Contacts of the helix formed by residues 81 - 86 (chain K) in PDB entry 1XFB
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 HIS 81 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K PHE 3.9 2.0 + - - -
80K PHE* 1.3 82.2 - - + +
82K GLU* 1.3 73.1 + - - +
84K LEU* 2.9 20.0 + - - +
85K TYR* 3.3 35.2 - + - -
107K ILE* 4.1 14.4 - - + +
108K LYS 5.0 5.7 + - - +
138K TYR* 2.6 37.6 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K VAL* 5.2 1.0 - - - +
53K GLU* 3.6 13.0 - - + +
56K ARG* 2.8 49.4 + - - +
60K ARG* 5.1 0.7 + - - -
80K PHE* 3.0 25.5 + - + -
81K HIS* 1.3 84.6 - - + +
83K THR* 1.3 64.3 + - - +
85K TYR* 2.9 25.0 + - - +
86K GLN* 3.5 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K ALA 5.3 0.7 - - - +
60K ARG* 3.3 33.8 + - + -
64K PHE* 3.6 22.9 - - + -
79K PHE* 3.5 21.2 - - + -
80K PHE* 2.8 23.0 + - - +
82K GLU* 1.3 75.6 + - - +
84K LEU* 1.3 57.1 + - - -
85K TYR 2.8 11.3 + - - -
86K GLN* 2.9 35.1 + - - +
94K PHE* 3.9 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K PHE* 3.7 21.0 - - + -
80K PHE 3.1 7.5 + - - +
81K HIS* 2.9 15.2 + - - +
83K THR* 1.3 73.5 - - - +
85K TYR* 1.3 91.4 + - + +
86K GLN 3.6 0.7 - - - +
93K PRO* 6.1 0.3 - - - +
95K VAL* 3.2 39.7 - - + +
105K VAL* 3.9 21.3 - - + -
106K GLY 5.0 0.7 - - - +
107K ILE* 4.1 15.5 - - + -
138K TYR* 3.7 24.0 - - + +
141K ASP* 4.7 13.0 - - + +
143K ALA* 5.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 85 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81K HIS* 3.3 42.9 - + - -
82K GLU* 2.9 8.8 + - - +
83K THR 2.9 1.2 - - - -
84K LEU* 1.3 102.3 - - + +
86K GLN* 1.3 61.9 + - - +
87K LYS* 4.2 8.9 + - - +
93K PRO* 6.4 0.4 - - - -
137K GLN* 4.6 2.3 + - - +
138K TYR* 3.6 19.1 - - - -
141K ASP* 2.6 37.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53K GLU* 3.5 17.0 + - - +
57K ARG* 3.4 41.2 + - + +
60K ARG* 4.2 1.6 - - - +
82K GLU* 3.5 37.1 + - + +
83K THR* 2.9 29.9 + - - +
84K LEU 5.0 0.9 - - - +
85K TYR* 1.3 83.5 - - - +
87K LYS* 1.3 66.1 + - - +
93K PRO* 3.6 2.1 - - - +
94K PHE* 3.1 40.7 + - + +
95K VAL 4.9 0.2 + - - -
----------------------------------------------------------
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