Contacts of the helix formed by residues 193 - 203 (chain D) in PDB entry 1P8J
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 193 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D MET 5.0 7.3 + - - -
190D ASN* 3.2 23.7 + - + +
191D ASP 3.4 2.6 - - - +
192D ASN* 1.3 75.2 - - - +
194D HIS* 1.3 66.8 + - - +
195D GLY 3.4 1.3 - - - -
196D THR* 3.4 5.7 + - - -
197D ARG* 3.1 58.2 + - - +
355D ASP* 3.5 16.1 + - - +
356D LEU* 3.5 20.6 - - + +
4018D SO4 3.1 41.7 + - - +
4019D SO4 3.0 45.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D ASP* 2.6 28.4 + - - +
154D ASP* 3.1 14.6 + - - +
191D ASP 4.5 1.0 + - - +
193D ARG* 1.3 84.0 - - - +
195D GLY* 1.3 64.3 + - - +
197D ARG* 3.3 5.7 + - - +
198D CYS* 3.2 29.5 + - - -
253D SER* 3.3 19.3 - - - -
364D HIS* 4.9 1.3 + - - -
368D SER* 2.9 17.2 - - - -
4018D SO4 3.1 25.8 - - - +
804M LYS* 3.5 19.7 - - + +
805M AR7 3.2 2.9 + - - -
806M 0QE 1.5 44.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
151D ILE* 3.9 9.0 - - - +
153D ASP* 3.5 20.1 + - - -
154D ASP* 2.7 17.5 + - - -
155D GLY 3.2 18.2 - - - -
156D ILE* 4.9 1.7 - - - +
193D ARG 3.4 0.2 - - - -
194D HIS* 1.3 72.8 - - - +
196D THR* 1.3 58.0 + - - +
198D CYS* 3.2 4.5 + - - +
199D ALA* 2.9 28.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
154D ASP* 4.6 0.2 + - - -
155D GLY 3.5 4.1 + - - -
156D ILE* 3.8 4.6 - - - +
157D GLU* 3.0 34.8 + - + +
160D HIS* 4.3 1.8 - - + -
163D LEU* 4.0 14.1 - - + -
184D PRO* 4.4 1.6 - - - +
192D ASN 4.9 1.0 + - - -
193D ARG 3.4 9.3 + - - -
194D HIS 3.3 0.2 - - - -
195D GLY* 1.3 75.6 - - - +
197D ARG* 1.3 62.0 + - - +
199D ALA* 3.2 7.4 + - - +
200D GLY 3.1 10.2 + - - -
354D THR* 2.9 43.3 + - - +
355D ASP 4.1 12.3 - - - +
356D LEU* 4.0 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D ARG* 3.1 56.1 + - - +
194D HIS 3.7 4.5 - - - +
195D GLY 3.3 0.2 - - - -
196D THR* 1.3 75.8 - - - +
198D CYS* 1.3 61.9 + - - +
201D GLU* 3.2 12.4 + - - +
353D THR* 2.7 27.2 + - + -
354D THR 3.2 17.7 - - - +
355D ASP* 2.8 38.7 + - - +
361D THR* 4.0 15.5 + - - +
363D SER* 3.9 21.2 + - - -
364D HIS* 3.6 28.1 - - + +
365D THR 5.2 0.2 - - - +
4018D SO4 2.9 26.1 + - - -
4019D SO4 4.1 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ILE* 3.8 18.6 - - + -
153D ASP* 4.2 7.4 - - - -
194D HIS* 3.2 17.7 + - - -
195D GLY 3.2 8.4 + - - +
197D ARG* 1.3 77.7 - - - +
199D ALA* 1.3 67.4 + - - +
201D GLU* 3.2 10.4 + - - -
202D VAL* 3.3 9.4 + - - +
251D SER* 5.5 0.2 - - - +
253D SER* 3.9 19.3 - - - -
364D HIS* 4.2 7.4 - - - -
368D SER 3.4 24.0 - - - -
372D PRO* 3.4 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ILE* 3.8 14.5 - - + +
156D ILE* 3.6 31.2 - - + -
163D LEU* 3.9 14.1 - - + +
195D GLY 2.9 13.4 + - - +
196D THR 3.2 8.3 + - - +
198D CYS* 1.3 75.6 - - - +
200D GLY* 1.3 63.8 + - - +
202D VAL* 2.9 14.6 + - - +
203D ALA* 3.0 13.2 + - - -
221D ILE* 4.0 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D LEU* 3.7 11.0 - - - +
196D THR 3.1 8.3 + - - -
197D ARG 3.5 0.2 + - - -
198D CYS 3.3 0.2 - - - -
199D ALA* 1.3 79.5 - - - +
201D GLU* 1.3 57.9 + - - +
204D ALA* 2.9 34.6 + - - +
213D VAL 4.3 0.9 - - - -
214D GLY* 3.4 4.5 - - - -
352D VAL 5.7 0.2 - - - -
353D THR* 3.3 10.3 - - - -
354D THR* 3.2 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D GLN* 6.2 0.4 - - - +
123D TYR* 5.3 0.7 - - - +
197D ARG 3.2 13.7 - - - +
198D CYS 3.2 7.4 + - - +
200D GLY* 1.3 76.3 - - - +
202D VAL* 1.3 58.7 + - - +
213D VAL 5.4 1.3 - - - -
214D GLY* 3.4 1.9 - - - -
215D VAL* 3.1 31.0 + - - +
351D ILE* 3.6 26.5 - - + +
352D VAL 4.6 3.8 - - - +
353D THR* 3.3 15.5 + - - +
364D HIS* 2.4 32.0 + - - -
369D ALA* 3.0 15.6 - - - +
372D PRO* 2.9 31.7 - - + +
373D LEU* 4.0 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D VAL* 3.8 33.9 - - + -
151D ILE* 4.0 14.1 - - + -
198D CYS 3.6 4.7 - - - +
199D ALA 2.9 6.3 + - - +
201D GLU* 1.3 78.1 - - - +
203D ALA* 1.3 63.3 + - + +
214D GLY* 3.9 0.9 - - - -
215D VAL 3.3 2.1 + - - +
216D ALA* 2.9 33.5 + - + +
219D ALA* 5.5 0.4 - - + -
221D ILE* 4.0 8.1 - - + -
372D PRO* 3.3 40.6 - - + +
375D ALA* 4.2 6.1 - - + -
376D GLY* 4.2 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ASP 4.2 1.6 - - - +
163D LEU* 4.4 6.2 - - - +
166D ASN* 2.9 18.8 + - - +
199D ALA 3.0 9.6 + - - -
202D VAL* 1.3 84.7 - - + +
204D ALA* 1.3 65.9 + - - +
205D VAL 3.3 0.3 + - - -
214D GLY* 4.2 0.4 - - - -
216D ALA 3.3 19.7 - - - +
219D ALA* 3.8 21.1 - - + +
221D ILE* 3.9 21.1 - - + -
----------------------------------------------------------
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