Contacts of the helix formed by residues 348 - 354 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ALA* 4.3 2.9 - - - -
23C GLY* 3.8 22.1 + - - -
344C SER 2.8 17.6 + - - -
345C ILE* 2.6 23.6 + - - -
346C LEU 2.8 2.6 + - - -
347C ALA* 1.3 75.0 - - - +
349C LEU* 1.3 66.4 + - - +
350C SER 3.7 1.4 + - - -
95K ASP* 3.9 16.6 + - - +
101K PHE* 5.4 0.5 - - - -
102K HIS* 5.2 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLN* 3.6 31.9 - - + +
143C TYR* 4.0 8.7 - - + +
345C ILE* 3.2 22.2 + - + +
346C LEU* 3.0 23.7 + - + +
347C ALA 4.7 1.0 - - - +
348C SER* 1.3 79.4 - - - +
350C SER* 1.3 60.5 + - - +
351C THR* 3.0 21.5 - - - +
352C PHE* 3.1 18.3 + - + +
353C GLN* 4.1 1.9 + - - +
95K ASP* 4.6 7.0 - - - +
101K PHE 4.4 6.5 - - - +
105K ALA* 3.1 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C SER 3.7 2.9 + - - -
349C LEU* 1.3 71.7 - - - +
351C THR* 1.3 61.8 + - - +
352C PHE 3.4 0.7 + - - -
353C GLN* 3.5 8.1 + - - +
354C GLN* 3.1 22.9 + - - -
95K ASP* 5.3 2.0 + - - -
109K LYS* 4.9 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN* 2.7 48.9 + - + +
49A GLN* 4.2 10.4 + - - +
346C LEU* 6.0 0.7 - - + -
349C LEU* 3.8 21.5 - - + +
350C SER* 1.3 75.8 + - - +
352C PHE* 1.3 61.9 + - - +
354C GLN* 3.0 28.7 + - - +
355C MET* 4.0 1.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU* 3.5 15.5 - - + -
133C TYR* 3.5 31.9 - + - -
346C LEU* 3.3 42.0 - - + +
347C ALA* 3.7 10.3 - - - -
349C LEU* 3.1 14.7 + - + +
351C THR* 1.3 74.4 - - - +
353C GLN* 1.3 63.1 + - - +
354C GLN 2.9 7.2 + - - -
355C MET* 2.9 56.6 + - + +
356C TRP* 3.2 55.4 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PRO* 4.2 12.9 - - - +
131C ALA* 4.9 5.7 - - - +
349C LEU 4.1 2.0 + - - +
350C SER* 3.5 7.6 + - - +
351C THR 3.3 1.4 + - - -
352C PHE* 1.3 76.8 - - - +
354C GLN* 1.3 74.2 + - - +
355C MET 3.3 3.5 + - - -
356C TRP* 2.9 56.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C SER* 3.1 24.0 + - - +
351C THR* 3.0 19.3 - - - +
353C GLN* 1.3 88.8 - - - +
355C 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