Contacts of the helix formed by residues 379 - 393 (chain D) in PDB entry 1EGE
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 SER 379 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349C GLN* 3.7 4.0 + - - -
333D LYS* 6.1 0.2 - - - +
334D ALA* 5.4 2.9 - - - +
338D ASP* 3.7 11.9 + - - -
373D GLN* 3.1 34.1 + - - +
377D GLY 3.8 0.6 + - - -
378D THR* 1.3 71.1 - - - +
380D GLN* 1.3 75.7 + - - +
382D GLN* 3.3 6.8 + - - +
383D ARG* 3.1 49.4 + - - +
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Residues in contact with GLN 380 (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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296A PHE* 3.5 28.4 - - + -
293C ALA* 4.3 4.0 - - + +
294C ILE* 4.1 6.0 - - + +
297C MET* 3.4 36.2 - - - +
349C GLN* 3.2 23.8 - - - +
378D THR 3.1 0.2 - - - -
379D SER* 1.3 81.1 + - - +
381D ILE* 1.3 64.5 + - - +
383D ARG* 3.1 4.5 + - - +
384D LEU* 3.1 24.5 + - - +
399D FAD 3.1 53.7 + - + +
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Residues in contact with ILE 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C PHE* 5.1 6.3 - - + -
142D SER* 3.7 31.4 - - - +
256D ARG* 4.2 6.5 - - - +
377D GLY* 3.5 18.2 - - - -
378D THR* 3.0 32.5 + - - +
380D GLN* 1.3 76.6 - - + +
382D GLN* 1.3 65.9 + - - +
384D LEU* 3.1 22.4 + - + +
385D ILE* 3.0 46.4 + - + +
399D FAD 4.6 13.2 - - + +
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Residues in contact with GLN 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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256D ARG* 3.3 12.2 + - - +
330D SER* 3.4 30.9 + - - +
333D LYS* 3.1 27.3 - - + +
334D ALA* 4.2 9.4 - - + +
376D GLU 2.9 20.0 + - - -
377D GLY* 2.9 36.4 + - - +
378D THR 2.9 10.5 + - - +
379D SER* 3.5 9.2 - - - +
380D GLN 3.1 0.2 + - - -
381D ILE* 1.3 77.0 - - - +
383D ARG* 1.3 58.6 + - - +
385D ILE* 3.0 14.8 + - - +
386D VAL* 3.0 32.5 + - - +
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Residues in contact with ARG 383 (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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295A SER 4.7 0.7 - - - +
296A PHE* 4.0 29.4 - - + -
299A ALA* 3.1 33.8 - - + +
300A GLU* 3.2 35.1 + - - +
303A MET* 4.1 25.3 - - + +
334D ALA* 3.7 21.9 + - + +
335D PHE* 5.7 0.2 - - - +
338D ASP* 2.8 28.4 + - - -
379D SER* 3.1 40.7 + - - +
380D GLN 3.1 7.1 + - - +
382D GLN* 1.3 74.8 - - - +
384D LEU* 1.3 61.6 + - - +
386D VAL* 4.3 4.3 - - - -
387D ALA* 3.1 12.1 + - - +
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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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292A GLN* 3.6 27.8 - - + +
295A SER* 5.4 8.1 - - - -
296A PHE* 3.7 16.6 - - + -
284C PHE* 6.0 1.6 - - + -
380D GLN 3.1 15.1 + - - +
381D ILE* 3.2 28.5 - - + +
382D GLN 3.1 0.4 - - - -
383D ARG* 1.3 77.8 - - - +
385D ILE* 1.3 57.9 + - + +
387D ALA* 4.0 3.9 - - - +
388D ARG* 3.0 28.3 + - - +
399D FAD 3.7 28.7 - - + +
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Residues in contact with ILE 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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256D ARG* 3.6 23.3 - - - +
326D THR* 4.2 11.2 - - - +
327D TYR* 6.1 0.2 - - - -
330D SER* 3.6 15.9 - - - +
381D ILE* 3.2 26.0 - - + +
382D GLN* 3.0 25.0 + - - +
384D LEU* 1.3 76.7 - - + +
386D VAL* 1.3 65.8 + - - +
388D ARG* 3.1 29.6 + - - +
389D GLU* 2.9 43.6 + - - +
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Residues in contact with VAL 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ALA* 4.0 25.4 - - + +
302A ALA* 4.7 4.3 - - + -
303A MET* 4.4 7.2 - - + -
327D TYR* 3.8 24.5 - - + +
330D SER* 3.4 34.3 - - - +
331D ILE* 4.2 17.7 - - + +
382D GLN 3.0 17.1 + - - +
383D ARG* 3.8 7.9 - - - +
384D LEU 3.4 0.2 - - - -
385D ILE* 1.3 77.7 - - - +
387D ALA* 1.3 56.3 + - - +
389D GLU* 3.3 4.9 + - - +
390D HIS* 2.8 29.1 + - - +
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Residues in contact with ALA 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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295A SER* 3.4 42.6 - - - +
299A ALA* 3.9 7.4 - - + +
383D ARG 3.1 14.9 + - - +
384D LEU* 4.0 3.8 - - - +
386D VAL* 1.3 74.4 - - - +
388D ARG* 1.3 58.7 + - - +
390D HIS* 3.9 7.4 - - - -
391D ILE* 2.7 47.0 + - + +
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Residues in contact with ARG 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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249D MET* 6.3 0.4 - - - +
324D ARG* 4.9 2.2 - - - +
326D THR* 4.2 4.9 + - - -
384D LEU 3.0 17.6 + - - +
385D ILE* 3.3 38.4 - - - +
387D ALA* 1.3 76.3 - - - +
389D GLU* 1.3 93.5 + - - +
391D ILE* 4.2 3.5 - - - +
392D ASP* 2.7 45.0 + - - +
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Residues in contact with GLU 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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324D ARG* 2.9 27.5 + - - +
326D THR* 3.9 21.1 - - + -
327D TYR* 3.5 27.1 - - + -
385D ILE* 2.9 27.9 + - - +
386D VAL 3.7 0.4 - - - +
388D ARG* 1.3 106.5 + - - +
390D HIS* 1.3 66.7 + - - +
392D ASP* 3.1 16.5 + - + +
393D LYS* 3.1 22.2 + - + +
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Residues in contact with HIS 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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268A GLN* 5.7 0.2 - - - -
271A LEU* 3.8 27.4 - - + +
275A THR* 3.0 25.7 + - + -
298A LEU* 4.6 10.1 - - + +
302A ALA* 3.8 16.8 - - + +
327D TYR* 3.9 7.0 + - + +
386D VAL* 2.8 19.1 + - + +
387D ALA* 3.5 7.2 - - - +
389D GLU* 1.3 76.2 - - - +
391D ILE* 1.3 80.7 + - + +
393D LYS* 3.0 31.9 + - - +
394D TYR* 2.9 50.8 - + - -
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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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275A THR* 4.4 6.7 - - + -
279A LEU* 3.7 23.9 - - + +
289A VAL* 3.2 27.6 - - + -
295A SER* 5.1 0.4 - - - +
298A LEU* 3.7 21.1 - - + -
387D ALA* 2.7 36.8 + - + +
388D ARG* 4.2 2.5 - - - +
390D HIS* 1.3 92.2 - - + +
392D ASP* 1.3 64.8 + - - +
394D TYR* 2.9 26.5 + - - +
395D LYS* 3.3 20.8 + - + +
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Residues in contact with ASP 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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388D ARG* 2.7 38.2 + - - +
389D GLU* 3.1 11.1 + - + +
391D ILE* 1.3 79.6 - - - +
393D LYS* 1.3 58.0 + - - +
394D TYR 3.0 4.4 + - - -
395D LYS* 3.5 40.3 + - + +
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Residues in contact with LYS 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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306A GLU* 5.2 4.2 + - - -
327D TYR* 3.7 22.0 + - + -
389D GLU* 3.1 18.6 - - + +
390D HIS* 3.0 44.3 + - - +
392D ASP* 1.3 76.2 - - + +
394D TYR* 1.3 70.0 + - + +
395D LYS 5.0 1.1 - - - -
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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