Contacts of the helix formed by residues 348 - 354 (chain H) in PDB entry 3LUE
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 SER 348 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H ALA* 4.3 2.2 - - - -
23H GLY* 3.8 22.3 + - - -
344H SER 2.8 19.4 + - - -
345H ILE* 2.6 23.4 + - - -
346H LEU 2.8 2.8 + - - -
347H ALA* 1.3 74.2 - - - +
349H LEU* 1.3 66.7 + - - +
350H SER 3.7 1.4 + - - -
95Q ASP* 4.0 16.4 + - - +
101Q PHE* 5.4 0.5 - - - -
102Q HIS* 5.2 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F GLN* 3.6 31.2 - - + +
143H TYR* 4.0 9.2 - - + +
345H ILE* 3.2 22.0 + - + +
346H LEU* 3.0 23.7 + - + +
347H ALA 4.7 0.9 - - - +
348H SER* 1.3 80.5 - - - +
350H SER* 1.3 60.4 + - - +
351H THR* 3.0 19.5 - - - +
352H PHE* 3.1 18.2 + - - +
353H GLN* 4.1 2.3 + - - +
95Q ASP* 4.6 6.7 - - - +
101Q PHE 4.4 6.5 - - - +
102Q HIS* 6.0 0.2 - - - -
104Q ILE* 6.3 0.4 - - + -
105Q ALA* 3.1 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 350 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348H SER 3.7 2.6 + - - -
349H LEU* 1.3 71.1 - - - +
351H THR* 1.3 62.6 + - - +
352H PHE 3.4 0.5 + - - -
353H GLN* 3.5 8.2 + - - +
354H GLN* 3.1 23.1 + - - -
95Q ASP* 5.3 2.0 + - - -
109Q LYS* 4.9 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 351 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F GLN* 2.7 49.5 + - + +
49F GLN* 4.2 10.2 + - - +
346H LEU* 6.0 1.1 - - + -
349H LEU* 3.8 21.2 - - + +
350H SER* 1.3 75.8 + - - +
352H PHE* 1.3 62.5 + - + +
354H GLN* 3.0 28.9 + - - +
355H MET* 4.0 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 352 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H LEU* 3.5 16.2 - - + -
133H TYR* 3.5 32.3 - + + -
346H LEU* 3.3 43.5 - - + +
347H ALA* 3.7 10.5 - - - +
349H LEU* 3.1 14.5 + - + +
351H THR* 1.3 73.4 - - - +
353H GLN* 1.3 63.2 + - - +
354H GLN 2.9 6.9 + - - -
355H MET* 2.9 56.8 + - + +
356H TRP* 3.2 55.3 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H PRO* 4.2 13.5 - - - +
131H ALA* 4.9 5.7 - - - +
349H LEU 4.1 2.4 + - - +
350H SER* 3.5 7.6 + - - +
351H THR 3.3 1.6 + - - -
352H PHE* 1.3 75.4 - - - +
354H GLN* 1.3 72.8 + - - +
355H MET 3.3 3.6 + - - -
356H TRP* 2.9 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 354 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350H SER* 3.1 23.4 + - - -
351H THR* 3.0 19.3 - - - +
352H PHE 2.9 0.2 - - - -
353H GLN* 1.3 88.6 - - - +
355H MET* 1.3 69.0 + - - +
----------------------------------------------------------
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