Contacts of the helix formed by residues 347 - 355 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187F ALA* 3.8 15.4 - - - +
215F ARG* 2.5 40.8 + - - -
216F CYS* 3.3 38.7 - - + +
345F HIS* 3.3 14.6 + - + -
346F PRO* 1.3 91.7 - - - +
348F HIS* 1.3 58.0 + - - +
349F HIS* 3.0 10.8 - - - -
350F ILE* 2.8 42.4 + - + +
351F ALA* 2.9 12.9 + - - +
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Residues in contact with HIS 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340F PRO 2.9 25.0 + - - -
341F GLY* 3.4 21.8 - - - -
342F LEU 3.0 13.8 + - - +
343F GLN* 3.5 40.6 - - + +
345F HIS* 2.9 23.2 + - + +
346F PRO 3.4 1.2 + - - -
347F GLU* 1.3 76.6 - - - +
349F HIS* 1.3 60.0 + - - +
351F ALA* 4.0 1.3 - - - -
352F LYS* 3.1 61.5 + - + +
358F PHE* 5.0 3.6 - + - -
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Residues in contact with HIS 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346F PRO 3.4 24.8 + - - -
347F GLU* 3.8 11.0 - - - -
348F HIS* 1.3 79.1 + - + +
350F ILE* 1.3 90.9 + - + +
352F LYS* 3.7 6.9 + - - +
353F LYS* 3.2 23.5 + - + +
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Residues in contact with ILE 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F ALA* 6.5 0.7 - - - -
216F CYS* 4.4 7.2 - - + +
217F VAL 4.0 2.0 - - - -
218F ASP* 3.6 51.6 - - + +
347F GLU* 2.8 28.4 + - + +
349F HIS* 1.3 101.5 - - + +
351F ALA* 1.3 65.8 + - - +
353F LYS* 2.9 20.2 + - + +
354F GLN* 2.9 30.7 + - - +
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Residues in contact with ALA 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216F CYS* 4.1 10.5 - - - +
340F PRO* 3.7 35.2 - - + +
347F GLU 2.9 14.4 + - - +
348F HIS* 4.0 1.3 - - - +
350F ILE* 1.3 78.0 - - - +
352F LYS* 1.3 57.5 + - - +
354F GLN* 4.5 2.5 - - - -
355F MET* 2.8 47.5 + - - +
358F PHE* 3.8 12.9 - - + -
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Residues in contact with LYS 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F GLN* 4.9 8.7 + - - +
348F HIS* 3.1 47.7 + - + +
349F HIS* 3.9 7.9 - - - +
351F ALA* 1.3 80.1 - - - +
353F LYS* 1.3 59.9 + - - +
355F MET 3.8 9.6 - - - +
358F PHE* 4.1 14.3 - - + -
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Residues in contact with LYS 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F ASP* 3.0 34.2 + - - +
220F GLU* 3.9 22.7 + - - -
221F LEU* 5.8 0.2 - - - +
250F LEU* 5.9 0.3 - - - +
349F HIS* 3.2 15.6 + - + +
350F ILE* 2.9 16.1 + - + +
352F LYS* 1.3 79.2 - - - +
354F GLN* 1.3 63.0 + - + +
355F MET 3.7 0.7 - - - -
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Residues in contact with GLN 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F SER* 3.7 12.3 + - - -
216F CYS* 4.5 1.2 - - - +
217F VAL 2.9 20.7 + - - +
218F ASP* 3.7 6.2 - - - +
219F ILE* 3.1 38.6 + - - +
220F GLU* 4.5 0.9 + - - +
244F ASN 4.1 0.5 - - - +
245F GLN* 3.6 24.2 + - - +
246F LYS 4.9 0.7 + - - -
250F LEU* 3.4 31.4 - - + +
350F ILE* 2.9 27.9 + - - +
351F ALA* 4.5 0.2 - - - -
353F LYS* 1.3 82.5 - - + +
355F MET* 1.3 71.9 + - + +
356F THR* 5.5 1.0 - - - +
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Residues in contact with MET 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F SER* 4.1 5.8 - - - +
209F PRO* 3.7 31.6 - - + -
216F CYS* 3.7 23.8 - - + -
240F ALA* 5.3 4.0 - - - -
244F ASN* 3.3 9.6 - - - +
245F GLN* 3.3 26.5 - - + +
340F PRO* 4.9 0.9 - - - -
351F ALA* 2.8 24.1 + - + +
352F LYS* 3.8 12.0 - - - +
353F LYS 3.7 0.5 - - - -
354F GLN* 1.3 90.9 - - + +
356F THR* 1.3 64.4 + - - +
357F GLY 3.3 22.2 - - - +
358F PHE* 4.3 19.9 - - + -
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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