Contacts of the helix formed by residues 194 - 206 (chain H) in PDB entry 3B4V
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 SER 194 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175H PRO 4.4 3.0 + - - -
177H PRO* 3.6 18.8 - - - -
182H GLN* 3.8 20.6 - - - -
184H LEU* 4.7 3.8 - - - -
192H TYR* 3.3 6.1 + - - +
193H ILE* 1.3 80.8 - - - +
195H SER* 1.3 64.7 + - - +
196H CYS* 3.3 16.7 + - - +
197H HIS* 2.8 37.4 + - - +
198H MET* 3.3 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E GLN* 3.5 19.0 + - - +
182H GLN* 4.4 7.8 + - - +
184H LEU* 4.1 18.9 - - - +
194H SER* 1.3 71.2 - - - +
196H CYS* 1.3 63.2 + - - +
198H MET* 3.2 3.7 + - - +
199H ARG* 2.9 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 196 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ASP* 6.3 1.3 - - + -
170H ARG* 3.5 26.4 - - - -
174H CYS* 2.1 51.3 - - + -
175H PRO* 4.5 6.5 - - + -
194H SER* 3.2 10.3 + - - +
195H SER* 1.3 77.2 - - - +
197H HIS* 1.3 56.4 + - - +
199H ARG* 3.3 20.0 + - - +
200H GLN* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 197 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H CYS* 3.2 44.3 + - + +
175H PRO 3.6 10.1 - - - -
176H VAL* 4.8 1.0 - - - +
192H TYR* 4.1 15.7 - - + -
193H ILE* 3.5 33.9 - - + +
194H SER* 2.8 36.0 + - - +
196H CYS* 1.3 74.9 - - - +
198H MET* 1.3 60.3 + - - +
200H GLN* 3.2 10.3 + - - +
201H ALA* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 198 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E GLY 3.9 3.8 - - - +
98E GLN* 3.8 17.0 - - + -
184H LEU* 3.9 14.4 - - + -
186H GLY* 4.1 5.6 - - - -
192H TYR* 3.9 36.2 - - + -
194H SER 3.3 4.1 + - - +
195H SER 3.2 7.7 + - - +
197H HIS* 1.3 77.8 - - - +
199H ARG* 1.3 57.1 + - - +
201H ALA* 3.3 3.2 + - - +
202H THR* 2.8 37.7 + - - +
209H ILE* 4.0 13.2 - - + -
210H GLY* 3.0 48.9 - - - +
211H VAL* 3.6 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ASP* 3.3 40.6 + - - +
28E TRP* 3.1 32.5 - - - +
94E TYR* 2.9 48.7 + - + +
98E GLN* 3.2 23.0 + - + +
195H SER* 2.9 41.2 + - - +
196H CYS* 3.4 20.7 - - - +
198H MET* 1.3 76.4 - - - +
200H GLN* 1.3 56.4 + - - +
202H THR* 3.7 1.3 - - - -
203H CYS* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H ARG* 2.7 42.0 + - + +
171H ALA 3.6 6.5 + - - -
172H ALA 2.9 25.3 + - - -
173H PRO* 4.5 3.1 - - - +
174H CYS* 4.3 14.8 + - - +
196H CYS 2.9 14.2 + - - +
197H HIS* 3.2 14.6 + - - +
199H ARG* 1.3 77.0 - - - +
201H ALA* 1.3 60.9 - - - +
203H CYS* 3.4 3.7 + - - +
204H PHE* 3.1 44.6 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
192H TYR* 3.5 42.2 - - + +
197H HIS 2.9 8.1 + - - +
198H MET 3.6 6.1 - - - +
200H GLN* 1.3 76.0 - - - +
202H THR* 1.3 61.2 + - - +
204H PHE* 3.7 2.7 + - - +
205H LEU* 3.1 26.0 + - - +
209H ILE* 4.0 6.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 202 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E TYR* 4.0 11.2 - - + -
98E GLN 3.8 18.1 + - - +
100E ILE* 4.0 13.0 - - + +
198H MET* 2.8 32.3 + - - +
199H ARG* 3.7 4.0 - - - -
201H ALA* 1.3 70.4 - - - +
203H CYS* 1.3 68.0 + - - +
205H LEU 3.4 0.7 + - - -
206H GLY 3.2 16.8 + - - -
207H ARG 3.4 26.3 + - - +
208H SER* 3.8 14.4 - - - -
209H ILE* 3.9 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 203 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ILE* 4.8 8.3 - - - -
94E TYR* 3.4 14.5 + - - +
100E ILE* 5.4 1.3 - - - -
155H SER* 4.6 1.7 - - - -
156H CYS 4.5 1.6 - - - +
157H VAL* 3.4 18.3 - - - +
167H VAL* 3.8 18.2 - - - -
168H VAL 4.7 0.4 - - - -
169H CYS* 2.0 60.1 - - + -
170H ARG 5.2 0.7 - - - +
199H ARG 2.8 18.1 + - - +
200H GLN* 3.9 4.0 - - - +
202H THR* 1.3 79.8 - - - +
204H PHE* 1.3 59.7 + - - +
206H GLY* 3.3 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H SER* 4.1 18.2 - - - -
156H CYS 5.6 0.3 - - - +
169H CYS* 3.5 26.9 - - + -
170H ARG 3.5 25.8 - - - -
171H ALA* 4.6 7.6 - - + -
200H GLN* 3.1 39.4 + - + +
201H ALA* 4.4 2.5 - - - +
203H CYS* 1.3 75.1 - - - +
205H LEU* 1.3 64.3 + - - +
206H GLY* 3.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188H ASN* 6.0 1.3 - - + +
201H ALA 3.1 19.5 + - - +
202H THR 3.8 4.3 - - - +
204H PHE* 1.3 76.9 - - - +
206H GLY* 1.3 57.9 + - - +
207H ARG* 3.7 55.2 + - + +
208H SER 4.8 0.7 - - - +
209H ILE* 3.4 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 206 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H CYS* 4.9 2.4 - - - -
156H CYS 3.6 22.4 - - - -
157H VAL* 3.4 8.9 - - - -
158H VAL* 3.0 27.3 + - - +
202H THR 3.2 4.8 + - - -
203H CYS 3.3 7.1 + - - -
204H PHE 3.2 3.2 - - - -
205H LEU* 1.3 78.1 - - - +
207H ARG* 1.3 64.3 + - - +
----------------------------------------------------------
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