Contacts of the helix formed by residues 193 - 205 (chain A) in PDB entry 1JPP
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 GLN 193 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A THR* 4.3 21.9 - - + +
191A SER* 2.7 11.6 + - - +
192A PRO* 1.3 82.6 - - + +
194A MET* 1.3 65.3 + - - +
195A VAL 3.3 1.3 - - - -
196A SER* 3.2 5.2 + - - -
197A ALA* 3.1 26.0 + - - +
200A ARG* 4.8 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE* 3.4 53.6 - - + +
156A LEU* 3.9 19.1 - - + -
157A THR* 3.8 15.8 + - - +
160A LEU* 3.9 24.2 - - - -
175A VAL* 4.5 8.3 - - + -
188A ILE* 4.2 23.3 - - + +
191A SER* 3.1 24.5 + - - +
193A GLN* 1.3 80.5 - - - +
195A VAL* 1.3 60.7 + - - +
197A ALA* 3.4 3.0 + - - +
198A ILE* 2.9 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 3.8 26.0 - - + +
189A MET* 4.1 11.9 - - - +
191A SER 3.4 9.3 + - - +
192A PRO* 5.1 3.8 - - + -
193A GLN 3.3 0.4 - - - -
194A MET* 1.3 76.5 - - - +
196A SER* 1.3 61.3 + - - +
198A ILE* 3.6 10.7 + - + +
199A VAL* 3.1 24.7 + - + +
218A LEU* 5.2 4.9 - - + +
221A LEU* 5.2 6.1 - - + -
230A ALA* 4.0 23.6 - - + +
231A ILE* 4.4 9.0 - - + +
234A SER* 3.2 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A PRO 2.9 20.6 + - - -
193A GLN* 3.2 9.5 + - - -
195A VAL* 1.3 76.2 - - - +
197A ALA* 1.3 65.2 + - - +
199A VAL* 3.1 12.9 + - - +
200A ARG* 3.3 31.6 + - - +
234A SER* 4.2 21.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A THR* 4.6 11.2 - - + +
160A LEU* 4.2 20.2 - - + -
161A ASN* 3.6 10.5 + - - +
193A GLN 3.1 13.1 + - - +
194A MET 3.9 3.8 - - - +
196A SER* 1.3 79.4 - - - +
198A ILE* 1.3 57.7 + - - +
200A ARG* 3.3 28.8 - - - +
201A THR* 2.7 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 4.2 15.3 - - + -
175A VAL* 4.1 11.0 - - + -
188A ILE* 5.1 7.6 - - + -
194A MET* 2.9 39.9 + - + +
195A VAL* 3.6 10.5 - - + +
196A SER 3.1 0.2 - - - -
197A ALA* 1.3 77.6 - - - +
199A VAL* 1.3 61.7 + - - +
201A THR* 3.4 5.9 + - - -
202A MET* 3.3 21.1 + - - +
214A THR* 4.5 15.3 - - + +
217A THR* 4.0 28.0 - - + -
218A LEU* 4.1 26.7 - - + -
221A LEU* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 3.1 17.9 - - + +
196A SER 3.1 6.0 + - - +
198A ILE* 1.3 72.8 - - - +
200A ARG* 1.3 63.0 + - - +
201A THR 3.0 4.6 + - - -
202A MET* 3.2 10.6 + - + +
203A GLN* 3.0 27.4 + - - +
218A LEU* 4.4 20.9 - - + -
231A ILE* 5.6 0.9 - - + +
234A SER* 4.1 22.4 - - - +
235A GLY 4.0 6.7 - - - +
236A GLY* 3.8 21.3 - - - +
239A ALA* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A THR* 5.9 2.0 - - - +
161A ASN* 3.3 25.0 - - - +
193A GLN* 4.8 2.0 + - - +
196A SER* 3.3 26.9 + - - +
197A ALA* 3.3 35.1 - - - +
199A VAL* 1.3 77.1 - - - +
201A THR* 1.3 56.6 + - - +
203A GLN* 3.8 16.2 - - - +
204A ASN* 2.9 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 3.7 16.1 + - + +
161A ASN* 3.5 21.2 + - - +
168A VAL* 5.1 13.2 - - + +
172A ALA* 5.4 2.0 - - + -
197A ALA 2.7 22.6 + - - -
198A ILE* 3.6 7.9 - - - -
199A VAL 3.0 0.8 - - - -
200A ARG* 1.3 75.5 - - - +
202A MET* 1.3 66.6 + - - +
203A GLN 3.0 1.1 - - - -
204A ASN* 5.3 0.4 - - - -
205A THR* 2.9 34.5 + - - +
210A THR* 4.1 24.5 - - + -
214A THR* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE 3.3 6.1 + - - +
199A VAL* 3.2 10.6 + - + +
201A THR* 1.3 79.1 - - - +
203A GLN* 1.3 60.7 + - - +
205A THR* 3.8 14.5 - - - +
211A ALA* 5.0 3.4 - - - +
214A THR* 3.1 32.0 + - - +
215A ALA* 4.2 20.0 - - + +
218A LEU* 3.9 29.6 - - + -
239A ALA* 3.6 38.4 - - + +
240A LEU* 3.9 16.2 - - + -
243A MET* 3.8 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A VAL* 3.0 17.7 + - - +
200A ARG* 3.8 13.3 - - - +
202A MET* 1.3 81.6 - - - +
204A ASN* 1.3 72.6 + - - +
205A THR 3.6 2.2 - - - +
235A GLY 5.8 0.8 + - - -
238A PRO* 5.1 3.8 - - - +
239A ALA* 4.2 29.7 + - + +
242A LYS* 2.9 50.1 + - + +
243A MET* 5.0 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLN* 5.7 1.7 + - - -
200A ARG* 2.9 30.4 + - - +
201A THR* 5.3 0.4 - - - -
203A GLN* 1.3 95.6 + - - +
205A THR* 1.3 67.9 + - - +
206A ASN* 4.9 1.6 - - - +
242A LYS* 5.0 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLN* 5.5 9.6 + - - +
169A ASN* 4.5 2.4 + - - -
201A THR* 2.9 22.9 + - - +
202A MET* 3.8 15.9 - - - +
203A GLN 3.6 2.3 - - - +
204A ASN* 1.3 83.3 - - - +
206A ASN* 1.3 68.2 + - - +
207A ASP* 3.2 23.1 + - - +
210A THR* 3.6 22.6 - - + +
211A ALA* 4.3 18.4 - - + +
----------------------------------------------------------
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