Contacts of the helix formed by residues 347 - 355 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187J ALA* 3.7 14.7 - - - +
215J ARG* 2.5 42.6 + - - -
216J CYS* 3.2 38.6 - - + +
345J HIS* 3.2 13.3 + - + -
346J PRO* 1.3 91.7 - - - +
348J HIS* 1.3 59.0 + - - +
349J HIS* 3.1 10.0 - - - -
350J ILE* 3.0 27.3 + - + +
351J ALA* 2.8 27.9 + - - +
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Residues in contact with HIS 348 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340J PRO 2.9 24.7 + - - +
341J GLY* 3.4 21.5 - - - -
342J LEU 3.0 13.4 + - - +
343J GLN* 3.5 41.1 + - - +
345J HIS* 2.9 20.5 + - + +
346J PRO 3.4 0.8 + - - -
347J GLU* 1.3 77.2 - - - +
349J HIS* 1.3 60.6 + - - +
351J ALA* 3.7 1.7 - - - +
352J LYS* 2.9 66.0 + - + +
358J PHE* 4.9 4.0 - + - -
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Residues in contact with HIS 349 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346J PRO 3.3 25.2 + - - -
347J GLU* 3.7 9.9 - - - -
348J HIS* 1.3 82.5 + - - +
350J ILE* 1.3 86.4 + - + +
352J LYS* 3.8 7.3 - - - +
353J LYS* 3.2 22.9 + - - +
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Residues in contact with ILE 350 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187J ALA* 6.4 1.8 - - + -
216J CYS* 4.3 11.4 - - + +
217J VAL 4.1 1.3 - - - -
218J ASP* 3.7 48.5 - - + +
347J GLU* 3.0 30.9 + - + +
349J HIS* 1.3 99.8 - - + +
351J ALA* 1.3 61.5 + - - +
353J LYS* 2.8 27.6 + - + +
354J GLN* 2.9 30.3 + - - +
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Residues in contact with ALA 351 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216J CYS* 4.2 13.0 - - - +
340J PRO* 3.7 32.1 - - + +
347J GLU 2.8 15.1 + - - +
348J HIS 3.7 4.3 - - - +
350J ILE* 1.3 76.7 - - - +
352J LYS* 1.3 57.8 + - - +
354J GLN* 4.6 2.7 - - - -
355J MET* 2.8 45.5 + - - +
358J PHE* 3.7 13.0 - - + -
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Residues in contact with LYS 352 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343J GLN* 4.8 9.7 + - - +
348J HIS* 2.9 52.2 + - + +
349J HIS* 3.8 7.2 - - - +
351J ALA* 1.3 76.4 - - - +
353J LYS* 1.3 58.4 + - - +
355J MET 4.0 10.0 - - - +
358J PHE* 4.2 14.5 - - + -
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Residues in contact with LYS 353 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218J ASP* 3.2 32.6 + - - +
220J GLU* 3.8 22.3 + - - +
349J HIS 3.2 14.3 + - - +
350J ILE* 2.8 17.3 + - + +
352J LYS* 1.3 80.5 - - - +
354J GLN* 1.3 61.5 + - + +
355J MET 3.6 1.1 - - - -
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Residues in contact with GLN 354 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208J SER* 3.7 11.9 + - - -
216J CYS* 4.6 1.4 - - - +
217J VAL 2.9 22.1 + - - +
218J ASP* 3.6 8.7 - - - +
219J ILE* 3.1 41.1 + - - +
220J GLU* 4.4 1.0 + - - +
245J GLN* 3.5 24.9 + - - +
246J LYS 4.9 0.3 + - - -
250J LEU* 3.4 27.9 - - + +
350J ILE* 2.9 27.6 + - - +
351J ALA* 4.6 0.4 - - - -
353J LYS* 1.3 82.2 - - + +
355J MET* 1.3 69.8 + - + +
356J THR* 5.5 1.0 - - - +
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Residues in contact with MET 355 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208J SER* 4.1 4.9 - - - +
209J PRO* 3.7 28.0 - - + -
216J CYS* 3.6 29.6 - - - -
240J ALA* 5.0 4.3 - - - -
244J ASN* 3.3 10.8 - - - +
245J GLN* 3.3 29.4 - - + +
340J PRO* 5.0 1.3 - - - -
351J ALA* 2.8 24.1 + - - +
352J LYS* 4.0 11.6 - - - +
353J LYS 3.6 0.5 - - - -
354J GLN* 1.3 87.5 - - + +
356J THR* 1.3 64.2 + - - +
357J GLY 3.3 21.3 - - - +
358J PHE* 4.3 18.4 - - + -
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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