Contacts of the helix formed by residues 341 - 350 (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 ARG 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A PRO* 3.6 38.6 + - + +
339A PRO 3.2 0.6 - - - -
340A LEU* 1.3 97.3 - - + +
342A TRP* 1.3 65.6 + - - +
343A LYS 3.2 2.9 - - - -
344A GLU* 2.9 40.6 + - + +
345A PHE* 3.0 11.8 + - - +
399A MET* 5.2 4.2 - - + +
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Residues in contact with TRP 342 (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* 3.2 28.7 - - + -
334A VAL* 3.4 18.6 - - - -
337A VAL* 3.4 14.4 - - + -
338A PRO 3.2 21.4 + - - +
339A PRO* 2.9 19.8 + - + +
340A LEU 3.2 0.2 - - - -
341A ARG* 1.3 76.5 - - - +
343A LYS* 1.3 53.1 + - - +
345A PHE* 2.8 15.9 + + - +
346A VAL* 2.6 75.3 + - + +
359A LEU* 6.3 0.9 - - + -
371A GLN* 2.9 56.2 - - + +
374A MET* 3.7 11.8 - - + +
375A LEU* 3.5 34.5 - - + -
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Residues in contact with LYS 343 (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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340A LEU 4.6 5.0 + - - +
341A ARG 3.2 1.0 - - - -
342A TRP* 1.3 77.6 - - - +
344A GLU* 1.3 54.4 + - + +
346A VAL* 2.8 11.4 + - - +
347A LYS* 2.6 69.7 + - + +
353A ASP* 4.4 11.4 + - - -
356A ILE* 3.5 23.3 - - + -
357A ASP* 3.2 31.1 + - - -
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Residues in contact with GLU 344 (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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341A ARG* 2.9 36.7 + - + +
343A LYS* 1.3 77.7 - - + +
345A PHE* 1.3 63.3 + - - +
347A LYS* 2.9 33.6 + - + +
348A ARG* 2.9 19.7 + - + +
399A MET* 4.7 4.9 - - + -
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Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A VAL* 4.1 6.7 - - + -
337A VAL* 3.5 36.6 - - + -
338A PRO* 5.8 0.4 - - + -
341A ARG 3.0 8.0 + - - +
342A TRP* 2.8 25.2 + + - +
344A GLU* 1.3 76.3 - - - +
346A VAL* 1.3 66.6 + - + +
348A ARG* 3.2 5.2 + - - +
349A LEU* 3.0 32.9 + - + +
375A LEU* 5.0 0.4 - - + -
392A LEU* 3.2 38.1 - - + -
395A VAL* 3.6 12.5 - - + +
396A LEU* 3.5 27.1 - - + -
399A MET* 3.4 38.4 - - + +
401A LEU* 4.1 2.5 - - + -
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A TRP* 2.6 56.6 + - + +
343A LYS* 3.1 13.7 - - - +
345A PHE* 1.3 74.2 - - + +
347A LYS* 1.3 59.2 + - - +
349A LEU* 2.7 29.7 + - - +
350A GLY 3.2 4.5 + - - -
351A LEU* 4.0 4.9 + - + -
356A ILE* 3.2 31.8 - - + +
359A LEU* 5.6 0.9 - - + -
374A MET* 3.1 37.9 - - + -
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Residues in contact with LYS 347 (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* 2.6 55.7 + - - +
344A GLU* 3.3 21.9 - - + +
346A VAL* 1.3 72.3 - - - +
348A ARG* 1.3 65.4 + - + +
350A GLY* 3.1 14.0 + - - -
351A LEU 5.5 1.6 - - - -
353A ASP* 3.7 20.2 - - - +
356A ILE* 4.4 11.9 - - + -
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Residues in contact with ARG 348 (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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344A GLU* 2.9 19.1 + - + +
345A PHE 3.4 2.2 - - - +
347A LYS* 1.3 78.6 - - + +
349A LEU* 1.3 61.9 + - - +
350A GLY* 3.2 1.2 + - - -
395A VAL* 3.2 35.3 - - + +
398A ASP* 5.0 21.9 + - + +
399A MET* 3.8 23.1 - - + +
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Residues in contact with LEU 349 (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* 3.0 32.6 + - + +
346A VAL* 2.7 20.0 + - + +
348A ARG* 1.3 79.8 - - - +
350A GLY* 1.3 56.9 + - - +
351A LEU 3.5 1.3 - - - +
374A MET* 3.2 29.4 - - + -
375A LEU* 5.1 0.4 - - + -
378A TRP* 3.1 58.4 - - + -
391A LEU* 3.6 14.8 - - + +
392A LEU* 3.5 23.3 - - + -
395A VAL* 3.5 20.4 - - + +
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Residues in contact with GLY 350 (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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346A VAL 3.2 0.6 + - - -
347A LYS 3.1 15.5 + - - -
348A ARG 3.1 1.5 - - - -
349A LEU* 1.3 79.6 - - - +
351A LEU* 1.3 64.9 + - - +
352A SER 3.8 0.5 + - - -
378A TRP* 4.5 2.9 - - - -
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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