Contacts of the helix formed by residues 191 - 202 (chain D) in PDB entry 3VZC
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 ARG 191 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D SER* 3.2 38.6 + - - -
113D GLY* 5.2 0.2 - - - -
178D ASP 4.3 4.9 + - - -
181D SER* 3.1 44.4 + - - +
183D LYS* 3.3 55.5 + - + +
184D TYR 5.3 0.2 - - - -
185D ARG* 3.8 8.0 + - - +
190D MET* 1.3 83.0 - - - +
192D PHE* 1.3 86.1 + - + +
194D LEU* 3.4 7.7 + - - +
195D GLY* 2.8 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D SER* 4.3 9.6 - - - -
113D GLY* 4.5 16.8 - - - -
177D VAL* 3.8 9.2 - - + +
178D ASP* 3.6 25.8 - - - -
181D SER* 4.8 2.5 - - - -
190D MET* 3.0 18.3 - - + -
191D ARG* 1.3 118.8 - - + +
193D THR* 1.3 58.6 + - - +
196D THR* 2.7 39.6 + - - +
268D LEU 6.1 0.7 - - - -
272D MET* 4.1 30.5 - - + -
303D PHE* 4.6 1.8 - - + -
1001D UUL 3.8 21.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D MET* 3.2 19.3 + - - +
192D PHE* 1.3 78.1 - - - +
194D LEU* 1.3 57.3 + - - +
196D THR* 3.4 3.8 + - - +
197D PHE* 2.9 27.6 + - + +
303D PHE* 3.9 30.0 - - + -
304D LEU* 5.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D LYS* 3.9 32.8 - - + +
190D MET 3.5 9.1 + - - +
191D ARG* 3.4 9.1 + - - +
192D PHE 3.3 0.4 - - - -
193D THR* 1.3 75.1 - - - +
195D GLY* 1.3 60.8 + - - +
197D PHE* 2.8 30.8 + - + +
198D LEU* 3.0 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D VAL* 3.6 17.8 - - - +
180D GLU 4.8 9.4 - - - -
183D LYS* 6.2 0.8 - - - +
191D ARG 2.8 20.3 + - - -
194D LEU* 1.3 72.8 - - - +
196D THR* 1.3 61.5 + - - +
198D LEU* 3.1 30.0 - - - +
199D ARG* 3.1 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D PHE* 3.5 6.0 - - + -
177D VAL* 3.6 7.9 - - - +
192D PHE 2.7 24.3 + - - -
193D THR 3.5 4.7 - - - +
194D LEU 3.1 0.2 - - - -
195D GLY* 1.3 76.8 - - - +
197D PHE* 1.3 57.8 + - - +
200D LEU* 3.0 36.8 + - + +
300D LEU* 5.7 1.3 - - + -
303D PHE* 3.7 36.8 - - + -
1001D UUL 2.9 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D THR* 2.9 12.1 + - + +
194D LEU* 2.8 24.6 + - + +
196D THR* 1.3 70.1 - - - +
198D LEU* 1.3 72.1 + - + +
200D LEU* 3.0 22.5 + - + +
201D ALA* 3.3 21.4 + - + +
300D LEU* 6.0 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D GLU* 3.3 30.7 - - - +
183D LYS* 5.5 5.4 - - - +
194D LEU* 3.0 47.9 + - + +
195D GLY* 3.1 35.0 - - - +
197D PHE* 1.3 82.1 - - + +
199D ARG* 1.3 64.9 + - + +
201D ALA* 3.0 10.7 + - - +
202D ALA* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D PHE* 3.8 21.3 - - + -
176D ASP* 3.4 42.2 + - - +
177D VAL* 3.9 12.1 - - + +
179D LEU* 5.5 4.4 - - - +
180D GLU* 2.9 48.8 + - - +
195D GLY* 3.1 19.3 + - - +
198D LEU* 1.3 80.3 - - + +
200D LEU* 1.3 57.0 - - - +
201D ALA 3.3 0.2 - - - -
202D ALA* 3.2 17.6 - - - +
203D LEU* 3.0 28.4 + - - -
204D ARG* 4.6 19.0 - - - +
206D TYR* 5.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D PHE* 4.0 10.1 - - + -
196D THR* 3.0 26.5 + - + +
197D PHE* 3.0 17.8 + - + +
199D ARG* 1.3 77.2 - - - +
201D ALA* 1.3 56.5 + - - +
203D LEU* 3.9 6.8 - - + +
296D ARG* 2.9 46.0 + - + +
299D LEU* 3.7 42.0 - - + -
300D LEU* 3.5 45.3 - - + -
303D PHE* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D PHE* 3.3 23.9 + - + +
198D LEU* 3.0 9.9 + - - +
200D LEU* 1.3 75.5 - - - +
202D ALA* 1.3 55.1 + - - +
203D LEU 3.2 2.5 - - - -
296D ARG* 2.5 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D LEU 2.9 15.7 + - - +
199D ARG* 3.2 18.7 - - - +
201D ALA* 1.3 75.9 - - + +
203D LEU* 1.3 63.7 + - - +
204D ARG* 3.3 10.0 + - - +
296D ARG* 4.3 0.4 - - - -
----------------------------------------------------------
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