Contacts of the helix formed by residues 899 - 907 (chain B) in PDB entry 3LMG
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 ALA 899 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897B ARG* 3.3 20.6 - - + +
898B LEU* 1.3 77.6 - - - +
900B GLU* 1.3 58.1 + - - +
902B PRO* 3.4 11.7 - - - +
903B ASP* 3.1 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 900 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896B LEU* 4.7 19.9 - - + +
897B ARG* 3.3 15.5 + - + +
898B LEU 3.0 1.0 - - - -
899B ALA* 1.3 77.3 - - - +
901B VAL* 1.3 54.3 + - - +
902B PRO 3.5 0.2 - - - -
903B ASP* 3.1 12.7 + - + +
904B LEU* 2.7 52.4 + - + +
907B LYS* 5.8 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 901 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856B ILE* 4.8 20.0 - - + +
857B LYS* 5.2 3.1 - - + -
864B ILE* 5.4 1.6 - - + -
893B TYR* 4.1 39.9 - - + -
896B LEU* 4.1 10.1 - - + +
897B ARG 4.1 4.0 - - - +
898B LEU* 2.7 40.0 + - + +
900B GLU* 1.3 70.0 - - - +
902B PRO* 1.4 67.0 - - + +
904B LEU* 2.9 10.1 + - - +
905B LEU* 2.9 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 902 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856B ILE* 5.1 9.2 - - + -
861B LEU* 3.7 18.0 - - + +
864B ILE* 4.0 27.4 - - + -
865B HIS* 4.6 9.4 - - + -
898B LEU 3.2 13.2 - - - +
899B ALA* 3.4 15.3 - - - +
901B VAL* 1.4 91.6 - - + +
903B ASP* 1.3 58.7 + - - +
905B LEU* 3.7 2.8 + - + -
906B GLU* 3.1 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 903 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899B ALA 3.1 17.8 - - - +
900B GLU* 3.1 16.0 + - + +
902B PRO* 1.3 80.3 - - - +
904B LEU* 1.3 60.0 + - - +
906B GLU* 3.4 11.1 + - - +
907B LYS* 3.0 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 904 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893B TYR* 4.0 32.5 - - + -
896B LEU* 5.0 16.6 - - + -
900B GLU* 2.7 33.2 + - + +
901B VAL* 3.3 10.3 - - - +
903B ASP* 1.3 71.3 - - - +
905B LEU* 1.3 64.4 + - - +
907B LYS* 3.4 17.2 + - + +
908B GLY 3.5 0.2 + - - -
909B GLU* 3.3 47.6 + - + +
910B ARG 5.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 905 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859B MET 5.7 0.7 - - - +
861B LEU* 3.8 24.0 - - + -
864B ILE* 5.1 6.1 - - + -
876B TRP* 3.8 21.8 - - + +
893B TYR* 3.5 25.6 - - + +
901B VAL* 2.9 51.5 + - + +
902B PRO* 4.3 3.1 - - + -
904B LEU* 1.3 74.5 - - - +
906B GLU* 1.3 59.8 + - - +
908B GLY 2.8 10.6 + - - -
909B GLU 3.7 9.4 - - - +
910B ARG* 2.6 54.8 + - - +
931B ILE* 4.4 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 906 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861B LEU* 3.8 19.9 - - + +
865B HIS* 3.2 27.7 + - - +
902B PRO 3.1 21.6 + - - +
903B ASP* 3.6 11.4 - - - +
904B LEU 3.3 0.2 - - - -
905B LEU* 1.3 76.0 - - - +
907B LYS* 1.3 59.8 + - + +
908B GLY* 3.1 5.0 + - - -
931B ILE* 5.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 907 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900B GLU* 5.8 3.0 + - - +
903B ASP* 3.0 26.8 + - - +
904B LEU* 3.7 14.1 - - + +
905B LEU 3.2 0.6 - - - -
906B GLU* 1.3 75.8 - - + +
908B GLY* 1.3 58.5 + - - +
909B GLU* 3.4 5.5 + - + +
----------------------------------------------------------
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