Contacts of the helix formed by residues 195 - 204 (chain E) in PDB entry 4HHM
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 THR 195 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E PRO* 3.3 14.4 - - - +
193E LEU 3.4 0.5 - - - +
194E PRO* 1.3 88.2 - - + +
196E ILE* 1.3 65.8 + - - +
197E GLY 3.2 1.4 + - - -
198E HIS* 2.7 40.9 + - + +
199E ALA 3.2 8.8 + - - -
221E GLU* 3.7 13.0 - - - +
224E ALA* 4.9 3.8 - - + -
226E LEU* 3.8 19.5 - - + -
195F THR* 4.6 0.7 - - + -
198F HIS* 3.1 23.4 - - + -
226F LEU* 4.3 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 196 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E PRO* 3.6 15.9 - - + -
195E THR* 1.3 72.7 - - - +
197E GLY* 1.3 63.2 + - - +
199E ALA* 3.3 3.5 + - - +
200E LEU* 3.0 44.9 + - + +
214E VAL* 4.1 18.2 - - + -
216E PRO* 3.2 36.8 - - + -
221E GLU* 3.1 36.8 + - + +
228E PHE* 5.4 0.9 - - + -
231E GLY* 3.9 29.6 - - - +
234E GLN* 5.9 0.2 - - + -
235E ALA* 4.2 3.1 - - + -
198F HIS* 4.4 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 197 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E THR* 3.1 4.6 + - - -
196E ILE* 1.3 79.7 - - - +
198E HIS* 1.3 56.3 + - - +
200E LEU* 3.2 11.1 + - - +
201E ALA 2.9 25.5 + - - -
197F GLY 2.9 28.9 - - - +
198F HIS* 3.4 22.7 + - - -
201F ALA* 3.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 198 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E LEU* 3.6 18.8 - - - +
194E PRO* 3.5 30.2 - - + +
195E THR* 2.7 30.1 + - + +
197E GLY* 1.3 75.0 - - - +
199E ALA* 1.3 58.1 + - - +
201E ALA* 4.4 0.2 - - - -
202E PHE* 2.9 26.9 + - - +
195F THR* 3.3 27.8 - - - -
196F ILE* 4.6 7.7 - - + +
197F GLY* 3.5 16.4 + - - -
221F GLU* 4.8 2.6 + - - -
226F LEU* 4.3 6.8 - - + +
231F GLY* 4.8 11.7 - - - -
234F GLN* 3.1 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E ILE* 4.1 19.7 - - + -
182E PRO* 4.0 20.6 - - + -
193E LEU* 4.3 10.2 - - + +
195E THR 3.2 3.4 + - - +
196E ILE 3.7 6.7 - - - +
198E HIS* 1.3 76.6 - - - +
200E LEU* 1.3 61.0 + - - +
202E PHE* 3.3 7.3 + - - +
203E ILE* 2.9 36.7 + - - +
214E VAL* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E ILE* 3.0 42.2 + - + +
197E GLY* 3.5 7.0 - - - +
199E ALA* 1.3 74.0 - - - +
201E ALA* 1.3 66.2 + - - +
203E ILE* 3.3 16.9 + - + +
204E GLU* 3.3 17.8 + - - +
214E VAL* 3.8 20.2 - - + -
234E GLN* 4.1 25.4 - - + +
235E ALA* 4.3 9.9 - - - -
238E ALA* 5.1 5.2 - - + -
240E LYS* 3.7 34.8 - - + -
201F ALA* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E GLY 2.9 17.2 + - - +
198E HIS* 4.4 0.2 - - - -
200E LEU* 1.3 75.5 - - - +
202E PHE* 1.3 65.0 + - - +
204E GLU* 3.2 20.6 + - - +
205E ARG* 3.8 7.8 + - - +
197F GLY 3.8 2.9 - - - +
200F LEU* 3.7 33.0 - - + -
201F ALA* 4.0 10.0 - - - +
204F GLU* 5.4 1.6 - - - +
234F GLN* 3.7 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 202 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E LEU* 4.0 8.3 - - + -
158E MET* 3.2 33.4 - - + -
159E LYS* 3.7 23.6 - - + -
162E PHE* 3.9 16.2 - + - -
180E ILE* 4.1 13.0 - - + -
193E LEU* 3.8 29.6 - - + -
198E HIS 2.9 18.2 + - - +
199E ALA 3.5 3.6 - - - +
201E ALA* 1.3 78.2 - - - +
203E ILE* 1.3 66.3 + - - +
205E ARG* 2.9 19.6 + - - +
206E LEU* 3.6 22.7 + - + +
234F GLN* 3.9 5.8 - - - +
237F TRP* 3.8 35.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E ILE* 3.6 22.7 - - + -
199E ALA 2.9 23.3 + - - +
200E LEU* 3.3 10.5 + - + +
202E PHE* 1.3 75.3 - - - +
204E GLU* 1.3 60.2 + - - +
205E ARG 3.1 0.2 - - - -
206E LEU* 3.1 29.8 + - + +
209E PRO* 3.6 21.6 - - + +
212E TYR* 3.4 30.1 - - + +
213E GLY* 3.1 36.1 - - - +
214E VAL* 3.9 11.2 - - + -
240E LYS* 4.2 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E LEU 3.3 13.8 + - - +
201E ALA* 3.2 11.4 + - - +
202E PHE 3.1 0.8 + - - -
203E ILE* 1.3 79.1 - - - +
205E ARG* 1.3 61.6 + - + +
206E LEU 3.4 0.6 + - - +
209E PRO* 4.1 24.4 - - - +
240E LYS* 4.4 19.9 - - - +
201F ALA* 5.6 1.8 - - - +
204F GLU* 4.0 41.9 - - + +
205F ARG* 6.5 0.9 - - - -
----------------------------------------------------------
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