Contacts of the helix formed by residues 195 - 204 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G THR* 4.5 1.8 - - + -
198G HIS* 3.3 12.7 - - - -
226G LEU* 4.3 17.0 - - + -
182H PRO* 3.3 13.4 - - - +
193H LEU 3.4 0.4 + - - +
194H PRO* 1.3 85.1 - - + +
196H ILE* 1.3 67.0 + - - +
197H GLY 3.2 8.7 + - - -
198H HIS* 2.8 37.2 + - + +
199H ALA 3.2 9.2 + - - -
221H GLU* 3.4 17.0 - - - +
224H ALA* 4.7 3.1 - - + -
226H LEU* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 196 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198G HIS* 4.3 8.1 - - + +
182H PRO* 3.8 8.1 - - + -
195H THR* 1.3 74.2 - - - +
197H GLY* 1.3 57.7 + - - +
199H ALA* 3.3 4.5 + - - +
200H LEU* 3.0 46.2 + - + +
214H VAL* 4.3 6.3 - - + +
216H PRO* 3.7 33.7 - - + -
221H GLU* 3.2 31.6 + - + +
228H PHE* 4.4 2.7 - - + -
231H GLY* 3.6 43.5 - - - +
232H ILE* 4.0 5.6 - - + +
234H GLN* 5.4 0.4 - - + -
235H ALA* 4.4 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 197 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G GLY 3.2 14.4 - - - +
198G HIS* 3.5 34.7 - - - -
195H THR* 3.1 6.1 + - - -
196H ILE* 1.3 79.1 - - - +
198H HIS* 1.3 56.5 + - - +
200H LEU* 3.1 10.2 + - - +
201H ALA 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 198 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G THR* 3.2 29.6 - - - -
196G ILE* 4.3 9.3 - - + +
197G GLY* 3.4 18.8 + - - -
221G GLU* 4.6 2.8 + - - -
226G LEU* 4.3 5.0 - - + +
231G GLY* 4.8 14.7 - - - -
234G GLN* 3.0 40.4 + - + +
193H LEU* 3.6 18.1 - - - +
194H PRO* 3.6 30.5 - - + +
195H THR* 2.8 26.2 + - + +
197H GLY* 1.3 73.6 - - - +
199H ALA* 1.3 58.3 + - - +
202H PHE* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180H ILE* 4.3 21.5 - - + -
182H PRO* 4.4 11.9 - - + -
193H LEU* 4.4 9.3 - - + +
195H THR 3.2 9.1 + - - +
196H ILE 3.6 7.9 - - - +
197H GLY 3.1 0.8 - - - -
198H HIS* 1.3 76.8 - - - +
200H LEU* 1.3 66.2 + - - +
202H PHE* 3.3 6.8 + - - +
203H ILE* 3.0 29.9 + - - +
214H VAL* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G ALA* 3.5 23.6 - - + -
196H ILE* 3.0 35.4 + - + +
197H GLY* 3.5 3.4 - - - +
199H ALA* 1.3 77.8 - - - +
201H ALA* 1.3 63.4 + - - +
203H ILE* 3.2 19.6 + - + +
204H GLU* 3.5 12.0 + - - +
214H VAL* 3.9 17.5 - - + -
234H GLN* 4.4 15.7 - - + +
235H ALA* 4.2 17.3 - - - +
238H ALA* 4.9 7.2 - - + -
240H LYS* 3.4 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G GLY 3.9 0.9 - - - +
200G LEU* 3.7 33.4 - - + -
201G ALA* 3.7 11.8 - - - +
204G GLU* 5.2 2.4 - - + +
234G GLN* 3.8 11.0 - - - +
237G TRP* 5.7 0.2 - - - -
197H GLY 2.9 15.5 + - - +
198H HIS* 3.8 4.9 - - - +
200H LEU* 1.3 75.5 - - - +
202H PHE* 1.3 64.8 + - - +
204H GLU* 3.0 21.5 + - - +
205H ARG* 3.9 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 202 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234G GLN* 3.8 5.8 - - - +
237G TRP* 3.5 36.3 - + - -
155H LEU* 4.1 17.7 - - + -
158H MET* 3.7 26.9 - - + -
159H LYS* 3.7 17.9 - - + -
162H PHE* 3.7 21.1 - + - -
180H ILE* 3.9 16.2 - - + -
193H LEU* 3.6 24.0 - - + -
198H HIS 2.9 18.9 + - - +
199H ALA 3.3 3.8 + - - +
201H ALA* 1.3 75.0 - - - +
203H ILE* 1.3 65.7 + - - +
205H ARG* 3.1 17.0 + - - +
206H LEU* 3.7 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180H ILE* 4.3 16.4 - - + -
199H ALA 3.0 19.5 + - - +
200H LEU* 3.4 14.6 - - + +
201H ALA 3.1 0.2 - - - -
202H PHE* 1.3 76.7 - - - +
204H GLU* 1.3 66.0 + - - +
205H ARG 3.1 4.4 + - - -
206H LEU* 3.2 24.0 + - + +
209H PRO* 3.6 30.8 - - + +
212H TYR* 3.8 24.7 - - + +
213H GLY* 3.5 34.5 - - - +
214H VAL* 4.1 10.3 - - + -
240H LYS* 4.0 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G ALA* 5.6 0.9 - - - +
204G GLU* 3.6 46.5 - - + +
205G ARG* 6.5 0.7 - - - -
200H LEU 3.5 11.4 + - - +
201H ALA 3.0 10.3 + - - +
203H ILE* 1.3 87.5 - - - +
205H ARG* 1.3 66.3 + - - +
206H LEU 3.4 1.0 - - - +
209H PRO* 4.2 23.2 - - - +
240H LYS* 4.1 14.0 - - - +
----------------------------------------------------------
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