Contacts of the helix formed by residues 185 - 191 (chain E) in PDB entry 1XBT
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 CYS 185 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E CYS* 3.4 9.1 - - + +
156E CYS* 3.6 7.6 - - - -
158E ARG* 5.2 1.8 - - + -
159E GLU 3.4 23.6 - - - +
160E ALA* 4.3 0.7 - - - +
161E ALA 4.6 1.1 - - - +
162E TYR* 3.8 4.0 - - - -
184E VAL* 1.3 79.4 - - - +
186E ARG* 1.3 65.6 + - - +
187E LEU* 3.8 5.4 - - - -
188E CYS* 3.5 15.0 - - - -
189E TYR* 3.0 20.1 + - - +
5193E ZN 2.4 35.7 - - - -
18G ARG* 3.8 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 186 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E ARG* 3.8 5.2 - - - +
162E TYR* 3.1 20.5 + - + -
185E CYS* 1.3 73.3 - - - +
187E LEU* 1.3 72.6 + - + +
189E TYR* 3.3 16.4 + - - +
190E PHE* 3.4 21.1 - - + -
19G GLY* 3.7 20.6 + - - +
21G ILE* 3.7 15.6 - - - +
110G GLU* 3.2 23.0 + - - -
113G ALA* 3.6 26.0 - - - +
114G ASN* 3.0 30.9 + - - +
142G LEU 2.9 28.1 + - - -
144G GLU* 2.9 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E CYS* 3.4 8.0 - - - +
186E ARG* 1.3 89.1 - - + +
188E CYS* 1.3 64.1 + - - +
190E PHE* 3.3 7.2 + - - +
191E LYS* 3.3 26.9 + - + +
18G ARG* 3.5 58.8 - - + +
19G GLY 5.7 2.0 - - - +
114G ASN 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 188 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E CYS* 3.6 11.7 - - - -
155E GLU* 4.0 16.2 - - - +
156E CYS* 3.6 13.7 - - - -
164E LYS* 2.8 26.3 + - - -
184E VAL* 3.9 12.1 - - + -
185E CYS* 3.5 5.4 - - - +
186E ARG 3.4 0.2 - - - -
187E LEU* 1.3 77.2 - - - +
189E TYR* 1.3 63.3 + - - +
190E PHE 3.3 0.3 + - - -
191E LYS* 3.4 23.8 + - - +
5193E ZN 2.3 36.8 - - - -
18G ARG* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 189 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E PHE 2.7 29.3 + - - -
129E GLN* 3.4 17.2 + - - -
130E ARG* 3.8 30.5 - - + -
162E TYR* 4.3 11.9 - - + -
163E THR 3.8 15.9 - - - -
164E LYS* 3.9 21.5 + - + +
184E VAL* 3.4 17.9 - - + +
185E CYS 3.0 19.9 + - - +
186E ARG* 3.4 8.5 - - - +
187E LEU 3.2 0.4 - - - -
188E CYS* 1.3 77.7 - - - +
190E PHE* 1.3 86.8 + + + +
191E LYS 3.7 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 190 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D ARG 5.9 2.2 - - - -
83D ASP 6.2 0.4 - - - -
86D GLN* 3.1 54.6 + - + +
130E ARG* 3.3 32.1 - - - -
186E ARG* 3.4 24.8 + - + +
187E LEU* 3.3 7.8 + - - +
188E CYS 3.2 0.4 - - - -
189E TYR* 1.3 97.8 - + + +
191E LYS* 1.3 64.0 + - - +
110G GLU* 3.7 4.7 - - - -
114G ASN* 3.6 29.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E GLU* 5.6 2.0 - - - +
164E LYS* 4.2 13.5 + - - +
187E LEU* 3.3 16.5 + - + +
188E CYS* 3.4 28.0 + - - +
189E TYR 3.4 0.9 - - - +
190E PHE* 1.3 82.7 - - - +
----------------------------------------------------------
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