Contacts of the helix formed by residues 278 - 294 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B MSE 3.0 47.8 - - + -
273B ASN* 3.9 26.9 + - + -
274B TYR 5.5 0.2 - - - +
275B GLU* 3.0 23.2 + - + +
277B ALA* 1.3 77.8 - - - +
279B GLN* 1.3 62.2 + - - +
280B TYR 3.4 1.8 - - - -
281B PHE* 3.2 17.3 + - + +
282B ALA* 3.2 12.1 + - - +
330B LEU* 4.2 26.4 - - + +
332B VAL* 4.1 24.5 - - + -
386B ILE* 4.6 4.9 - - + -
389B LEU* 4.2 9.9 - - + -
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Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLN* 4.2 19.5 + - - +
280A TYR* 4.8 10.9 + - - -
283A GLU* 5.9 2.4 + - - -
94B GLU* 5.4 2.5 - - - +
273B ASN* 4.1 1.9 - - - +
276B PRO* 3.0 19.2 + - - +
277B ALA 3.3 1.0 - - - -
278B LEU* 1.3 75.2 - - - +
280B TYR* 1.3 77.2 + - + +
282B ALA* 3.1 20.6 + - - +
283B GLU* 3.3 16.4 + - + +
306B ASN* 3.8 37.9 + - - +
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Residues in contact with TYR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLN* 4.9 9.8 + - - -
86B TYR* 3.5 11.7 + + - -
87B LEU* 4.1 26.6 - - + +
90B ARG* 3.4 56.6 + - + +
91B ALA* 3.6 26.9 - - - +
94B GLU* 3.3 27.3 + - + +
277B ALA 4.5 2.8 + - - -
278B LEU 3.4 0.4 - - - -
279B GLN* 1.3 88.3 - - + +
281B PHE* 1.3 65.4 + - - +
283B GLU* 3.1 17.5 + - + +
284B TRP* 3.1 18.2 + - - +
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Residues in contact with PHE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA* 3.6 15.7 + - + +
95B MSE 3.6 31.0 - - + -
271B LEU* 4.7 2.0 - - + -
277B ALA 5.1 0.4 + - - -
278B LEU* 3.2 13.6 + - + +
280B TYR* 1.3 77.6 - - - +
282B ALA* 1.3 60.1 + - - +
284B TRP* 3.2 36.6 + + - +
285B TRP* 2.9 27.4 + - + +
330B LEU* 4.0 20.4 - - + -
394B PHE* 4.0 21.8 - + - -
397B LEU* 3.7 31.0 - - + -
398B VAL* 4.2 8.1 - - + -
401B PHE* 3.8 23.6 - + - -
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 3.8 23.1 - - + +
273B ASN* 5.1 6.5 - - - +
278B LEU 3.2 7.7 + - - +
279B GLN* 3.1 14.0 + - + +
281B PHE* 1.3 80.2 - - - +
283B GLU* 1.3 55.9 + - - +
285B TRP* 3.3 2.8 + - - +
286B LYS* 2.9 34.6 + - - +
304B SER* 3.9 27.6 - - - +
306B ASN* 5.6 1.1 - - - +
330B LEU* 6.1 0.4 - - + -
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASN* 6.2 2.5 - - - -
310A ASP* 4.4 18.0 - - - +
313A SER* 4.6 5.7 + - - -
87B LEU* 3.6 31.2 - - + +
279B GLN* 3.3 19.1 + - + +
280B TYR* 3.1 26.6 + - + +
282B ALA* 1.3 76.4 - - - +
284B TRP* 1.3 62.0 + - - +
286B LYS* 2.9 39.4 + - - +
287B GLN* 3.2 17.7 + - - +
304B SER* 4.4 3.3 + - - -
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Residues in contact with TRP 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLY* 6.6 0.2 - - - -
87B LEU* 4.1 22.1 - - + +
88B GLY* 3.6 27.1 - - - -
91B ALA* 4.3 4.7 - - + -
208B ARG* 3.9 19.3 + - - -
211B VAL* 4.2 16.1 - - + +
280B TYR 3.1 11.4 + - - +
281B PHE* 3.4 42.6 - + - +
283B GLU* 1.3 76.2 - - - +
285B TRP* 1.3 75.2 + - - +
287B GLN* 3.3 7.6 + - - +
288B LEU* 3.0 53.8 + - + +
394B PHE* 6.2 1.6 - + - -
398B VAL* 3.8 42.8 - - + -
401B PHE* 4.0 9.0 - + + -
402B GLU* 4.1 10.1 - - + -
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Residues in contact with TRP 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TYR* 3.4 15.2 + - - -
258B ARG* 4.8 2.7 - - - -
269B GLU* 3.5 52.5 - - + -
271B LEU* 3.6 34.6 - - + +
281B PHE* 2.9 15.7 + - + +
282B ALA* 3.5 7.4 - - - +
283B GLU 3.2 0.2 - - - -
284B TRP* 1.3 85.0 - - + +
286B LYS* 1.3 85.8 + - + +
288B LEU* 3.2 4.0 + - - +
289B PHE* 3.0 53.1 + + - +
302B PRO* 3.5 24.7 - - + -
303B SER 3.4 21.8 - - - -
304B SER* 5.5 0.4 - - - -
401B PHE* 3.7 26.0 - + + -
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Residues in contact with LYS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A SER 5.3 6.7 + - - -
313A SER* 4.0 6.2 - - - +
314A LEU* 4.3 22.1 - - + +
282B ALA 2.9 17.6 + - - +
283B GLU* 2.9 45.6 + - - +
285B TRP* 1.3 94.5 - - + +
287B GLN* 1.3 57.3 + - - +
290B GLY* 2.8 30.7 + - - -
302B PRO* 3.6 30.4 - - + +
303B SER* 4.3 4.9 - - - +
304B SER* 3.3 25.1 + - - +
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Residues in contact with GLN 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A HIS 3.0 24.5 + - - +
313A SER* 3.5 24.5 - - - -
83B GLY 3.3 7.3 - - - +
84B GLY* 3.3 31.8 + - - +
87B LEU* 3.4 14.1 - - + +
207B GLY* 4.8 0.6 - - - -
208B ARG* 3.8 23.9 - - + +
283B GLU 3.2 9.7 + - - +
284B TRP* 3.6 10.6 - - + +
286B LYS* 1.3 76.8 - - - +
288B LEU* 1.3 62.8 + - - +
291B GLU* 3.0 43.4 + - - +
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ARG* 3.8 27.0 - - + +
209B PHE* 3.7 37.7 - - + -
284B TRP* 3.0 44.1 + - + +
285B TRP* 3.2 8.3 + - - +
287B GLN* 1.3 79.6 - - - +
289B PHE* 1.3 65.4 + - + +
292B SER* 2.6 31.0 + - - -
401B PHE* 3.6 32.5 - - + +
402B GLU* 3.9 2.9 - - + +
405B CYS* 3.4 9.5 - - - -
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Residues in contact with PHE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TYR* 3.8 19.1 - + - -
258B ARG* 3.5 48.9 - - - +
285B TRP* 3.0 51.8 + + + +
286B LYS 4.8 0.2 - - - +
288B LEU* 1.3 90.7 - - + +
290B GLY* 1.3 60.4 + - - +
293B GLU* 3.0 39.6 + - - +
300B ILE 5.4 3.5 - - - +
302B PRO* 4.7 8.7 - - + -
401B PHE* 3.8 14.1 - + - -
404B ALA 4.4 1.1 - - - -
405B CYS* 3.6 36.1 - - + -
408B SER* 4.4 3.1 - - - -
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Residues in contact with GLY 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A SER 4.3 5.8 - - - -
314A LEU* 4.9 0.9 - - - -
317A TYR* 3.9 18.8 + - - +
286B LYS 2.8 23.1 + - - -
289B PHE* 1.3 74.0 - - - +
291B GLU* 1.3 55.5 + - - +
294B GLY* 3.0 29.1 + - - -
300B ILE 5.5 0.4 - - - -
302B PRO* 3.8 20.0 - - - +
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU 4.9 0.2 - - - +
312A HIS* 3.2 20.3 - - - +
313A SER 3.4 18.1 + - - +
316A GLN* 3.7 23.0 + - + +
208B ARG* 2.8 36.6 + - - +
287B GLN* 3.0 40.2 + - + +
290B GLY* 1.3 73.5 - - - +
292B SER* 1.3 62.2 + - - +
295B LYS* 3.0 24.8 + - - -
418B ASP 3.7 3.1 - - - +
419B GLN* 4.7 10.4 - - + +
422B VAL* 4.4 13.3 - - - +
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Residues in contact with SER 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ARG* 2.8 17.1 + - - +
209B PHE* 4.1 4.5 - - - -
288B LEU 2.6 24.2 + - - -
289B PHE 4.2 0.7 - - - -
291B GLU* 1.3 79.1 - - - +
293B GLU* 1.3 60.9 + - - +
295B LYS* 3.0 19.8 + - - +
405B CYS* 3.2 23.7 - - - -
414B VAL* 3.6 3.3 - - - +
415B ASN 3.5 7.4 - - - +
416B PRO* 3.2 31.2 + - - +
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Residues in contact with GLU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ARG* 2.7 29.9 + - - -
259B ASN* 4.8 0.5 + - - -
289B PHE* 3.0 21.2 + - + +
292B SER* 1.3 85.4 - - - +
294B GLY* 1.3 59.4 + - - +
295B LYS* 2.8 13.9 + - - +
298B LYS 3.3 10.3 - - - +
299B GLY* 3.8 5.6 - - - -
300B ILE* 4.6 11.8 + - - +
405B CYS 5.1 1.6 - - - +
408B SER* 2.4 44.0 + - - +
409B GLY* 4.1 11.9 - - - +
412B LEU* 3.7 25.5 - - + +
414B VAL* 4.3 5.1 - - - +
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Residues in contact with GLY 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLN* 2.9 34.6 + - - +
317A TYR* 3.5 24.4 - - - -
320A GLU 3.6 2.6 - - - -
321A GLY* 3.9 6.7 - - - -
290B GLY 3.0 20.5 + - - -
291B GLU 4.3 0.4 + - - -
292B SER 3.8 1.2 - - - -
293B GLU* 1.3 71.6 - - - +
295B LYS* 1.3 59.4 + - - -
298B LYS 3.6 4.9 - - - -
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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
------------------------------------------------------------
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