Contacts of the helix formed by residues 380 - 393 (chain D) in PDB entry 1FM9
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 ASP 380 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230D LYS* 4.5 4.7 - - - +
378D GLU 3.7 2.1 + - - +
379D LEU* 1.3 74.0 - - - +
381D ASP* 1.3 60.5 + - - +
382D SER* 2.7 27.0 + - - -
383D ASP* 2.8 34.0 + - - +
384D LEU* 2.9 16.5 + - - +
424D ASN* 2.9 24.1 + - - +
425D HIS* 5.1 1.6 - - + -
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Residues in contact with ASP 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D TYR* 4.1 16.0 - - + +
222D TYR* 2.6 40.5 + - + -
223D ILE* 5.2 1.7 - - + +
229D THR* 3.2 14.0 - - - -
230D LYS* 2.8 27.0 + - - +
231D ALA* 2.9 32.7 + - - +
380D ASP* 1.3 74.5 - - - +
382D SER* 1.3 56.8 + - - +
384D LEU* 3.7 4.2 - - - +
385D ALA* 2.9 29.5 + - - +
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Residues in contact with SER 382 (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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215D ALA 5.2 3.0 - - - +
219D TYR* 3.6 29.9 - - - -
380D ASP* 2.7 23.4 + - - -
381D ASP* 1.3 76.7 - - - +
383D ASP* 1.3 65.8 + - - +
385D ALA* 3.7 5.4 + - - +
386D ILE* 3.6 21.3 + - - +
420D GLN* 3.0 23.9 + - - -
424D ASN* 3.8 1.4 + - - -
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Residues in contact with ASP 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D LEU* 3.4 17.0 - - + -
380D ASP* 2.8 28.9 + - - +
382D SER* 1.3 78.5 - - - +
384D LEU* 1.3 63.0 + - - +
386D ILE* 3.3 6.6 + - - +
387D PHE* 3.2 19.9 + - - +
417D LEU* 3.8 5.2 - - + +
420D GLN* 3.0 34.1 + - - +
421D LEU* 4.0 12.7 - - + +
424D ASN* 3.2 9.0 - - - +
425D HIS* 2.7 34.4 + - - -
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Residues in contact with LEU 384 (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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222D TYR* 4.0 20.9 - - + +
230D LYS* 3.9 22.0 - - + +
328D THR* 4.2 13.9 - - + +
329D MET* 6.1 2.9 - - + -
332D SER* 3.6 24.0 - - - +
374D PHE* 3.7 35.0 - - + -
379D LEU* 3.9 16.8 - - + +
380D ASP 2.9 18.0 + - - +
381D ASP 3.8 4.0 - - - +
382D SER 3.3 0.2 - - - -
383D ASP* 1.3 75.9 - - - +
385D ALA* 1.3 66.3 + - - +
387D PHE* 3.2 6.0 + - + +
388D ILE* 2.9 34.4 + - + +
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Residues in contact with ALA 385 (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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218D LEU* 3.7 27.1 - - + +
219D TYR* 3.9 12.1 - - - +
222D TYR* 3.6 25.0 - - + -
299D TYR* 2.5 22.5 + - - +
381D ASP 2.9 18.0 + - - +
382D SER 3.9 6.1 - - - +
383D ASP 3.3 0.2 - - - -
384D LEU* 1.3 76.8 - - - +
386D ILE* 1.3 61.4 + - + +
388D ILE* 3.8 1.0 + - - +
389D ALA* 3.4 9.4 + - - +
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Residues in contact with ILE 386 (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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215D ALA* 3.6 30.3 - - + +
218D LEU* 4.0 24.0 - - + -
382D SER 3.6 11.2 - - - +
383D ASP 3.3 4.2 + - - +
384D LEU 3.1 0.8 - - - -
385D ALA* 1.3 77.7 - - + +
387D PHE* 1.3 67.6 + - - +
389D ALA* 2.9 5.2 + - - +
390D VAL* 2.9 25.5 + - + +
413D LEU* 3.5 27.6 - - + +
416D ALA* 3.9 10.3 - - + +
417D LEU* 3.6 15.7 - - + +
420D GLN* 3.6 36.8 - - + -
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Residues in contact with PHE 387 (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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328D THR* 3.9 24.7 - - + -
374D PHE* 3.9 21.1 - + - -
379D LEU* 5.0 1.1 - - + -
383D ASP 3.2 10.7 + - - +
384D LEU* 3.2 12.1 + - + +
386D ILE* 1.3 80.1 - - - +
388D ILE* 1.3 61.7 + - - +
390D VAL* 3.1 7.6 + - + +
391D ILE* 3.0 40.4 + - + +
417D LEU* 4.2 14.3 - - + +
435D LEU* 3.6 52.7 - - + -
436D LEU* 4.9 2.2 - - + -
438D LYS* 4.7 0.4 - - + -
439D MET* 3.6 40.2 - - + -
442D LEU* 4.6 5.8 - - + -
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Residues in contact with ILE 388 (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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222D TYR* 3.7 24.9 - - + -
226D PHE* 4.8 2.0 - - + -
299D TYR* 3.7 21.1 - - + -
325D ILE* 3.5 32.1 - - + -
328D THR* 4.6 15.7 - - + -
329D MET* 3.6 37.5 - - + -
384D LEU* 2.9 20.5 + - + +
385D ALA 4.0 4.0 - - - +
387D PHE* 1.3 75.7 - - + +
389D ALA* 1.3 64.0 + - - +
391D ILE* 3.0 10.3 + - + +
392D ILE* 3.0 23.3 + - + +
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Residues in contact with ALA 389 (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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218D LEU* 4.0 8.7 - - + -
299D TYR* 4.0 4.5 - - - +
303D ILE* 3.8 27.8 - - + -
385D ALA 3.4 11.2 + - - +
386D ILE 2.9 9.7 + - - +
388D ILE* 1.3 79.3 - - - +
390D VAL* 1.3 61.7 + - - +
392D ILE* 3.4 0.7 + - - -
393D LEU* 3.1 22.5 + - - +
413D LEU* 3.4 32.4 - - + +
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Residues in contact with VAL 390 (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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420A LEU* 4.9 0.4 - - + -
386D ILE 2.9 22.2 + - - +
387D PHE* 3.1 13.0 + - + +
389D ALA* 1.3 78.8 - - - +
391D ILE* 1.3 61.8 + - - +
393D LEU 3.7 4.5 + - - -
394D SER* 3.7 1.0 + - - -
410D GLN* 3.4 28.3 + - + +
413D LEU* 3.7 39.0 - - + +
414D LEU* 3.5 27.4 - - + +
417D LEU* 4.3 10.1 - - + -
436D LEU* 4.8 2.0 - - + -
439D MET* 4.1 18.0 - - - +
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Residues in contact with ILE 391 (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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321D GLY* 4.2 2.5 - - - +
324D GLU* 3.2 37.5 - - + +
325D ILE* 4.1 18.2 - - + -
328D THR* 3.8 15.5 - - - +
387D PHE* 3.0 50.4 + - + +
388D ILE* 3.0 13.0 + - - +
390D VAL* 1.3 78.4 - - - +
392D ILE* 1.3 61.5 + - - +
394D SER* 2.5 21.7 + - - +
397D ARG* 3.4 10.1 + - - +
439D MET* 3.9 21.5 - - + -
442D LEU* 4.6 7.6 - - + -
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Residues in contact with ILE 392 (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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296D ILE* 4.4 6.3 - - + -
299D TYR* 4.3 8.3 - - + -
300D ALA* 4.1 17.3 - - + -
303D ILE* 3.9 19.3 - - + -
306D PHE* 3.9 20.9 - - + -
317D LEU* 3.4 31.9 - - + +
318D LEU* 4.6 7.2 - - + -
321D GLY* 5.2 4.3 - - - -
325D ILE* 3.1 33.2 - - + -
388D ILE* 3.0 15.4 + - + +
389D ALA 3.7 6.7 - - - +
390D VAL 3.3 0.2 - - - -
391D ILE* 1.3 78.1 - - - +
393D LEU* 1.3 71.4 + - + +
394D SER* 2.9 8.2 + - - -
397D ARG* 5.0 1.0 + - - -
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Residues in contact with LEU 393 (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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303D ILE* 3.9 20.4 - - + -
306D PHE* 4.1 9.6 - - + -
309D LEU* 4.2 16.2 - - + -
317D LEU* 4.3 1.8 - - + -
389D ALA 3.1 16.5 + - - +
390D VAL 3.9 5.2 - - - +
391D ILE 3.4 0.2 - - - -
392D ILE* 1.3 91.9 - - + +
394D SER* 1.3 58.3 + - - +
395D GLY 3.6 1.4 + - - -
406D ILE* 3.6 22.6 - - + +
409D ILE* 3.9 34.1 - - + -
410D GLN* 3.1 31.5 + - + +
413D LEU* 3.8 19.5 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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