Contacts of the helix formed by residues 278 - 294 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D MSE 3.0 43.7 - - + -
273D ASN* 3.8 28.9 + - + +
275D GLU* 3.0 22.5 + - + +
277D ALA* 1.3 76.5 - - - +
279D GLN* 1.3 63.2 + - - +
280D TYR 3.4 1.6 - - - -
281D PHE* 3.1 13.4 + - + +
282D ALA* 3.1 20.6 + - - +
330D LEU* 4.2 25.1 - - + +
332D VAL* 4.2 24.9 - - + -
386D ILE* 4.8 6.1 - - + -
389D LEU* 4.4 7.6 - - + -
397D LEU* 5.6 0.2 - - + -
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Residues in contact with GLN 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C GLN* 3.7 24.0 - - - +
280C TYR* 4.9 11.0 + - - -
94D GLU* 5.3 3.1 - - - +
273D ASN* 4.0 1.6 - - - +
276D PRO* 3.2 21.6 + - - +
277D ALA 3.3 1.0 - - - -
278D LEU* 1.3 76.2 - - - +
280D TYR* 1.3 78.6 + - + +
282D ALA* 3.2 20.9 - - - +
283D GLU* 3.4 13.2 + - + +
306D ASN* 3.9 36.1 + - - +
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Residues in contact with TYR 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C GLN* 5.0 10.2 + - - -
86D TYR* 3.6 14.0 + + - -
87D LEU* 4.0 27.5 - - + +
90D ARG* 3.4 55.2 + - + +
91D ALA* 3.6 26.2 - - - +
94D GLU* 3.4 24.1 + - + +
277D ALA 4.5 3.6 + - - +
278D LEU 3.4 0.2 - - - -
279D GLN* 1.3 91.9 - - + +
281D PHE* 1.3 66.2 + - - +
282D ALA 3.1 1.6 - - - -
283D GLU* 3.0 26.4 + - + +
284D TRP* 3.0 9.5 + - - +
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Residues in contact with PHE 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ALA* 3.4 16.1 + - + +
95D MSE 3.6 31.6 - - + -
271D LEU* 4.6 3.4 - - + -
277D ALA 5.1 0.4 + - - -
278D LEU* 3.1 13.1 + - + +
280D TYR* 1.3 77.0 - - - +
282D ALA* 1.3 58.1 + - - +
284D TRP* 3.1 39.0 + + - +
285D TRP* 2.8 29.4 + - + -
330D LEU* 3.9 21.3 - - + -
394D PHE* 4.1 12.8 - + - -
397D LEU* 3.8 24.0 - - + -
398D VAL* 4.2 17.0 - - + -
401D PHE* 3.7 31.0 - + - -
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Residues in contact with ALA 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D LEU* 3.9 21.3 - - + +
273D ASN* 5.1 6.5 - - - +
278D LEU 3.1 10.9 + - - +
279D GLN* 3.2 16.2 - - - +
280D TYR 3.1 0.2 - - - -
281D PHE* 1.3 77.7 - - - +
283D GLU* 1.3 56.0 + - - +
285D TRP* 3.2 3.1 + - - +
286D LYS* 2.8 34.7 + - - +
304D SER* 3.9 27.8 - - - +
306D ASN* 5.4 2.0 - - - +
330D LEU* 6.4 0.4 - - + -
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Residues in contact with GLU 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ASN* 5.9 1.5 + - - -
310C ASP* 4.3 18.5 - - - +
313C SER* 4.7 5.0 + - - -
87D LEU* 3.5 30.3 - - + +
279D GLN* 3.9 15.0 - - + +
280D TYR* 3.0 27.6 + - + +
282D ALA* 1.3 76.6 - - - +
284D TRP* 1.3 62.4 + - - +
286D LYS* 3.1 38.1 + - - +
287D GLN 3.1 18.4 + - - -
304D SER* 4.4 5.2 + - - -
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Residues in contact with TRP 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D GLY* 6.5 0.9 - - - -
87D LEU* 4.1 15.6 - - + +
88D GLY* 3.6 26.6 - - - -
91D ALA* 4.2 11.2 - - + -
208D ARG* 3.9 18.6 + - - -
211D VAL* 4.2 15.5 - - + +
280D TYR 3.0 11.0 + - - +
281D PHE* 3.3 45.3 - + - +
283D GLU* 1.3 76.7 - - - +
285D TRP* 1.3 73.0 + - - +
287D GLN* 3.4 5.9 + - + +
288D LEU* 3.0 55.0 + - + +
394D PHE* 6.3 1.3 - + - -
398D VAL* 3.8 43.1 - - + -
401D PHE* 4.0 9.4 - + + -
402D GLU* 4.1 10.1 - - + -
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Residues in contact with TRP 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D TYR* 3.4 12.2 + - - -
258D ARG* 4.7 1.1 - - - -
269D GLU* 3.3 51.6 - - + -
271D LEU* 3.4 37.2 - - + +
281D PHE* 2.8 14.8 + - + +
282D ALA 3.4 6.7 - - - +
284D TRP* 1.3 84.3 - - + +
286D LYS* 1.3 73.5 + - + +
288D LEU* 3.3 4.1 + - - +
289D PHE* 3.0 59.8 + + - +
302D PRO* 3.6 22.9 - - + -
303D SER 3.3 21.1 - - - -
304D SER* 5.5 0.2 - - - -
401D PHE* 3.5 27.0 - + + -
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Residues in contact with LYS 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C SER 5.0 8.3 + - - -
310C ASP* 5.7 2.2 + - - -
313C SER* 5.6 2.5 - - - +
314C LEU* 4.0 30.1 - - + +
282D ALA 2.8 16.0 + - - +
283D GLU* 3.1 45.5 + - - +
285D TRP* 1.3 93.0 - - + +
287D GLN* 1.3 55.9 + - - +
290D GLY* 2.8 31.2 + - - -
302D PRO* 3.6 30.5 - - + +
303D SER* 4.2 4.4 - - - +
304D SER* 3.9 20.4 + - - +
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Residues in contact with GLN 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C HIS 3.0 25.6 + - - +
313C SER* 3.5 24.1 - - - -
83D GLY* 3.3 20.3 - - - +
84D GLY* 3.4 17.5 + - - +
87D LEU* 3.6 13.2 - - + +
207D GLY* 4.7 0.6 - - - -
208D ARG* 3.7 21.9 - - + +
283D GLU 3.1 11.2 + - - +
284D TRP* 3.8 9.1 - - + +
286D LYS* 1.3 74.6 - - - +
288D LEU* 1.3 64.9 + - - +
291D GLU* 2.9 47.1 + - - +
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Residues in contact with LEU 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D ARG* 4.0 26.0 - - + +
209D PHE* 3.6 39.7 - - + -
284D TRP* 3.0 50.0 + - + +
285D TRP* 3.3 5.6 + - - +
287D GLN* 1.3 79.4 - - - +
289D PHE* 1.3 63.3 + - + +
292D SER* 2.8 30.7 + - - -
401D PHE* 3.7 30.3 - - + +
402D GLU* 3.9 2.5 - - + +
405D CYS* 3.5 9.8 - - - -
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Residues in contact with PHE 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C TYR* 5.8 0.2 - - - -
254D TYR* 3.9 18.8 - + - -
258D ARG* 3.4 50.7 - - - +
285D TRP* 3.0 50.7 + + + +
288D LEU* 1.3 83.7 - - + +
290D GLY* 1.3 61.3 + - - +
293D GLU* 3.0 39.2 + - - +
300D ILE 5.3 3.2 - - - +
302D PRO* 4.6 10.5 - - + -
401D PHE* 3.8 20.4 - + - -
404D ALA* 4.4 1.8 - - + -
405D CYS* 3.7 37.9 - - + -
408D SER* 4.4 3.1 - - - -
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Residues in contact with GLY 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C SER 4.4 2.9 - - - -
314C LEU* 4.6 6.3 - - - -
316C GLN* 4.3 0.2 - - - +
317C TYR* 3.9 15.6 + - - +
286D LYS 2.8 23.3 + - - -
289D PHE* 1.3 73.4 - - - +
291D GLU* 1.3 56.1 + - - +
294D GLY* 3.0 29.5 + - - -
300D ILE 5.4 0.2 - - - -
302D PRO* 3.7 20.9 - - - +
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Residues in contact with GLU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C LEU 4.9 0.3 - - - +
312C HIS* 3.6 15.3 - - - +
313C SER 3.4 18.9 + - - +
316C GLN* 3.6 24.1 + - + +
208D ARG* 3.0 31.5 + - - +
287D GLN* 2.9 44.7 + - + +
290D GLY* 1.3 70.7 - - - -
292D SER* 1.3 62.4 + - - +
295D LYS* 3.0 23.7 + - - -
418D ASP 3.7 3.6 - - - +
419D GLN* 4.3 10.2 - - + +
422D VAL* 4.3 17.0 - - - +
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Residues in contact with SER 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D ARG* 2.7 22.7 + - - +
209D PHE* 3.9 5.5 - - - -
288D LEU 2.8 19.8 + - - -
289D PHE 4.2 0.7 - - - -
291D GLU* 1.3 79.4 - - - +
293D GLU* 1.3 60.3 + - - +
295D LYS* 3.1 18.2 + - - -
405D CYS* 3.4 22.5 - - - -
414D VAL* 3.6 5.0 - - - +
415D ASN 3.5 7.6 - - - +
416D PRO* 3.1 29.4 + - - +
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Residues in contact with GLU 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C TYR* 6.2 0.2 - - + -
258D ARG* 2.8 28.8 + - - -
259D ASN* 4.6 0.5 + - - -
289D PHE* 3.0 22.9 + - + +
292D SER* 1.3 86.2 - - - +
294D GLY* 1.3 55.7 + - - +
295D LYS* 2.9 16.8 + - - +
298D LYS 3.3 10.7 - - - +
299D GLY* 4.5 5.8 - - - -
300D ILE* 4.6 12.0 + - - +
405D CYS 5.2 1.3 - - - +
408D SER* 2.6 43.7 + - - +
409D GLY* 3.5 13.4 - - - -
412D LEU* 3.7 25.7 - - + +
414D VAL* 4.2 5.1 - - - +
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Residues in contact with GLY 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C GLN* 2.9 36.4 + - - +
317C TYR* 3.4 25.9 - - - -
320C GLU 3.7 2.3 - - - -
321C GLY* 3.9 6.5 - - - -
290D GLY 3.0 18.6 + - - -
291D GLU 4.4 0.4 + - - -
292D SER 3.8 0.6 - - - -
293D GLU* 1.3 72.4 - - - +
295D LYS* 1.3 59.4 + - - -
298D 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