Contacts of the helix formed by residues 1106 - 1115 (chain B) in PDB entry 3LJ1
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 ASP1106 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996B ARG* 4.0 15.9 + - - -
1103B LEU* 2.8 58.4 - - - +
1104B SER 3.2 5.1 + - - -
1105B ASP* 1.3 73.6 - - - +
1107B GLN* 1.3 52.2 + - - +
1108B ILE* 3.3 3.4 + - - +
1109B LEU* 2.7 28.4 + - + +
1110B ARG* 2.5 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1105B ASP 3.8 4.4 + - - +
1106B ASP* 1.3 72.5 + - - +
1108B ILE* 1.3 63.5 + - + +
1110B ARG* 3.5 20.5 - - + +
1111B GLU* 3.7 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992B LYS* 4.2 31.0 - - + +
1106B ASP* 2.9 4.1 + - - +
1107B GLN* 1.3 76.3 - - + +
1109B LEU* 1.3 80.0 + - + +
1111B GLU* 3.4 23.1 + - - +
1112B PHE* 3.7 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989B PHE* 4.4 9.6 - - + -
992B LYS* 4.1 25.1 - - + +
993B VAL* 4.4 11.2 - - + +
996B ARG* 4.7 9.0 - - + -
1099B VAL* 3.9 22.9 - - + -
1103B LEU* 3.5 33.0 - - + +
1106B ASP* 2.7 27.1 + - + +
1108B ILE* 1.3 90.4 - - + +
1110B ARG* 1.3 62.5 + - - +
1111B GLU 3.1 2.0 - - - -
1112B PHE* 3.2 11.7 + - + +
1113B LEU* 2.9 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104B SER 3.1 23.8 + - - -
1105B ASP* 3.7 20.7 - - - +
1106B ASP* 2.5 39.7 + - - +
1107B GLN* 3.5 14.8 - - + +
1109B LEU* 1.3 73.0 - - - +
1111B GLU* 1.3 59.5 + - - +
1113B LEU* 3.1 0.8 + - - -
1114B TYR* 2.7 66.3 + - + +
1115B SER* 3.9 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985B LYS* 4.9 1.9 + - - -
1107B GLN 3.7 14.0 - - - +
1108B ILE* 3.5 15.9 - - - +
1109B LEU 3.1 0.6 - - - -
1110B ARG* 1.3 81.1 - - - +
1112B PHE* 1.3 64.6 + - + +
1115B SER* 3.1 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976B ARG* 5.0 0.9 - - - +
981B TRP* 3.2 24.6 + + + -
985B LYS* 3.5 52.6 + - + +
988B GLU* 3.9 25.8 - - + -
989B PHE* 3.5 43.1 - + + -
992B LYS* 3.9 23.6 - - + -
1108B ILE* 3.7 20.4 - - + -
1109B LEU* 3.2 11.5 + - + +
1111B GLU* 1.3 84.2 - - + +
1113B LEU* 1.3 61.8 + - - +
1115B SER 4.7 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976B ARG* 3.8 20.6 - - - +
989B PHE* 3.8 25.8 - - + -
1096B TYR* 3.9 33.4 + - + +
1099B VAL* 4.0 14.6 - - + -
1100B LYS* 3.9 22.1 - - + -
1103B LEU 4.2 2.0 - - - +
1104B SER* 3.8 22.2 - - - +
1109B LEU 2.9 20.9 + - - +
1112B PHE* 1.3 80.6 - - - +
1114B TYR* 1.3 97.4 + - + +
1115B SER 3.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973B LYS* 6.4 0.2 - - - -
976B ARG* 3.3 27.7 + - - +
1100B LYS* 3.7 29.7 + - - +
1104B SER* 3.1 42.0 - - - -
1110B ARG* 2.7 47.4 + - + +
1113B LEU* 1.3 104.0 - - + +
1115B SER* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976B ARG* 4.1 13.6 + - - +
985B LYS* 4.0 16.4 + - - -
1110B ARG 4.2 0.3 + - - -
1111B GLU* 3.1 47.8 + - - +
1112B PHE 4.8 1.2 - - - +
1113B LEU 3.8 1.2 - - - -
1114B TYR* 1.3 82.4 - - - +
----------------------------------------------------------
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