Contacts of the helix formed by residues 387 - 399 (chain A) in PDB entry 1ICH
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 ALA 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384A ARG* 5.7 1.8 - - - +
386A GLU* 1.3 86.8 - - + +
388A THR* 1.3 66.5 + - - +
389A LEU* 3.2 3.1 - - - +
390A GLU* 2.8 47.8 + - + +
391A LEU* 3.3 5.5 + - - +
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Residues in contact with THR 388 (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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330A LEU* 4.9 9.9 - - + -
375A LEU 4.8 6.3 - - - +
378A TRP* 3.5 35.6 + - + +
379A ARG* 4.3 25.8 - - + +
384A ARG* 4.6 13.3 + - + +
386A GLU* 3.3 5.7 - - - -
387A ALA* 1.3 77.9 + - - +
389A LEU* 1.3 63.2 + - - +
391A LEU* 3.3 12.2 + - - +
392A LEU* 3.1 25.7 + - + +
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Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A THR* 3.0 37.9 - - + +
330A LEU* 6.0 1.0 - - + +
333A VAL* 3.4 24.2 - - + -
387A ALA* 3.2 0.6 - - - +
388A THR* 1.3 81.3 - - - +
390A GLU* 1.3 51.7 + - - +
392A LEU* 3.0 12.3 + - + +
393A GLY* 2.5 35.7 + - - -
396A LEU* 5.2 0.7 - - + -
405A LEU* 3.6 37.0 - - + -
408A ILE* 3.8 4.9 - - + -
409A GLU* 5.3 3.1 - - + +
412A LEU* 4.2 15.3 - - + -
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Residues in contact with GLU 390 (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* 2.8 39.7 + - + +
389A LEU* 1.3 78.8 - - - +
391A LEU* 1.3 62.5 + - - +
393A GLY* 3.1 10.5 + - - +
394A ARG* 3.1 49.8 + - - +
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Residues in contact with LEU 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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349A LEU* 3.6 27.4 - - + +
378A TRP* 3.1 47.3 - - + +
384A ARG* 3.2 34.8 - - + +
387A ALA 3.3 5.6 + - - +
388A THR* 3.8 7.2 - - - +
389A LEU 3.3 0.6 - - - -
390A GLU* 1.3 79.8 - - - +
392A LEU* 1.3 65.6 + - + +
394A ARG* 3.3 12.2 + - + +
395A VAL* 3.2 27.7 + - + +
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Residues in contact with LEU 392 (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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330A LEU* 5.1 4.0 - - + -
333A VAL* 3.7 18.2 - - + -
345A PHE* 3.2 38.0 - - + -
349A LEU* 3.5 16.2 - - + -
375A LEU* 3.9 22.2 - - + -
378A TRP* 5.4 3.8 - - + +
388A THR* 3.1 37.4 + - + +
389A LEU* 3.0 21.1 + - + +
391A LEU* 1.3 82.8 - - + +
393A GLY* 1.3 55.9 + - - +
395A VAL* 3.1 10.7 + - - +
396A LEU* 2.9 32.7 + - + +
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Residues in contact with GLY 393 (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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389A LEU* 2.5 20.7 + - - +
390A GLU* 3.1 3.3 + - - -
392A LEU* 1.3 73.8 - - - +
394A ARG* 1.3 61.7 + - - +
396A LEU* 2.8 18.5 + - - +
397A ARG* 2.8 29.3 + - - +
405A LEU* 4.3 13.1 - - - +
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Residues in contact with ARG 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 GLU* 3.1 43.4 + - + +
391A LEU* 3.6 12.5 - - + +
393A GLY* 1.3 74.1 - - - +
395A VAL* 1.3 60.7 + - + +
397A ARG* 3.2 15.8 + - - +
398A ASP* 2.5 36.9 + - - +
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Residues in contact with VAL 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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345A PHE* 3.6 18.8 - - + +
348A ARG* 3.2 47.6 - - + +
349A LEU* 3.5 22.2 - - + -
391A LEU* 3.2 18.4 - - + +
392A LEU 3.1 7.8 + - - +
394A ARG* 1.3 78.6 - - + +
396A LEU* 1.3 63.2 + - - +
398A ASP* 3.2 7.4 + - - +
399A MET* 3.0 40.7 + - - +
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Residues in contact with LEU 396 (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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333A VAL* 5.6 0.9 - - + -
337A VAL* 3.9 11.7 - - + -
345A PHE* 3.5 16.6 - - + -
389A LEU* 5.2 0.4 - - + -
392A LEU* 2.9 23.6 + - + +
393A GLY* 2.8 8.6 + - - +
395A VAL* 1.3 77.1 - - - +
397A ARG* 1.3 54.8 + - + +
399A MET 3.0 1.7 + - - -
400A ASP 2.8 10.6 + - - -
401A LEU* 2.5 73.8 + - + +
402A LEU* 4.5 1.1 - - - +
404A CYS* 4.5 3.8 - - + -
405A LEU* 3.4 42.8 - - + -
408A ILE* 3.8 12.1 - - + -
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Residues in contact with ARG 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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393A GLY 2.8 18.7 + - - +
394A ARG* 3.2 16.6 + - - +
396A LEU* 1.3 76.7 - - + +
398A ASP* 1.3 64.5 + - - +
400A ASP* 2.9 18.7 + - - +
401A LEU 4.5 2.0 - - - +
402A LEU* 3.9 49.8 - - + +
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Residues in contact with ASP 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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348A ARG* 5.0 21.9 + - + +
394A ARG* 2.5 27.5 + - - +
395A VAL* 3.6 10.5 - - - +
397A ARG* 1.3 78.3 - - - +
399A MET* 1.3 62.4 + - + +
400A ASP* 3.2 9.2 + - - +
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Residues in contact with MET 399 (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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337A VAL* 5.6 0.7 - - + -
338A PRO* 5.8 4.9 - - + -
341A ARG* 5.2 4.7 - - + +
344A GLU* 4.7 5.2 - - + -
345A PHE* 3.4 55.6 - - + +
348A ARG* 3.8 21.8 - - + +
395A VAL* 3.0 25.4 + - - +
396A LEU 3.0 0.4 + - - +
398A ASP* 1.3 78.5 - - + +
400A ASP* 1.3 75.7 + - - +
401A LEU* 3.2 22.8 - - + +
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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