Contacts of the helix formed by residues 202 - 210 (chain E) in PDB entry 1MKD
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 202 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E GLU* 4.5 8.0 - - - +
200E GLY 3.3 4.7 + - - +
201E LEU* 1.3 74.8 - - - +
203E VAL* 1.3 60.2 + - - +
204E PHE* 3.2 37.7 + + + -
205E ARG* 3.1 54.4 + - + +
206E ILE* 3.2 25.8 + - - +
424E GLN* 3.1 27.8 + - - -
425E LEU* 4.0 12.7 - - + +
428E GLN* 3.7 5.4 + - - -
510L SER* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201E LEU* 3.0 17.9 + - + +
202E HIS* 1.3 73.3 + - - +
204E PHE* 1.3 69.8 + - + +
206E ILE* 3.2 11.3 + - - +
207E ALA* 2.8 26.2 + - - +
214E PRO* 4.5 2.9 - - + -
218E ILE* 4.0 23.3 - - + -
260E ILE* 3.8 26.9 - - + +
263E ALA* 4.2 5.8 - - + -
264E ASP* 4.4 16.4 - - + +
267E GLN* 6.5 0.2 - - + -
425E LEU* 4.8 4.5 - - + -
429E TRP* 4.0 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E HIS* 3.2 11.7 + - + -
203E VAL* 1.3 75.9 - - + +
205E ARG* 1.3 65.5 + - - +
207E ALA* 3.2 19.0 + - + +
208E GLU* 3.3 14.3 + - - +
260E ILE* 4.0 13.0 - - + -
425E LEU* 3.8 19.3 - - + -
428E GLN* 3.3 48.0 - - + +
429E TRP* 3.5 50.9 - + - -
432E ARG* 3.1 42.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 205 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E VAL* 5.7 3.4 - - - -
192E GLU* 3.1 29.5 + - - +
202E HIS* 3.1 50.4 + - + +
204E PHE* 1.3 72.5 - - - +
206E ILE* 1.3 67.2 + - - +
208E GLU* 2.9 18.4 + - - +
209E LEU* 2.9 43.9 + - + +
424E GLN* 4.5 4.9 + - - +
510L SER* 4.4 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 206 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E LEU* 3.9 11.2 - - + +
192E GLU* 3.7 24.9 - - + -
193E LEU* 3.9 30.7 - - + -
201E LEU* 3.6 38.8 - - + -
202E HIS 3.2 13.0 + - - +
203E VAL* 3.2 9.4 + - - +
205E ARG* 1.3 76.1 - - - +
207E ALA* 1.3 59.8 + - - +
209E LEU* 3.9 7.8 - - - -
210E SER* 2.8 28.1 + - - -
214E PRO* 4.5 8.1 - - + -
217E VAL* 4.5 4.5 - - + -
218E ILE* 4.3 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E VAL 2.8 13.4 + - - +
204E PHE* 3.2 16.2 - - - +
205E ARG 3.0 0.4 - - - -
206E ILE* 1.3 78.8 - - - +
208E GLU* 1.3 56.0 + - + +
210E SER* 3.1 8.3 + - - -
212E ASN* 2.8 36.2 + - - +
214E PRO* 3.9 22.7 - - + -
260E ILE* 4.3 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E PHE 3.3 13.1 + - - +
205E ARG* 2.9 17.8 + - - +
207E ALA* 1.3 73.4 - - + +
209E LEU* 1.3 57.8 + - + +
210E SER 2.8 14.9 + - - -
211E GLY* 2.8 16.2 + - - -
212E ASN 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E GLN* 4.3 38.3 - - + +
186E GLU* 5.7 2.1 - - - +
188E VAL* 4.0 13.9 - - + -
189E LEU* 3.6 41.3 - - + +
192E GLU* 3.8 28.3 - - + -
205E ARG* 2.9 37.7 + - + +
206E ILE* 4.6 1.6 - - - +
208E GLU* 1.3 73.8 - - + +
210E SER* 1.3 56.2 + - - +
211E GLY 3.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E LEU* 3.9 8.3 - - - -
206E ILE 2.8 21.0 + - - -
207E ALA 3.1 3.6 + - - -
208E GLU 2.8 1.6 + - - -
209E LEU* 1.3 80.3 - - - +
211E GLY* 1.3 62.3 + - - +
213E ARG* 2.9 38.5 + - - +
214E PRO 3.3 0.7 - - - -
217E VAL* 3.7 27.6 - - - -
----------------------------------------------------------
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