Contacts of the helix formed by residues 352 - 363 (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 SER 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A GLY 3.8 1.0 + - - -
351A LEU* 1.3 76.2 - - - +
353A ASP* 1.3 64.7 + - - +
354A HIS* 3.7 14.7 + - - +
355A GLU* 3.2 27.5 + - - +
356A ILE* 3.2 15.1 + - - +
381A ARG* 5.5 5.4 - - - -
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Residues in contact with ASP 353 (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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343A LYS* 4.4 8.3 + - - -
347A LYS* 3.7 30.2 - - + +
351A LEU 3.0 4.1 + - - +
352A SER* 1.3 72.8 + - - +
354A HIS* 1.3 75.9 + - + +
356A ILE* 3.0 28.9 + - - +
357A ASP* 3.4 13.9 + - - +
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Residues in contact with HIS 354 (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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352A SER* 3.3 7.9 + - - +
353A ASP* 1.3 86.9 + - + +
355A GLU* 1.3 64.2 + - - +
357A ASP* 3.1 21.7 + - - +
358A ARG* 3.2 20.1 + - + +
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Residues in contact with GLU 355 (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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351A LEU* 3.1 34.1 - - + +
352A SER* 3.2 21.6 + - - +
354A HIS* 1.3 79.7 - - - +
356A ILE* 1.3 63.8 + - - +
358A ARG* 3.1 20.9 + - + +
359A LEU* 3.0 36.6 + - + +
377A THR* 3.7 17.6 - - - +
381A ARG* 2.9 41.0 + - - +
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Residues in contact with ILE 356 (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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342A TRP* 6.2 0.2 - - + -
343A LYS* 3.5 32.1 - - + -
346A VAL* 3.2 40.2 - - + -
347A LYS* 4.3 20.6 - - + +
351A LEU* 4.1 11.2 - - + +
352A SER 3.2 10.8 - - - +
353A ASP* 3.0 26.0 + - - +
355A GLU* 1.3 78.2 - - - +
357A ASP* 1.3 64.0 + - - +
359A LEU* 3.2 29.0 + - + +
360A GLU* 4.1 1.4 + - - +
374A MET* 4.6 3.8 - - + -
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Residues in contact with ASP 357 (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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343A LYS* 3.2 32.6 + - - +
353A ASP* 3.4 12.7 + - - +
354A HIS* 3.1 15.2 + - - +
356A ILE* 1.3 77.9 - - - +
358A ARG* 1.3 64.5 + - + +
359A LEU 3.2 0.5 + - - -
360A GLU* 3.3 19.8 + - - +
361A LEU* 4.1 2.1 + - - +
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Residues in contact with ARG 358 (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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354A HIS* 3.4 18.4 - - + +
355A GLU* 3.1 21.8 + - + +
357A ASP* 1.3 75.7 - - + +
359A LEU* 1.3 67.7 + - + +
361A LEU* 3.0 26.4 + - + +
362A GLN* 3.1 10.7 + - - +
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Residues in contact with LEU 359 (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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342A TRP* 6.3 0.7 - - + -
346A VAL* 5.3 1.6 - - + -
351A LEU* 5.1 0.7 - - + -
355A GLU* 3.0 38.0 + - + +
356A ILE* 3.2 25.8 - - + +
357A ASP 3.1 0.4 - - - -
358A ARG* 1.3 79.3 - - + +
360A GLU* 1.3 64.2 + - - +
362A GLN* 3.0 25.8 + - + +
363A ASN 3.4 5.7 + - - +
370A ALA* 4.9 12.9 - - + +
373A SER* 4.8 16.2 + - - -
374A MET* 3.8 41.5 - - + +
377A THR* 5.1 11.0 - - + +
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Residues in contact with GLU 360 (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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356A ILE 4.1 1.5 + - - +
357A ASP* 3.3 12.1 + - - +
358A ARG 3.1 0.4 - - - -
359A LEU* 1.3 78.7 - - - +
361A LEU* 1.3 63.1 + - - +
363A ASN 3.1 1.2 + - - -
364A GLY* 3.0 38.4 + - - +
370A ALA* 5.3 6.0 - - + +
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Residues in contact with LEU 361 (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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357A ASP 4.1 1.2 + - - +
358A ARG* 3.0 22.6 + - + +
360A GLU* 1.3 80.4 + - - +
362A GLN* 1.3 65.3 + - - +
363A ASN* 3.1 1.7 + - - -
364A GLY 4.9 0.2 + - - -
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Residues in contact with GLN 362 (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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358A ARG 3.1 9.4 + - - +
359A LEU* 3.0 16.6 + - + +
361A LEU* 1.3 77.3 - - - +
363A ASN* 1.3 81.1 + - + +
369A GLU* 6.0 0.7 - - - -
373A SER* 2.6 37.8 + - - -
377A THR* 4.2 13.3 + - - +
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Residues in contact with ASN 363 (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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359A LEU 3.4 2.0 + - - -
360A GLU 3.1 3.4 + - - -
361A LEU 3.1 3.7 + - - -
362A GLN* 1.3 94.3 + - + +
364A GLY* 1.3 61.6 + - - +
365A ARG* 3.3 37.0 + - - +
366A CYS 3.7 13.3 - - - +
369A GLU* 2.6 43.2 + - + +
370A ALA* 3.9 13.3 + - - +
373A SER* 5.4 0.9 - - - +
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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