Contacts of the helix formed by residues 385 - 398 (chain A) in PDB entry 2D7I
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 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A GLU* 5.7 1.3 - - - +
384A VAL* 1.3 79.2 - - - +
386A LEU* 1.3 65.3 + - - +
387A ALA* 3.2 24.2 - - - +
388A ARG* 3.3 19.0 + - - +
389A ASN* 3.8 13.7 + - - -
415A LEU* 5.3 1.7 - - - +
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Residues in contact with LEU 386 (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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292A MET 5.9 2.2 - - - +
293A TYR* 5.3 14.6 - - + +
342A TRP* 3.7 28.5 - - + +
343A GLY* 3.4 34.5 - - - -
344A GLY 4.3 0.2 - - - +
385A SER* 1.3 73.4 - - - +
387A ALA* 1.3 63.8 + - - +
389A ASN* 3.1 8.3 + - - +
390A LEU* 2.9 50.0 + - + +
409A ARG* 5.5 6.1 - - - +
412A TYR* 5.7 0.4 - - - +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A SER* 3.1 14.1 + - - +
386A LEU* 1.3 77.3 - - - +
388A ARG* 1.3 53.3 + - - +
390A LEU* 3.1 4.0 + - - +
391A LYS* 2.7 36.7 + - - +
411A GLU* 6.1 0.7 - - + -
412A TYR* 3.4 41.7 + - + +
415A LEU* 4.0 16.2 - - + -
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Residues in contact with ARG 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLY* 3.5 24.9 + - - -
340A GLU* 4.5 13.6 + - + +
385A SER* 3.3 17.5 + - - +
386A LEU 3.3 0.6 - - - -
387A ALA* 1.3 77.7 - - - +
389A ASN* 1.3 65.5 + - - +
391A LYS* 3.3 5.9 + - - +
392A ARG* 3.1 41.5 + - - +
415A LEU* 4.6 10.6 - - + +
416A SER* 3.0 28.1 + - - +
417A ALA* 3.4 16.3 - - - +
418A GLY* 3.1 28.7 - - - +
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Residues in contact with ASN 389 (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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218A ILE* 5.8 0.2 - - - +
338A GLY 4.1 1.9 - - - +
339A LEU* 3.1 18.7 - - + +
340A GLU* 2.7 42.1 + - - +
342A TRP 2.9 27.5 + - - +
343A GLY 3.5 20.8 + - - +
344A GLY* 4.8 0.2 - - - -
384A VAL* 5.6 1.2 - - - +
385A SER 3.8 14.6 + - - -
386A LEU* 3.1 9.0 + - - +
388A ARG* 1.3 76.7 + - - +
390A LEU* 1.3 66.3 + - - +
392A ARG* 3.0 17.0 + - - +
393A VAL* 3.1 16.1 + - - +
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU 4.0 8.5 - - - +
292A MET* 3.6 36.8 - - + +
344A GLY* 4.0 21.1 - - - +
347A TYR* 4.5 11.9 - - + -
386A LEU* 2.9 47.3 + - + +
387A ALA 3.5 7.4 - - - +
389A ASN* 1.3 76.9 - - - +
391A LYS* 1.3 56.8 + - - +
393A VAL* 2.9 9.1 + - + +
394A ALA* 2.8 32.0 + - - +
405A ILE* 5.6 3.3 - - + +
409A ARG* 4.6 1.6 - - - +
412A TYR* 4.3 23.1 - - + +
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Residues in contact with LYS 391 (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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387A ALA 2.7 21.2 + - - +
388A ARG* 3.5 8.3 - - - +
389A ASN 3.2 0.2 - - - -
390A LEU* 1.3 72.1 - - - +
392A ARG* 1.3 62.1 - - - +
394A ALA* 3.9 4.2 - - - +
395A GLU* 3.1 44.5 + - + +
406A TYR* 3.1 30.1 - - + +
412A TYR* 2.6 43.7 + - + +
413A ARG* 3.5 11.1 + - - +
415A LEU* 3.0 25.3 + - + +
416A SER 5.6 0.2 - - - +
417A ALA* 3.8 18.0 - - + +
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ASP* 2.7 46.7 + - - +
337A PRO* 5.9 0.2 - - - +
338A GLY* 3.8 20.2 - - - -
339A LEU* 4.4 6.3 - - + -
388A ARG* 3.1 39.3 + - - +
389A ASN* 3.0 8.6 + - - +
391A LYS* 1.3 77.2 - - - +
393A VAL* 1.3 60.8 + - - +
395A GLU* 4.5 0.2 - - - +
396A VAL* 3.0 30.8 + - - +
417A ALA* 2.6 51.4 + - + +
418A GLY* 4.1 1.2 - - - -
419A ASP 2.9 33.9 + - - +
420A VAL* 3.4 14.4 - - + +
423A GLN* 3.8 13.7 - - - +
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Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A MET* 5.9 1.1 - - + -
336A ASP* 5.9 0.4 - - + +
339A LEU* 4.3 10.5 - - + -
344A GLY* 3.6 26.0 - - - +
347A TYR* 4.1 13.9 - - + -
348A GLU* 3.8 35.0 - - + +
351A PHE* 4.2 14.4 - - + -
389A ASN 3.1 13.2 + - - +
390A LEU* 2.9 10.1 + - + +
392A ARG* 1.3 77.8 - - - +
394A ALA* 1.3 66.8 + - - +
396A VAL 3.5 0.9 + - - -
397A TRP* 3.1 29.5 + - + +
398A MET* 3.9 3.4 + - - +
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Residues in contact with ALA 394 (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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390A LEU 2.8 18.7 + - - +
391A LYS* 3.9 5.2 - - - +
393A VAL* 1.3 72.1 - - - +
395A GLU* 1.3 60.5 + - - +
398A MET* 2.7 52.5 + - - +
399A ASP 3.9 2.8 + - - -
402A ALA* 3.7 23.8 - - + +
405A ILE* 3.8 12.3 - - + -
406A TYR* 4.1 9.0 - - + +
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Residues in contact with GLU 395 (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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391A LYS* 3.1 42.6 + - + +
392A ARG* 4.5 4.0 - - - +
394A ALA* 1.3 77.3 - - - +
396A VAL* 1.3 63.9 + - + +
399A ASP* 5.2 3.8 + - - -
402A ALA* 4.6 4.5 - - - +
406A TYR* 3.0 23.5 + - - +
417A ALA* 5.1 3.8 - - + -
420A VAL* 5.3 6.5 - - + -
424A LYS* 4.1 27.1 + - - -
427A ARG* 5.5 0.5 + - - -
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ASP* 5.8 0.7 - - - +
392A ARG 3.0 20.4 - - - +
393A VAL 3.5 0.8 + - - -
394A ALA 3.2 0.6 - - - -
395A GLU* 1.3 78.2 - - + +
397A TRP* 1.3 87.9 + - + +
399A ASP 5.4 0.2 - - - -
420A VAL* 4.1 20.9 - - + -
423A GLN* 4.1 26.0 - - + +
424A LYS* 4.0 31.9 - - + +
427A ARG* 2.8 27.3 + - + -
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Residues in contact with TRP 397 (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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348A GLU* 4.0 24.1 + - + +
351A PHE* 4.3 22.9 - - + -
352A LYS* 3.3 44.1 - - + +
355A MET* 3.9 19.0 - - + +
356A CYS* 3.6 27.1 - - - -
393A VAL* 3.1 22.1 + - + +
396A VAL* 1.3 101.2 - - + +
398A MET* 1.3 61.3 + - - +
399A ASP 3.3 3.4 + - - -
423A GLN* 5.4 2.8 + - - +
426A LEU* 5.0 4.7 - - + -
427A ARG* 3.3 60.5 + - + +
430A LEU* 4.8 4.7 - - + -
432A CYS* 3.8 2.9 - - + -
435A PHE* 3.1 24.8 - - - +
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Residues in contact with MET 398 (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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288A PHE* 4.4 2.0 - - + -
290A TRP* 3.9 20.9 - - + -
292A MET* 3.8 31.9 - - + -
351A PHE* 3.9 19.7 - - + -
390A LEU 5.6 0.2 - - - +
393A VAL* 4.2 3.1 - - - +
394A ALA* 2.7 37.2 + - - +
397A TRP* 1.3 73.4 - - - +
399A ASP* 1.3 67.9 + - - +
400A GLU 3.2 0.3 + - - -
401A TYR* 2.8 24.0 + - + +
402A ALA 3.9 8.7 - - - +
405A ILE* 3.6 29.4 - - + -
435A PHE* 3.8 27.6 - - + -
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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