Contacts of the helix formed by residues 342 - 349 (chain D) in PDB entry 3IML
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 LYS 342 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D TYR* 6.3 0.8 - - - -
272D SER* 6.5 0.9 - - - -
340D ARG* 3.3 0.6 - - - +
341D PRO* 1.3 82.4 - - + +
343D GLY* 1.3 64.9 + - - +
344D ILE 3.1 1.8 - - - -
345D ILE* 3.2 44.4 + - + +
346D GLN* 3.3 11.8 + - - +
351D LEU* 5.7 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D ASP* 3.7 33.4 - - - +
340D ARG* 2.9 12.6 + - - +
342D LYS* 1.3 76.5 - - - +
344D ILE* 1.3 57.5 + - - +
346D GLN* 3.9 7.7 - - - +
347D MET* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D VAL* 6.4 0.2 - - + -
277D SER* 3.4 33.2 - - - +
278D ALA* 4.0 11.2 - - + +
281D ALA* 3.6 29.4 - - + -
304D TYR* 3.9 16.6 - - - +
338D ASP 3.9 11.9 - - - +
339D LEU* 3.8 19.7 - - + +
340D ARG 2.7 16.5 + - - +
341D PRO* 3.8 9.9 - - + +
342D LYS 3.1 0.2 - - - -
343D GLY* 1.3 74.5 - - - +
345D ILE* 1.3 64.8 + - - +
347D MET* 3.2 6.2 + - + +
348D LEU* 3.1 29.8 + - + +
350D LEU* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D PRO* 4.0 39.0 - - + +
272D SER* 4.0 11.0 - - - +
277D SER* 4.9 1.8 - - - -
341D PRO 4.3 9.0 - - - +
342D LYS* 3.2 38.6 + - + +
344D ILE* 1.3 78.3 - - - +
346D GLN* 1.3 57.1 + - - +
349D ASP* 2.9 26.0 + - - -
350D LEU* 3.2 19.7 + - + +
351D LEU* 3.8 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 346 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D ASP* 5.9 0.7 - - - +
342D LYS 3.3 9.0 + - - +
343D GLY* 3.9 10.8 - - - +
344D ILE 3.3 0.4 - - - -
345D ILE* 1.3 80.4 - - - +
347D MET* 1.3 63.5 + - - +
349D ASP* 3.2 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D ALA* 4.8 8.7 - - + +
284D TYR* 3.8 38.0 + - + +
285D VAL* 6.0 1.1 - - + -
337D PHE* 4.0 14.4 - - + -
338D ASP* 3.1 45.5 - - + +
339D LEU* 4.9 2.9 - - + -
343D GLY 3.0 15.7 + - - +
344D ILE* 3.2 18.8 + - + +
346D GLN* 1.3 78.3 - - - +
348D LEU* 1.3 66.5 + - + +
349D ASP* 3.9 0.7 + - - +
372D SER* 5.4 0.9 - - - -
378D LYS* 4.7 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 348 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D TYR* 4.1 19.1 - - + -
281D ALA* 4.1 17.0 - - + +
284D TYR* 3.7 38.1 - - + -
344D ILE* 3.1 20.6 + - + +
347D MET* 1.3 81.1 - - + +
349D ASP* 1.3 73.0 + - - +
350D LEU* 3.4 18.1 + - + +
352D ARG* 3.9 1.6 + - - -
372D SER* 2.6 43.0 + - - +
373D TRP* 3.7 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 349 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345D ILE 2.9 13.6 + - - -
346D GLN* 3.2 10.1 + - - +
347D MET 5.3 0.4 - - - +
348D LEU* 1.3 80.6 - - - +
350D LEU* 1.3 58.1 + - - +
351D LEU* 3.4 8.5 + - - +
352D ARG* 2.9 51.3 + - - +
372D SER* 5.7 0.7 - - - -
----------------------------------------------------------
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