Contacts of the helix formed by residues 200 - 204 (chain E) in PDB entry 1WUR
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 VAL 200 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ILE* 3.9 27.8 - - + -
167E GLN* 3.0 51.9 + - + +
168E GLY* 3.7 5.4 - - - +
198E LEU 3.4 0.2 + - - -
199E GLY* 1.3 71.2 - - - -
201E PHE* 1.3 62.3 + - + +
202E ARG 3.2 0.2 - - - -
203E GLU* 4.3 16.4 - - + +
204E ASN* 2.8 40.7 + - + +
207E THR* 3.9 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 201 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E MET* 3.7 18.4 - - + -
122E GLY 3.5 26.7 - - - -
123E TYR* 3.5 8.5 - - - -
124E ILE* 3.8 17.5 - - + -
168E GLY* 3.4 29.4 - - - -
169E VAL 3.4 17.3 - - - +
170E GLY* 3.6 14.4 - - - -
197E MET* 3.8 11.9 - - - +
198E LEU 3.2 3.2 + - - +
199E GLY 3.1 1.0 + - - -
200E VAL* 1.3 80.9 - - + +
202E ARG* 1.3 58.2 + - - +
204E ASN 4.8 0.4 - - - -
207E THR* 4.0 12.1 - - + -
208E ARG* 2.8 36.9 + - - +
211E PHE* 3.6 38.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER* 3.2 28.8 + - - +
95A GLU* 4.3 13.5 + - - +
197E MET* 3.4 33.9 + - + +
198E LEU* 3.9 14.2 + - - +
199E GLY 2.9 10.7 + - - +
201E PHE* 1.3 80.8 - - - +
203E GLU* 1.3 67.6 + - + +
204E ASN 3.6 0.2 - - - -
208E ARG* 3.1 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E GLY* 3.1 26.9 + - - +
200E VAL* 4.3 12.3 + - + +
202E ARG* 1.3 88.5 - - + +
204E ASN* 1.3 58.4 + - + +
205E GLN 3.7 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 204 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E VAL* 2.8 29.6 + - + +
203E GLU* 1.3 71.5 - - + +
205E GLN* 1.3 64.3 + - - +
206E LYS* 3.0 29.3 - - - +
207E THR* 3.1 24.2 + - - +
208E ARG* 3.1 24.9 + - - +
----------------------------------------------------------
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