Contacts of the helix formed by residues 386 - 397 (chain B) in PDB entry 4Z2C
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 HIS 386 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382B ILE* 2.9 30.0 + - + +
383B ALA* 3.0 4.9 + - - -
385B ASP* 1.3 94.9 - - + +
387B ILE* 1.3 56.8 + - - +
388B ASP 3.4 2.0 - - - -
389B GLU* 3.5 23.0 + - + +
390B VAL* 2.9 29.3 + - - +
411B PHE* 3.5 28.0 - + + -
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Residues in contact with ILE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A ARG* 4.9 17.5 - - - +
383B ALA 2.9 12.2 + - - +
384B LEU* 3.8 16.8 + - + +
385B ASP 3.7 2.6 + - - -
386B HIS* 1.3 74.7 - - - +
388B ASP* 1.3 64.5 + - - +
390B VAL* 3.2 3.8 + - - +
391B ILE* 2.9 44.8 + - + +
429B LEU* 6.1 4.3 - - + -
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Residues in contact with ASP 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ILE* 6.0 1.7 - - - +
395A ARG* 5.1 11.6 + - - -
386B HIS 3.4 0.4 - - - -
387B ILE* 1.3 80.1 + - - +
389B GLU* 1.3 58.6 + - - +
391B ILE* 3.5 7.3 + - - +
392B ARG* 2.9 41.6 + - - +
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Residues in contact with GLU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B HIS* 3.5 22.0 + - + +
387B ILE 3.3 0.4 - - - -
388B ASP* 1.3 76.0 - - - +
390B VAL* 1.3 60.7 + - - +
392B ARG* 3.3 30.1 + - - +
393B ILE* 2.9 41.7 + - + +
410B LYS* 4.9 8.1 - - - +
411B PHE* 3.7 28.9 - - + -
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A LEU* 5.9 6.3 - - + -
383B ALA* 4.5 14.1 - - + +
386B HIS 2.9 20.6 + - - +
387B ILE* 3.4 7.2 - - - +
389B GLU* 1.3 75.9 - - - +
391B ILE* 1.3 60.4 + - + +
393B ILE* 3.1 6.1 + - - +
394B ILE* 2.9 27.1 + - - +
407B LEU* 4.3 17.3 - - + +
411B PHE* 4.2 14.1 - - + -
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Residues in contact with ILE 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A ILE* 5.8 0.4 - - + -
388A ASP* 5.9 1.3 - - - +
391A ILE* 3.6 46.9 - - + -
426A LEU* 4.4 24.7 - - + -
429A LEU* 5.4 7.0 - - + -
387B ILE* 2.9 32.7 + - + +
388B ASP* 4.0 7.2 - - - +
390B VAL* 1.3 74.4 - - + +
392B ARG* 1.3 60.8 + - - +
394B ILE* 3.8 7.6 - - + +
395B ARG* 2.9 47.7 + - + +
426B LEU* 6.0 0.4 - - + -
429B LEU* 6.2 3.6 - - + -
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Residues in contact with ARG 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B ASP* 2.9 31.2 + - - +
389B GLU* 3.3 39.2 - - - +
390B VAL 3.2 0.2 - - - -
391B ILE* 1.3 77.7 - - - +
393B ILE* 1.3 64.4 + - + +
395B ARG* 3.9 4.6 - - - +
396B ALA* 2.9 33.9 + - + +
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Residues in contact with ILE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B GLU* 2.9 29.5 + - + +
390B VAL* 3.1 8.3 + - - +
392B ARG* 1.3 82.9 - - + +
394B ILE* 1.3 62.3 + - - +
396B ALA* 3.4 8.3 + - + +
397B SER* 3.1 22.3 + - - -
403B ALA* 4.2 4.3 - - - +
406B GLU* 3.6 32.8 - - + +
407B LEU* 4.0 25.4 - - + +
410B LYS* 5.3 10.5 - - + -
411B PHE* 5.0 4.3 - - + -
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Residues in contact with ILE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A LEU* 4.6 20.4 - - + +
427A ARG* 5.9 0.2 - - - -
429A LEU* 4.5 4.9 - - + -
430A THR* 3.7 15.3 - - + +
390B VAL 2.9 16.1 + - - +
391B ILE* 3.8 9.2 - - + +
392B ARG 3.3 0.2 - - - -
393B ILE* 1.3 78.6 - - - +
395B ARG* 1.3 63.4 + - + +
397B SER* 3.3 22.5 + - - +
403B ALA* 4.7 6.1 - - + -
407B LEU* 5.9 3.1 - - + -
422B LEU* 5.1 13.9 - - + -
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Residues in contact with ARG 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A ILE* 4.2 22.4 - - + -
388A ASP* 5.0 11.7 - - - -
429A LEU* 3.6 25.4 - - + +
431A GLY* 4.0 10.2 + - - -
391B ILE* 2.9 37.6 + - + +
392B ARG* 3.9 4.5 - - - +
394B ILE* 1.3 74.0 - - - +
396B ALA* 1.3 66.7 + - - +
397B SER 3.1 8.9 + - - +
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Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B ARG* 2.9 22.2 + - + +
393B ILE* 3.7 9.2 - - + +
395B ARG* 1.3 77.5 - - - +
397B SER* 1.3 60.8 + - - +
398B GLU* 3.9 0.9 + - - +
402B GLU* 4.6 0.9 - - - +
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Residues in contact with SER 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A THR* 3.8 2.7 - - - -
431A GLY* 3.3 14.6 + - - -
393B ILE 3.1 10.5 + - - -
394B ILE 3.5 13.9 - - - +
395B ARG 3.1 13.1 - - - +
396B ALA* 1.3 79.2 - - - +
398B GLU* 1.3 60.5 + - - +
399B THR 4.1 2.9 - - - -
402B GLU* 3.5 14.4 - - - -
403B ALA* 3.6 34.5 - - - -
406B GLU* 6.3 0.4 - - - -
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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