Contacts of the helix formed by residues 347 - 355 (chain A) in PDB entry 1I43
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 GLU 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A ALA* 3.9 14.4 - - - +
215A ARG* 2.5 46.4 + - - -
216A CYS* 3.2 38.3 - - + +
345A HIS* 3.1 14.5 + - + -
346A PRO* 1.3 87.5 - - - +
348A HIS* 1.3 58.5 + - - +
349A HIS* 3.1 10.2 - - - -
350A ILE* 3.0 26.4 + - + +
351A ALA* 2.8 27.5 + - - +
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Residues in contact with HIS 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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340A PRO 2.9 26.6 + - - +
341A GLY* 3.4 20.9 - - - -
342A LEU 3.0 15.0 + - - +
343A GLN* 3.6 38.6 - - + +
345A HIS* 2.9 21.4 + - + +
346A PRO 3.3 1.4 + - - -
347A GLU* 1.3 77.9 - - - +
349A HIS* 1.3 60.8 + - - +
351A ALA* 3.9 0.4 - - - +
352A LYS* 3.0 65.7 + - + +
358A PHE* 5.0 3.6 - + - -
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Residues in contact with HIS 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A HIS 5.4 0.2 + - - -
346A PRO 3.3 25.3 + - - -
347A GLU* 4.0 8.1 - - - -
348A HIS* 1.3 83.1 + - + +
350A ILE* 1.3 86.0 + - + +
352A LYS* 3.8 7.1 - - - +
353A LYS* 3.2 22.9 + - - +
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Residues in contact with ILE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ALA* 6.4 2.0 - - + -
216A CYS* 4.3 9.9 - - + +
217A VAL 4.1 1.8 - - - -
218A ASP* 3.8 39.7 - - + +
347A GLU* 3.0 29.5 + - + +
349A HIS* 1.3 100.9 - - + +
351A ALA* 1.3 61.9 + - - +
353A LYS* 2.8 26.7 + - + +
354A GLN* 2.9 39.3 + - - +
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Residues in contact with ALA 351 (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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216A CYS* 4.0 11.0 - - - +
340A PRO* 3.7 32.1 - - + +
347A GLU 2.8 18.8 + - - +
348A HIS 3.9 3.6 - - - +
350A ILE* 1.3 73.4 - - - +
352A LYS* 1.3 58.2 + - - +
354A GLN* 4.4 7.4 - - - -
355A MET* 2.8 43.0 + - - +
358A PHE* 3.8 12.2 - - + -
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Residues in contact with LYS 352 (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 GLN* 4.9 10.1 + - - +
348A HIS* 3.0 52.6 + - + +
349A HIS* 3.8 7.6 - - - +
351A ALA* 1.3 76.8 - - - +
353A LYS* 1.3 60.3 + - - +
355A MET 3.9 9.8 - - - +
358A PHE* 4.2 14.8 - - + -
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Residues in contact with LYS 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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218A ASP* 3.2 33.3 + - - +
220A GLU* 3.9 22.9 + - - -
221A LEU* 5.9 0.2 - - - +
349A HIS 3.2 15.9 + - - +
350A ILE* 2.8 12.2 + - + +
352A LYS* 1.3 81.4 - - - +
354A GLN* 1.3 63.7 + - + +
355A MET 3.7 0.7 - - - -
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Residues in contact with GLN 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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208A SER* 3.7 15.0 + - - -
216A CYS* 4.4 0.6 - - - +
217A VAL 2.9 23.2 + - - +
218A ASP* 3.6 8.8 - - - +
219A ILE* 3.2 36.3 + - - +
220A GLU* 4.6 0.7 + - - +
245A GLN* 3.6 21.8 + - - +
246A LYS 5.0 0.3 + - - -
250A LEU* 3.5 29.0 - - + +
350A ILE* 2.9 26.7 + - - +
351A ALA* 4.4 0.7 - - - +
353A LYS* 1.3 83.1 - - + +
355A MET* 1.3 74.9 + - + +
356A THR* 5.6 1.0 - - - +
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Residues in contact with MET 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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208A SER* 4.1 2.2 - - - +
209A PRO* 3.8 25.8 - - + -
216A CYS* 3.7 27.1 - - - -
240A ALA* 5.3 3.1 - - - -
244A ASN* 3.3 15.0 - - + +
245A GLN* 3.3 24.7 - - + +
340A PRO* 4.9 1.1 - - - -
351A ALA* 2.8 29.7 + - + +
352A LYS* 3.9 11.4 - - - +
353A LYS 3.7 0.9 - - - -
354A GLN* 1.3 97.5 - - + +
356A THR* 1.3 64.4 + - - +
357A GLY 3.2 20.6 - - - +
358A PHE* 4.3 12.9 - - + -
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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