C SER* 2.6 31.5 + - - -
401C PHE* 3.5 37.7 - - + +
402C GLU* 3.9 2.9 - - + +
405C CYS* 3.9 7.6 - - - -
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Residues in contact with PHE 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C TYR* 3.8 18.4 - + - -
258C ARG* 3.5 48.0 - - - +
285C TRP* 2.9 57.4 + + + +
288C LEU* 1.3 86.3 - - + +
290C GLY* 1.3 60.7 + - - +
293C GLU* 3.0 41.1 + - - +
300C ILE 5.3 2.8 - - - +
302C PRO* 4.6 9.2 - - + -
401C PHE* 3.8 15.3 - + - -
404C ALA* 4.5 0.9 - - + -
405C CYS* 3.6 36.1 - - + -
408C SER* 4.4 3.1 - - - -
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Residues in contact with GLY 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C LYS 2.8 23.3 + - - -
289C PHE* 1.3 73.2 - - - +
291C GLU* 1.3 55.5 + - - +
294C GLY* 3.0 28.8 + - - -
300C ILE 5.4 0.4 - - - -
302C PRO* 3.6 21.1 - - - +
313D SER 4.4 6.5 - - - -
314D LEU* 5.7 1.1 - - - -
316D GLN* 4.4 0.2 - - - +
317D TYR* 3.8 18.6 + - - +
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ARG* 2.9 33.1 + - - +
287C GLN* 3.0 39.8 + - - +
290C GLY* 1.3 74.4 - - - +
292C SER* 1.3 61.7 + - - +
295C LYS* 3.0 23.0 + - - -
418C ASP 3.7 1.6 - - - +
419C GLN* 4.5 9.9 - - + +
422C VAL* 4.3 16.5 - - - +
312D HIS* 3.4 17.7 - - - +
313D SER 3.4 18.7 + - - +
316D GLN* 3.7 23.8 + - + +
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Residues in contact with SER 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ARG* 2.8 17.1 + - - +
209C PHE* 4.1 4.7 - - - -
288C LEU 2.6 25.1 + - - -
289C PHE 4.1 1.6 - - - -
290C GLY 3.4 0.2 - - - -
291C GLU* 1.3 77.5 - - - +
293C GLU* 1.3 61.4 + - - +
295C LYS* 3.0 19.5 + - - +
405C CYS* 3.2 24.4 - - - -
414C VAL* 3.7 3.1 - - - +
415C ASN 3.5 1.0 - - - +
416C PRO* 3.2 35.2 + - - +
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Residues in contact with GLU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C ARG* 2.9 28.4 + - - -
259C ASN* 4.6 0.9 + - - -
289C PHE* 3.0 23.6 + - + +
292C SER* 1.3 86.2 - - - +
294C GLY* 1.3 58.8 + - - +
295C LYS* 2.9 14.6 + - - +
298C LYS 3.3 9.9 - - - +
299C GLY* 3.8 10.1 - - - -
300C ILE* 4.7 11.3 + - - +
405C CYS 5.1 0.9 - - - +
408C SER* 2.4 43.3 + - - +
409C GLY* 4.0 14.4 - - - +
412C LEU* 3.9 22.2 - - + +
414C VAL* 4.2 4.7 - - - -
317D TYR* 5.1 0.2 - - - -
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Residues in contact with GLY 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C GLY 3.0 19.4 + - - -
291C GLU 4.4 0.6 + - - -
292C SER 3.8 1.0 - - - -
293C GLU* 1.3 71.9 - - - +
295C LYS* 1.3 58.0 + - - -
298C LYS 3.6 5.2 - - - -
316D GLN* 2.9 36.4 + - - +
317D TYR* 3.5 24.3 - - - -
320D GLU 3.6 2.4 - - - -
321D GLY* 3.8 7.0 - - - -
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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