Contacts of the helix formed by residues 174 - 189 (chain J) in PDB entry 2HPC
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 ASP 174 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172J GLU* 4.2 1.0 - - - +
173J VAL* 1.3 69.4 - - - +
175J LEU* 1.3 64.6 + - - +
176J LYS* 3.7 8.8 - - - +
177J ASP* 2.9 44.2 + - + +
178J TYR* 3.7 8.7 + - - -
178K LYS* 4.5 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148J LYS* 3.9 27.3 - - + +
151J GLU* 5.6 1.1 - - + -
152J VAL* 3.8 26.9 - - + -
173J VAL* 2.7 25.4 + - + +
174J ASP* 1.3 72.2 - - - +
176J LYS* 1.3 64.5 + - - +
178J TYR* 3.1 27.4 + - + +
179J GLU* 3.6 6.7 + - + +
426K MET* 3.3 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 176 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174J ASP* 3.0 8.9 + - - +
175J LEU* 1.3 78.8 - - - +
177J ASP* 1.3 54.9 + - - +
178J TYR 2.7 0.7 + - - -
179J GLU* 2.5 39.2 + - + +
180J ASP* 3.1 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 177 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174J ASP* 2.9 35.6 + - + +
176J LYS* 1.3 77.3 - - - +
178J TYR* 1.3 60.6 + - - +
179J GLU 3.3 0.2 - - - -
180J ASP* 3.8 11.5 - - - +
181J GLN* 2.7 50.8 + - - +
174K ASN* 3.9 6.0 + - - -
178K LYS* 3.0 25.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 178 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J LEU* 4.1 19.4 - - + +
147J MET* 3.4 37.0 - - + +
148J LYS* 3.7 31.4 - - + -
151J GLU* 2.5 52.1 + - + +
173J VAL* 5.3 1.1 - - + -
174J ASP 4.0 6.5 - - - -
175J LEU* 3.1 21.5 + - + +
176J LYS 2.7 4.6 + - - -
177J ASP* 1.3 73.4 - - - +
179J GLU* 1.3 68.4 + - - +
181J GLN* 3.3 8.1 + - - +
182J GLN* 3.1 23.8 + - - +
175K LEU* 4.1 4.0 - - + -
178K LYS* 3.2 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148J LYS* 4.3 16.1 - - - -
175J LEU* 4.4 5.2 - - + +
176J LYS* 2.5 23.4 + - + +
178J TYR* 1.3 70.3 - - - +
180J ASP* 1.3 61.0 + - - +
182J GLN* 2.6 39.0 + - - +
183J LYS* 2.8 28.9 + - + +
425K ASP* 4.9 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 180 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176J LYS* 3.1 21.8 + - - +
177J ASP* 3.8 15.7 - - - +
179J GLU* 1.3 79.1 - - - +
181J GLN* 1.3 58.7 + - + +
183J LYS* 3.2 15.3 - - - +
184J GLN* 2.9 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 181 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J LEU* 4.1 20.9 - - + +
177J ASP* 2.7 33.1 + - - +
178J TYR* 3.3 9.3 + - - +
179J GLU 2.7 4.8 + - - -
180J ASP* 1.3 77.7 - - + +
182J GLN* 1.3 51.1 + - - +
184J GLN* 2.8 21.0 + - - +
185J LEU* 2.7 34.3 + - - +
170K SER* 5.9 2.0 - - - +
171K ILE* 3.7 29.9 - - + +
174K ASN* 2.5 47.3 + - - +
175K LEU* 4.3 1.6 - - - +
178K LYS* 4.2 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 182 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J ARG* 4.5 7.0 + - + +
144J LEU* 3.2 35.3 - - + +
145J VAL* 3.2 35.8 - - - +
148J LYS* 4.0 21.2 - - - +
178J TYR* 3.1 13.1 + - - +
179J GLU* 2.6 19.8 + - - +
181J GLN* 1.3 68.7 - - - +
183J LYS* 1.3 65.2 + - - +
185J LEU* 4.1 3.3 - - - +
186J GLU* 3.0 36.4 + - + +
425K ASP* 5.0 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179J GLU* 2.8 31.9 + - + +
180J ASP* 3.2 16.2 - - - +
182J GLN* 1.3 79.2 - - + +
184J GLN* 1.3 64.0 + - + +
186J GLU* 3.5 10.5 + - - +
187J GLN* 3.6 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 184 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180J ASP* 2.9 26.5 + - - +
181J GLN* 2.8 19.6 + - - +
183J LYS* 1.3 74.3 - - + +
185J LEU* 1.3 54.1 + - - +
186J GLU 2.9 4.3 - - - -
187J GLN* 2.7 38.1 + - - +
188J VAL* 3.8 6.9 + - - +
167K VAL* 4.1 25.2 - - + +
170K SER* 5.0 8.5 + - - -
171K ILE* 4.6 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J GLN* 3.4 20.2 - - + +
140J VAL* 3.4 25.8 - - + -
141J ARG* 4.5 8.5 - - + +
144J LEU* 4.5 5.6 - - + -
181J GLN 2.7 14.2 + - - +
182J GLN* 4.1 8.3 - - - +
184J GLN* 1.3 72.1 - - - +
186J GLU* 1.3 60.7 + - - +
187J GLN 3.5 0.7 + - - -
188J VAL* 3.7 6.0 + - + +
189J ILE* 3.2 42.8 + - + +
167K VAL* 4.3 10.8 - - + -
168K LEU* 4.2 16.8 - - + -
171K ILE* 3.5 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 186 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J ARG* 2.4 49.6 + - - -
182J GLN* 3.0 29.1 + - + +
183J LYS* 3.7 8.3 - - - +
184J GLN 2.8 1.8 + - - -
185J LEU* 1.3 79.6 - - - +
187J GLN* 1.3 61.6 + - - +
188J VAL 3.4 0.2 - - - -
189J ILE* 3.1 25.1 + - - +
190J ALA* 4.2 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 187 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183J LYS 3.7 14.5 - - - +
184J GLN* 2.7 21.3 + - - +
186J GLU* 1.3 74.4 - - - +
188J VAL* 1.3 61.6 + - + +
190J ALA* 3.9 8.1 + - - +
191J LYS* 3.8 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J GLN* 5.7 0.7 - - - +
137J GLN* 3.3 23.7 + - + +
184J GLN 4.0 10.5 - - - +
185J LEU* 3.7 8.7 + - + +
186J GLU 3.4 0.2 - - - -
187J GLN* 1.3 80.5 - - + +
189J ILE* 1.3 63.3 + - - +
190J ALA* 2.9 7.1 + - - -
191J LYS* 3.5 20.6 + - + +
192J ASP 5.2 0.2 + - - -
163K THR 5.4 2.0 - - - +
164K ASN* 3.1 39.7 + - + +
167K VAL* 3.9 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J GLN* 4.3 18.5 + - - +
137J GLN* 3.2 33.9 - - + +
138J LYS* 4.9 7.0 - - - +
141J ARG* 3.7 24.5 - - - +
185J LEU* 3.2 35.4 + - + +
186J GLU* 3.1 29.6 + - - +
187J GLN 3.5 0.6 - - - -
188J VAL* 1.3 77.9 - - - +
190J ALA* 1.3 57.5 + - + +
191J LYS 3.6 3.3 + - - -
192J ASP 5.4 1.2 + - - +
----------------------------------------------------------
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