Contacts of the helix formed by residues 128 - 132 (chain P) in PDB entry 6LTJ
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 MET 128 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1958L GLU* 5.0 2.2 - - - +
2096L SER 4.3 0.4 - - - +
2097L ALA* 3.7 25.7 - - + +
2100L GLN* 4.0 17.7 - - + -
2101L ASP* 3.2 24.8 + - - +
126P LYS* 5.2 4.9 - - - +
127P LYS* 1.3 71.1 - - - +
129P ALA* 1.3 61.7 - - - +
130P ASP 3.3 1.3 - - - -
131P LYS* 3.4 24.5 + - - +
132P ILE* 3.6 26.6 - - + +
151P LEU* 6.3 2.2 - - + -
155P ARG* 4.2 38.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2097L ALA* 4.1 16.4 - - + +
2098L GLU* 6.5 0.7 - - - -
2101L ASP* 3.2 14.6 + - + +
127P LYS* 3.3 7.5 - - + -
128P MET* 1.3 74.1 - - - +
130P ASP* 1.3 59.9 + - - +
131P LYS 3.1 10.0 + - - -
132P ILE* 3.5 26.1 + - + +
428P ILE* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P LYS 5.6 0.5 - - - +
126P LYS* 5.2 1.4 - - - -
127P LYS* 3.7 37.6 + - - +
128P MET 3.3 0.8 - - - -
129P ALA* 1.3 80.4 - - - +
131P LYS* 1.3 60.9 + - - +
132P ILE 3.8 0.4 - - - -
425P HIS* 3.8 29.2 - - + +
428P ILE* 4.2 17.9 - - - +
429P GLU* 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895N GLN* 6.2 0.2 - - - +
898N LYS* 4.6 18.4 - - - +
126P LYS* 3.6 28.5 - - - +
127P LYS 3.1 22.2 + - - -
128P MET* 3.4 21.5 + - - +
129P ALA 3.1 1.0 - - - -
130P ASP* 1.3 79.3 - - - +
132P ILE* 1.3 61.4 + - + +
147P TYR* 2.4 37.1 + - - +
151P LEU* 3.3 19.2 - - + +
154P GLU* 6.1 2.0 - - - -
421P ASP* 5.3 2.9 - - + -
424P ILE* 4.7 7.9 - - + -
425P HIS* 3.3 29.7 + - + +
428P ILE* 3.5 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1958L GLU* 3.5 37.9 - - + +
2097L ALA* 4.1 12.3 - - + -
2098L GLU* 5.4 3.6 - - - +
128P MET* 3.6 21.5 - - + +
129P ALA* 3.5 21.3 - - + +
131P LYS* 1.3 82.5 - - - +
133P LEU* 1.3 69.3 + - - +
134P PRO* 3.8 5.2 - - - +
138P ARG* 5.2 2.2 - - - +
148P MET* 4.1 17.0 - - + -
151P LEU* 4.0 17.9 - - + -
428P ILE* 4.0 11.7 - - - +
----------------------------------------------------------
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