Contacts of the helix formed by residues 278 - 294 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A MSE 3.1 47.6 - - + -
273A ASN* 3.8 29.1 + - + -
274A TYR 5.2 0.4 - - - +
275A GLU* 2.9 22.0 + - + +
277A ALA* 1.3 76.9 - - - +
279A GLN* 1.3 62.4 + - - +
280A TYR 3.4 2.0 - - - -
281A PHE* 3.2 10.7 + - + +
282A ALA* 3.1 21.5 + - - +
330A LEU* 4.3 24.9 - - + +
332A VAL* 4.0 24.7 - - + -
386A ILE* 4.8 6.1 - - + -
389A LEU* 4.2 10.8 - - + -
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Residues in contact with GLN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 5.3 3.1 - - - +
273A ASN* 4.1 2.1 - - - +
276A PRO* 3.1 19.6 + - - +
277A ALA 3.2 0.8 - - - -
278A LEU* 1.3 76.6 - - - +
280A TYR* 1.3 88.1 + - + +
282A ALA* 3.2 15.6 + - - +
283A GLU* 3.4 17.5 + - + +
306A ASN* 4.1 32.0 + - - +
279B GLN* 4.2 20.0 - - - +
280B TYR* 4.9 9.0 + - - -
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Residues in contact with TYR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR* 3.7 11.2 + + - -
87A LEU* 4.1 23.1 - - + +
90A ARG* 3.4 57.7 + - + +
91A ALA* 3.7 27.8 - - - +
94A GLU* 3.3 24.8 + - + +
277A ALA 4.5 2.8 + - - -
278A LEU 3.4 0.4 - - - -
279A GLN* 1.3 100.5 + - + +
281A PHE* 1.3 66.6 + - - +
283A GLU* 3.0 21.0 + - + +
284A TRP* 3.0 18.7 + - - +
279B GLN* 4.8 12.2 + - - -
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Residues in contact with PHE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA* 3.6 16.6 + - + +
95A MSE 3.5 31.4 - - + -
271A LEU* 4.5 2.7 - - + -
277A ALA 5.1 0.2 + - - -
278A LEU* 3.2 12.3 + - + +
280A TYR* 1.3 76.2 - - - +
282A ALA* 1.3 57.2 + - - +
284A TRP* 3.2 36.8 + + - +
285A TRP* 2.9 28.7 + - + +
330A LEU* 3.9 21.8 - - + -
394A PHE* 4.0 12.1 - + - -
397A LEU* 3.5 33.7 - - + -
398A VAL* 4.2 15.9 - - + -
401A PHE* 3.7 24.0 - + - -
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 3.6 26.7 - - + +
273A ASN* 5.1 7.0 - - - +
278A LEU 3.1 11.2 + - - +
279A GLN* 3.4 11.4 - - - +
280A TYR 3.1 0.4 - - - -
281A PHE* 1.3 79.1 - - - +
283A GLU* 1.3 56.6 + - - +
285A TRP* 3.2 3.1 + - - +
286A LYS* 2.9 33.7 + - - +
304A SER* 3.8 25.1 - - - +
306A ASN* 5.5 1.6 - - - +
330A LEU* 6.0 0.9 - - + -
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 3.4 30.3 - - + +
279A GLN* 3.4 18.3 + - + +
280A TYR* 3.0 27.2 + - + +
282A ALA* 1.3 76.7 - - - +
284A TRP* 1.3 62.9 + - - +
286A LYS* 2.9 38.0 + - - +
287A GLN 3.1 17.5 + - - -
304A SER* 4.2 4.0 + - - -
279B GLN* 5.9 2.4 + - - -
306B ASN* 5.8 2.7 + - - -
310B ASP* 4.5 17.5 - - - +
313B SER* 4.8 4.3 + - - -
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Residues in contact with TRP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY* 6.5 1.1 - - - -
87A LEU* 4.1 16.3 - - + +
88A GLY* 3.6 28.0 - - - -
91A ALA* 4.3 11.4 - - + -
208A ARG* 3.8 19.2 + - - +
211A VAL* 4.2 15.5 - - + +
280A TYR 3.0 12.3 + - - +
281A PHE* 3.3 42.4 - + - +
283A GLU* 1.3 75.5 - - - +
285A TRP* 1.3 78.2 + - - +
287A GLN* 3.3 6.7 + - + +
288A LEU* 3.0 52.2 + - + +
394A PHE* 6.2 1.1 - + - -
398A VAL* 3.8 44.2 - - + -
401A PHE* 4.0 9.4 - + + -
402A GLU* 4.1 10.1 - - + -
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Residues in contact with TRP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 3.3 15.6 + - - -
258A ARG* 4.8 2.0 - - - -
269A GLU* 3.4 51.8 - - + -
271A LEU* 3.5 36.6 - - + +
281A PHE* 2.9 15.3 + - + +
282A ALA 3.5 7.6 - - - +
284A TRP* 1.3 87.1 - - + +
286A LYS* 1.3 82.2 + - + +
288A LEU* 3.3 5.1 + - - +
289A PHE* 3.0 55.0 + + - +
302A PRO* 3.6 24.7 - - + -
303A SER 3.3 20.9 - - - -
304A SER* 5.5 0.2 - - - -
401A PHE* 3.7 25.2 - + + -
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Residues in contact with LYS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ALA 2.9 16.2 + - - +
283A GLU* 2.9 45.7 + - - +
284A TRP 3.2 0.2 - - - -
285A TRP* 1.3 90.5 - - + +
287A GLN* 1.3 60.1 + - - +
290A GLY* 2.8 30.3 + - - -
302A PRO* 3.5 33.6 - - + +
303A SER* 4.2 4.9 - - - +
304A SER* 3.4 23.4 + - - +
304B SER 5.1 7.9 + - - -
313B SER* 4.2 5.3 - - - +
314B LEU* 4.2 20.9 - - + +
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Residues in contact with GLN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY 3.4 20.1 - - - +
84A GLY* 3.4 15.5 + - - +
87A LEU* 3.4 14.6 - - + +
207A GLY* 4.6 0.8 - - - -
208A ARG* 3.6 25.3 - - + +
283A GLU 3.1 10.5 + - - +
284A TRP* 3.7 9.5 - - + +
286A LYS* 1.3 76.5 - - - +
288A LEU* 1.3 58.5 + - - +
291A GLU* 2.8 54.8 + - - +
312B HIS 3.1 21.7 + - - +
313B SER* 3.6 24.1 - - - -
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ARG* 3.8 25.6 - - + +
209A PHE* 3.8 37.9 - - + -
284A TRP* 3.0 44.9 + - + +
285A TRP* 3.4 9.6 - - - +
287A GLN* 1.3 79.2 - - - +
289A PHE* 1.3 63.1 + - + +
292A SER* 2.6 32.4 + - - -
401A PHE* 3.6 33.0 - - + +
402A GLU* 3.9 2.7 - - + +
405A CYS* 3.5 8.9 - - - -
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 3.9 18.6 - + - -
258A ARG* 3.5 48.9 - - - +
285A TRP* 3.0 48.5 + + + +
288A LEU* 1.3 88.0 - - + +
290A GLY* 1.3 60.7 + - - +
293A GLU* 3.0 39.4 + - - +
300A ILE 5.3 3.8 - - - +
302A PRO* 4.6 10.8 - - + -
401A PHE* 3.8 28.0 - + - -
404A ALA 4.5 1.1 - - - -
405A CYS* 3.6 28.9 - - + -
408A SER* 4.4 3.1 - - - -
317B TYR* 5.7 0.2 - - - -
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Residues in contact with GLY 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LYS 2.8 24.3 + - - -
289A PHE* 1.3 74.6 - - - +
291A GLU* 1.3 55.5 + - - +
294A GLY* 3.1 28.6 + - - -
300A ILE 5.5 0.2 - - - -
302A PRO* 3.7 20.0 - - - +
313B SER 4.3 6.1 - - - -
314B LEU* 4.5 4.7 - - - -
316B GLN* 4.3 0.2 - - - +
317B TYR* 3.9 15.9 + - - +
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ARG* 3.0 33.2 + - - +
287A GLN* 2.8 45.0 + - + +
290A GLY* 1.3 73.2 - - - -
292A SER* 1.3 61.7 + - - +
295A LYS* 3.2 20.1 + - - -
418A ASP 3.7 1.4 - - - +
419A GLN* 4.4 10.0 - - + +
422A VAL* 4.3 17.5 - - - +
311B LEU 4.9 0.3 - - - +
312B HIS* 3.5 16.8 - - - +
313B SER 3.3 19.4 + - - +
316B GLN* 3.6 22.9 - - + +
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Residues in contact with SER 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ARG* 2.9 17.3 + - - +
209A PHE* 4.1 5.0 - - - -
288A LEU 2.6 25.2 + - - -
289A PHE 4.1 0.9 - - - -
291A GLU* 1.3 78.6 - - - +
293A GLU* 1.3 60.6 + - - +
295A LYS* 3.1 19.8 + - - +
405A CYS* 3.2 24.8 - - - -
414A VAL* 3.7 2.9 - - - +
415A ASN 3.6 0.9 - - - +
416A PRO* 3.2 35.6 + - - +
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Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 2.8 29.7 + - - -
259A ASN* 4.8 0.2 + - - -
289A PHE* 3.0 23.1 + - + +
292A SER* 1.3 86.0 - - - +
294A GLY* 1.3 61.5 + - - +
295A LYS* 2.8 14.7 + - - +
298A LYS 3.3 13.7 - - - +
299A GLY* 4.5 5.8 - - - -
300A ILE* 4.7 11.7 + - - +
405A CYS 5.1 0.9 - - - +
408A SER* 2.5 43.5 + - - +
409A GLY* 3.1 12.5 + - - -
412A LEU* 3.8 22.7 - - + +
414A VAL* 4.2 4.9 - - - -
317B TYR* 5.0 0.4 - - + -
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Residues in contact with GLY 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLY 3.1 13.2 + - - -
291A GLU 4.5 0.6 + - - -
292A SER 3.8 1.0 - - - -
293A GLU* 1.3 72.9 - - - +
295A LYS* 1.3 57.8 + - - -
298A LYS 3.5 5.4 - - - -
316B GLN* 2.9 34.0 + - - +
317B TYR* 3.4 31.7 - - - -
320B GLU 3.7 2.3 - - - -
321B GLY* 3.9 7.9 - - - -
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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