Contacts of the helix formed by residues 169 - 196 (chain A) in PDB entry 4DJH
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 PHE 169 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 1.3 81.7 + - - +
170A ARG* 1.3 68.1 + - + +
171A THR 3.6 0.2 - - - -
172A PRO* 3.6 9.1 - - - +
173A LEU* 3.9 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LYS* 4.3 25.6 - - - +
168A ASP* 3.6 27.1 + - - +
169A PHE* 1.3 81.6 - - + +
171A THR* 1.3 58.1 + - - +
172A PRO 3.2 2.9 - - - -
173A LEU* 2.7 15.4 + - + -
174A LYS* 2.6 60.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 3.8 24.3 - - + +
155A ASP* 4.7 5.2 - - - +
165A LYS* 2.6 40.9 + - + +
166A ALA* 3.7 19.7 - - - +
168A ASP* 3.2 8.4 - - - +
170A ARG* 1.3 76.8 - - - +
172A PRO* 1.3 69.6 - - - +
174A LYS* 3.6 11.6 + - + +
175A ALA* 3.3 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LYS* 3.4 29.6 - - + +
92A THR* 4.7 4.3 - - - -
93A ALA 4.3 7.4 - - - +
96A ILE* 3.8 11.5 - - + +
166A ALA 5.2 1.6 - - - +
168A ASP 3.4 22.7 - - - +
169A PHE 3.6 5.8 - - - +
170A ARG 3.4 3.6 - - - -
171A THR* 1.3 96.6 - - - +
173A LEU* 1.3 60.7 + - - +
175A ALA* 3.2 10.3 - - + +
176A LYS* 3.1 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE 3.9 11.6 + - - +
170A ARG* 2.7 23.1 + - + +
172A PRO* 1.3 71.4 - - - +
174A LYS* 1.3 67.3 + - + +
175A ALA 3.0 1.6 - - - -
176A LYS* 2.9 42.2 + - + +
177A ILE* 3.0 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LYS* 4.0 23.2 - - - +
170A ARG* 2.6 47.6 + - + +
171A THR* 3.8 9.0 - - + +
173A LEU* 1.3 72.9 - - + +
175A ALA* 1.3 57.8 + - - +
177A ILE* 3.1 12.6 + - + +
178A ILE* 2.9 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 3.9 10.3 - - + +
96A ILE* 3.4 22.4 - - + -
97A TYR* 3.9 29.3 - - + +
171A THR 3.3 10.3 + - - +
172A PRO 3.2 12.5 + - - +
173A LEU 3.0 0.4 - - - -
174A LYS* 1.3 78.6 - - - +
176A LYS* 1.3 62.9 + - - +
178A ILE* 3.2 2.8 + - - +
179A ASN* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LYS* 6.5 0.4 - - + -
96A ILE* 3.8 21.3 - - + -
172A PRO* 3.1 20.6 + - + +
173A LEU* 2.9 31.2 + - + +
175A ALA* 1.3 78.1 - - - +
177A ILE* 1.3 64.3 + - + +
179A ASN* 3.2 17.1 + - - +
180A ILE* 3.3 14.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU* 3.0 35.6 + - + +
174A LYS* 3.5 12.1 - - + +
176A LYS* 1.3 76.6 - - + +
178A ILE* 1.3 66.2 + - + +
180A ILE* 2.9 24.6 + - + +
181A CYS* 3.0 25.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 3.3 27.4 - - + +
151A MET* 3.8 41.3 - - + -
174A LYS* 2.9 25.4 + - + +
175A ALA 3.6 6.5 - - - +
177A ILE* 1.3 77.7 - - + +
179A ASN* 1.3 64.2 + - - +
181A CYS* 2.8 14.0 + - + +
182A ILE* 2.8 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 2.8 37.8 + - - +
97A TYR* 3.3 24.6 - - - -
99A PHE* 4.8 5.7 - - - -
100A ASN* 3.4 36.0 + - - +
175A ALA 2.9 12.4 + - - -
176A LYS* 3.2 10.8 + - - +
178A ILE* 1.3 74.1 - - - +
180A ILE* 1.3 64.5 + - + +
182A ILE* 3.2 7.5 + - - +
183A TRP* 3.0 29.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LYS* 3.5 15.3 - - + +
177A ILE* 2.9 16.1 + - + +
179A ASN* 1.3 76.3 - - + +
181A CYS* 1.3 59.9 + - - +
183A TRP* 2.7 30.9 + - + +
184A LEU* 2.8 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 3.0 31.2 + - - -
178A ILE* 2.8 14.2 + - + +
180A ILE* 1.3 77.1 - - - +
182A ILE* 1.3 58.0 + - + +
184A LEU* 3.3 12.2 + - - +
185A LEU* 2.9 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 5.6 0.4 - - + -
100A ASN* 4.2 11.2 - - - +
144A THR* 3.8 16.8 - - - +
147A PHE* 3.5 29.4 - - + +
148A THR* 3.8 30.1 - - - +
151A MET* 3.9 21.8 - - + -
178A ILE* 2.8 26.7 + - + +
179A ASN* 3.4 12.1 - - - +
181A CYS* 1.3 79.4 - - + +
183A TRP* 1.3 53.6 + - - +
185A LEU* 3.3 7.3 + - + +
186A SER* 2.7 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASN* 2.5 26.2 + - - -
103A LEU* 3.7 29.6 - - + +
104A ALA* 4.7 8.1 - - + -
107A LEU* 4.1 22.9 - - + -
140A TYR* 3.6 49.8 - + + -
141A ASN 5.6 0.2 - - - -
144A THR* 3.7 30.7 - - + -
179A ASN* 3.0 27.0 + - + -
180A ILE* 2.7 18.3 + - + +
182A ILE* 1.3 69.6 - - - +
184A LEU* 1.3 57.7 + - + +
186A SER* 4.3 1.3 - - - -
187A SER* 2.6 34.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ILE* 2.8 34.6 + - + +
181A CYS* 3.7 14.4 - - - +
183A TRP* 1.3 78.6 - - + +
185A LEU* 1.3 70.0 + - + +
187A SER* 3.0 25.0 + - - +
188A SER* 3.7 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PHE* 5.8 0.7 - - - -
147A PHE* 4.4 23.0 - - + -
181A CYS* 2.9 31.9 + - + +
182A ILE* 3.8 6.1 - - + +
184A LEU* 1.3 81.4 - - + +
186A SER* 1.3 57.6 + - - +
188A SER* 2.4 33.6 + - - +
189A VAL* 5.3 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 3.4 24.1 - - - -
143A PHE* 3.7 21.2 - - - +
144A THR* 3.4 28.7 + - - -
147A PHE* 4.1 4.1 - - - -
182A ILE* 2.7 25.6 + - - +
183A TRP* 4.0 2.2 - - - -
185A LEU* 1.3 72.2 - - - +
187A SER* 1.3 51.1 + - - +
188A SER 3.0 5.6 + - - -
189A VAL* 3.1 7.6 + - - +
190A GLY* 2.7 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 3.0 23.4 + - - -
183A TRP 2.6 23.7 + - - -
184A LEU* 3.0 19.8 + - - +
186A SER* 1.3 74.4 - - - +
188A SER* 1.3 62.7 + - - +
190A GLY 3.5 0.2 - - - -
191A ILE* 2.6 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU 3.7 2.8 + - - -
185A LEU* 2.4 27.5 + - - +
187A SER* 1.3 79.8 - - - +
189A VAL* 1.3 66.5 + - - +
191A ILE* 4.7 0.5 - - - +
192A SER* 3.4 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TYR* 3.2 42.9 - - + +
143A PHE* 3.7 40.8 - - + -
185A LEU 5.3 0.7 - - - +
186A SER 3.1 5.9 + - - +
188A SER* 1.3 83.6 - - - +
190A GLY* 1.3 63.5 + - - +
191A ILE 3.3 0.7 - - - -
192A SER* 3.2 10.4 + - - +
193A ALA* 3.0 28.9 + - - +
226A MET* 6.0 6.1 - - + -
230A VAL* 6.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A SER* 3.0 31.5 - - - -
139A TYR* 4.7 0.7 - - - -
140A TYR* 3.7 30.1 - - - -
186A SER 2.7 16.9 + - - -
189A VAL* 1.3 82.5 - - - +
191A ILE* 1.3 60.1 + - - +
193A ALA* 3.4 6.6 - - - +
194A ILE* 3.5 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 3.9 13.0 + - - +
187A SER* 2.6 36.1 + - - +
188A SER 4.7 0.4 - - - +
190A GLY* 1.3 68.1 - - - -
192A SER* 1.3 54.8 + - - +
193A ALA 3.0 4.5 - - - -
194A ILE* 2.7 38.2 + - + +
195A VAL* 3.1 21.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A SER 3.4 13.2 + - - -
189A VAL* 3.2 22.6 + - - +
191A ILE* 1.3 79.9 - - - +
193A ALA* 1.3 56.0 + - - +
194A ILE 3.2 0.2 - - - -
195A VAL* 3.7 9.0 - - - +
196A LEU* 2.9 44.7 + - - +
226A MET* 4.6 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LYS* 3.9 6.6 - - - +
135A LEU* 3.8 11.5 - - + +
136A SER* 3.6 23.6 - - - +
139A TYR* 4.2 12.3 - - + -
189A VAL 3.0 18.8 + - - +
190A GLY 3.4 7.9 - - - +
192A SER* 1.3 77.7 + - - +
194A ILE* 1.3 57.5 - - - +
197A GLY* 2.9 27.9 + - - -
212A LEU* 3.9 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LYS* 2.9 54.5 + - + +
133A ILE* 5.4 3.1 - - + -
136A SER* 3.4 26.5 - - - +
140A TYR* 5.4 4.7 - - + -
190A GLY 3.5 9.4 - - - +
191A ILE* 2.7 24.4 + - + +
193A ALA* 1.3 79.1 - - - +
195A VAL* 1.3 57.7 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
132A LYS* 3.9 11.5 + - - +
191A ILE* 3.1 27.0 + - + +
192A SER* 4.0 7.2 - - - +
193A ALA 3.3 0.2 - - - -
194A ILE* 1.3 82.3 - - + +
196A LEU* 1.3 66.3 + - + +
197A GLY 3.6 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A SER* 2.9 27.5 + - - +
195A VAL* 1.3 79.6 - - + +
197A GLY* 1.3 67.0 + - - +
198A GLY 3.3 0.5 + - - -
212A LEU* 3.9 18.8 - - + -
213A GLN* 2.7 53.6 + - - +
214A PHE* 3.7 33.2 - - + -
215A PRO* 6.0 0.9 - - + -
226A MET* 4.4 14.1 - - + -
----------------------------------------------------------
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