Contacts of the helix formed by residues 401 - 413 (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 LEU 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A VAL* 4.7 7.2 - - + -
338A PRO* 4.8 13.0 - - + -
345A PHE* 4.1 6.3 - - + -
396A LEU* 2.5 50.6 + - + +
399A MET* 3.7 42.8 - - + +
400A ASP* 1.3 75.1 - - - +
402A LEU* 1.3 64.8 + - - +
403A GLY 3.0 3.8 - - - +
404A CYS* 2.8 38.2 + - + +
405A LEU 3.0 8.8 + - - -
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Residues in contact with LEU 402 (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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396A LEU* 4.0 5.1 + - - -
397A ARG* 3.9 52.5 - - + +
400A ASP* 3.3 5.2 - - - +
401A LEU* 1.3 77.9 - - - +
403A GLY* 1.3 62.6 + - - +
405A LEU* 3.2 16.0 + - + +
406A GLU* 3.0 45.3 + - + +
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Residues in contact with GLY 403 (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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400A ASP 5.0 1.2 + - - -
401A LEU* 3.0 1.2 - - - +
402A LEU* 1.3 79.9 - - - +
404A CYS* 1.3 61.6 + - - +
406A GLU* 3.3 16.6 + - - +
407A ASP* 3.2 18.9 + - - +
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Residues in contact with CYS 404 (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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336A ASN* 3.1 48.0 - - + -
396A LEU* 4.5 3.1 - - + -
401A LEU* 2.8 36.6 + - + +
403A GLY* 1.3 75.6 - - - +
405A LEU* 1.3 60.1 + - - +
407A ASP* 2.9 5.4 + - - +
408A ILE* 2.7 35.1 + - + +
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Residues in contact with LEU 405 (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* 3.6 40.2 - - + -
393A GLY* 4.3 11.2 - - - +
396A LEU* 3.4 28.7 - - + +
401A LEU 3.0 8.2 + - - +
402A LEU* 3.2 20.8 + - + +
404A CYS* 1.3 76.0 - - - +
406A GLU* 1.3 55.6 + - + +
408A ILE* 3.4 7.3 - - + +
409A GLU* 2.5 54.9 + - + +
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Residues in contact with GLU 406 (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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402A LEU* 3.0 34.7 + - + +
403A GLY* 3.5 14.5 - - - +
405A LEU* 1.3 78.7 - - + +
407A ASP* 1.3 63.0 + - - +
409A GLU* 3.4 16.1 - - - +
410A GLU* 3.0 21.7 + - - +
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Residues in contact with ASP 407 (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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335A GLU* 6.0 0.2 - - - +
336A ASN* 2.4 40.5 + - - +
403A GLY 3.2 9.1 + - - +
404A CYS* 2.9 4.3 + - - +
406A GLU* 1.3 79.8 - - - +
408A ILE* 1.3 60.5 + - - +
410A GLU* 3.0 28.9 + - - +
411A ALA* 3.2 10.2 + - - +
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Residues in contact with ILE 408 (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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329A THR* 3.6 29.8 - - + +
332A ALA* 3.0 28.0 - - + -
333A VAL* 4.0 13.7 - - + -
336A ASN* 2.9 33.2 - - + +
337A VAL* 5.1 0.2 - - + -
389A LEU* 3.8 8.3 - - + -
396A LEU* 3.8 13.5 - - + -
404A CYS* 2.7 25.7 + - + +
405A LEU* 3.4 25.1 - - + +
407A ASP* 1.3 72.2 - - - +
409A GLU* 1.3 65.7 + - - +
411A ALA* 2.8 20.4 + - - +
412A LEU* 3.3 5.4 + - - +
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Residues in contact with GLU 409 (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* 5.4 2.0 - - + -
405A LEU* 2.5 36.3 + - + +
406A GLU* 3.4 15.7 - - - +
408A ILE* 1.3 73.0 - - - +
410A GLU* 1.3 63.7 + - - +
412A LEU* 3.0 26.7 + - + +
413A CYS* 3.1 19.8 + - - +
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Residues in contact with GLU 410 (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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406A GLU 3.0 12.9 + - - +
407A ASP* 3.2 24.0 - - - +
409A GLU* 1.3 77.3 + - - +
411A ALA* 1.3 61.4 + - - +
413A CYS* 2.7 39.0 + - + +
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Residues in contact with ALA 411 (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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328A ALA* 4.4 19.1 - - + +
332A ALA* 3.7 22.7 - - + -
407A ASP 3.2 6.9 + - - +
408A ILE* 2.8 15.3 + - + +
410A GLU* 1.3 79.0 - - - +
412A LEU* 1.3 62.3 + - + +
413A CYS 3.1 4.0 + - - -
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Residues in contact with LEU 412 (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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328A ALA* 4.5 8.7 - - + -
329A THR* 2.6 47.6 - - + +
389A LEU* 4.2 14.1 - - + -
408A ILE 3.3 7.8 + - - +
409A GLU* 3.0 15.7 + - + +
411A ALA* 1.3 77.8 - - - +
413A CYS* 1.3 64.2 + - - +
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Residues in contact with CYS 413 (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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409A GLU* 3.1 20.7 + - - +
410A GLU* 2.7 32.9 + - + +
411A ALA 4.0 3.4 - - - -
412A LEU* 1.3 85.5 - - - +
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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