Contacts of the helix formed by residues 347 - 355 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L ALA* 3.8 14.0 - - - +
215L ARG* 2.7 47.7 + - - -
216L CYS* 3.3 36.8 - - + +
345L HIS* 3.3 14.7 + - + -
346L PRO* 1.3 89.2 - - - +
348L HIS* 1.3 54.4 + - - +
349L HIS* 3.0 10.9 - - - -
350L ILE* 2.7 47.0 + - + +
351L ALA* 2.9 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 348 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340L PRO 2.8 26.5 + - - +
341L GLY* 3.2 23.1 + - - -
342L LEU 3.0 17.8 + - - +
343L GLN* 3.7 32.2 - - - +
345L HIS* 3.1 21.3 + - + +
346L PRO 3.5 0.8 + - - -
347L GLU* 1.3 77.2 - - - +
349L HIS* 1.3 59.0 + - - +
351L ALA* 4.4 1.6 - - - -
352L LYS* 3.0 63.4 + - + +
358L PHE* 4.8 5.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 349 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345L HIS 5.3 0.2 + - - -
346L PRO 3.3 26.0 + - - -
347L GLU* 3.7 9.2 - - - -
348L HIS* 1.3 81.6 + - + +
350L ILE* 1.3 90.5 + - + +
352L LYS* 3.9 6.7 - - - +
353L LYS* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 350 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L ALA* 6.4 0.9 - - - -
216L CYS* 4.2 11.2 - - + +
217L VAL 4.1 1.3 - - - -
218L ASP* 3.8 39.5 - - + +
347L GLU* 2.7 32.1 + - + +
349L HIS* 1.3 100.3 - - + +
351L ALA* 1.3 67.1 + - - +
353L LYS* 2.8 21.3 + - + +
354L GLN* 2.9 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216L CYS* 3.9 14.1 - - - +
340L PRO* 3.7 32.5 - - + +
347L GLU 2.9 12.8 + - - +
348L HIS* 4.0 4.5 - - - +
350L ILE* 1.3 76.3 - - - +
352L LYS* 1.3 57.3 + - - +
354L GLN* 4.5 2.7 - - - -
355L MET* 2.8 46.2 + - - +
358L PHE* 3.7 12.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 352 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343L GLN* 5.2 7.1 + - - +
348L HIS* 3.0 54.4 + - + +
349L HIS* 3.9 7.2 - - - +
350L ILE 3.1 0.2 - - - -
351L ALA* 1.3 78.0 - - - +
353L LYS* 1.3 59.6 + - - +
355L MET 3.9 9.7 - - - +
358L PHE* 4.1 14.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 353 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218L ASP* 3.2 32.6 + - - +
220L GLU* 3.8 25.7 + - - -
221L LEU* 5.8 0.2 - - - +
349L HIS 3.2 15.5 + - - +
350L ILE* 2.8 13.7 + - + +
352L LYS* 1.3 80.9 - - - +
354L GLN* 1.3 65.2 + - + +
355L MET 3.7 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 354 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208L SER* 3.6 17.0 + - - -
216L CYS* 4.4 1.0 - - - +
217L VAL 3.0 20.5 + - - +
218L ASP* 3.8 7.1 - - - +
219L ILE* 3.2 35.2 + - - +
220L GLU* 4.6 1.2 + - - +
244L ASN 4.0 0.2 - - - +
245L GLN* 3.5 25.2 + - - +
246L LYS 4.9 0.5 + - - -
250L LEU* 3.5 28.7 - - + +
350L ILE* 2.9 28.1 + - - +
353L LYS* 1.3 83.7 - - + +
355L MET* 1.3 71.3 + - + +
356L THR* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 355 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208L SER* 4.0 7.0 - - - +
209L PRO* 3.7 32.8 - - + -
216L CYS* 3.7 23.1 - - - -
240L ALA* 5.3 3.1 - - - -
244L ASN* 3.2 11.2 - - - +
245L GLN* 3.3 26.5 - - + +
340L PRO* 4.9 1.1 - - - -
351L ALA* 2.8 32.9 + - + +
352L LYS* 3.9 11.3 - - - +
353L LYS 4.9 0.5 - - - -
354L GLN* 1.3 90.2 - - + +
356L THR* 1.3 66.5 + - - +
357L GLY 3.2 21.1 - - - +
358L PHE* 4.2 12.9 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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