Contacts of the helix formed by residues 157 - 180 (chain A) in PDB entry 6AGF
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 SER 157 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PHE* 6.6 0.2 - - - -
153A PRO* 4.3 18.3 - - - +
154A PRO* 3.4 16.1 + - - -
155A PRO* 3.3 1.8 - - - +
156A TRP* 1.3 78.1 - - - +
158A LYS* 1.3 64.9 + - - +
159A ASN 3.3 2.7 - - - -
160A VAL* 3.6 7.6 - - - -
161A GLU* 2.6 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PRO* 5.0 19.5 + - + +
156A TRP 3.6 1.2 - - - -
157A SER* 1.3 84.9 + - - +
159A ASN* 1.3 59.6 + - - +
161A GLU* 3.9 8.7 + - - +
162A TYR* 3.2 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TRP* 3.0 21.6 + - - +
158A LYS* 1.3 74.7 - - - +
160A VAL* 1.3 74.6 + - - +
161A GLU 3.2 0.2 - - - -
162A TYR* 2.8 12.2 + - - +
163A THR* 2.7 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PHE* 3.5 37.5 - - + -
156A TRP 3.3 12.8 - - - +
157A SER* 3.1 10.6 + - - +
159A ASN* 1.3 92.3 + - - +
161A GLU* 1.3 64.3 + - - +
163A THR* 2.9 25.4 + - + +
164A PHE* 3.3 24.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A SER* 2.6 25.6 + - - +
158A LYS* 3.9 11.2 - - - +
160A VAL* 1.3 72.8 - - - +
162A TYR* 1.3 72.2 + - + +
164A PHE* 4.1 6.6 - - - +
165A THR* 2.9 25.8 + - - +
207A THR* 4.9 11.3 - - - +
222A ARG* 3.0 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS* 3.2 26.2 - - + +
159A ASN* 2.8 11.4 + - - +
161A GLU* 1.3 96.6 - - + +
163A THR* 1.3 54.0 + - + +
164A PHE 3.3 0.4 - - - -
165A THR* 3.2 10.2 + - - -
166A GLY* 2.7 30.7 + - - -
208A GLU* 3.4 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ASN* 2.7 27.4 + - + +
160A VAL* 2.9 25.2 + - + +
162A TYR* 1.3 68.6 - - + +
164A PHE* 1.3 71.0 + - - +
166A GLY* 3.1 4.8 + - - +
167A ILE* 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A THR* 4.2 24.5 - - + -
143A THR* 4.0 16.6 - - + -
144A ASN* 3.6 46.7 - - + -
147A PHE* 3.8 26.9 - + + -
160A VAL* 3.3 20.5 + - + +
161A GLU* 4.1 6.7 - - - +
162A TYR 3.3 0.6 - - - -
163A THR* 1.3 87.3 + - - +
165A THR* 1.3 58.8 + - - +
167A ILE* 3.0 13.7 + - + +
168A TYR* 3.0 47.5 + + + -
222A ARG* 5.8 1.3 - - - -
225A ARG* 4.5 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLU* 2.9 15.6 + - - +
162A TYR* 3.2 15.0 + - - -
164A PHE* 1.3 77.5 - - - +
166A GLY* 1.3 52.1 + - - +
168A TYR* 4.4 7.2 - - - -
169A THR* 2.6 49.3 + - + -
201A ILE* 5.4 4.0 - - + -
204A ALA* 4.5 16.7 - - + +
205A TYR* 4.3 20.2 - - + +
222A ARG* 5.0 2.6 + - - -
225A ARG* 3.7 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A TYR 2.7 14.0 + - - -
163A THR* 3.1 8.6 + - - -
165A THR* 1.3 77.9 - - - +
167A ILE* 1.3 59.8 + - - +
169A THR* 3.6 10.8 + - - -
170A PHE* 3.6 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 3.7 34.8 - - + -
137A ILE* 4.2 11.1 - - + +
140A THR* 3.5 38.6 - - + +
163A THR* 3.3 19.5 - - - +
164A PHE* 3.0 15.9 + - + +
166A GLY* 1.3 80.0 - - - +
168A TYR* 1.3 63.8 + - + +
169A THR 3.3 0.4 - - - -
170A PHE* 3.5 7.4 + - + +
171A GLU* 3.2 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 5.1 3.4 - - + -
140A THR* 3.7 21.4 + - + -
141A ILE* 3.7 29.4 - - + +
144A ASN* 3.2 31.1 + - - +
164A PHE* 3.0 35.8 + - + +
165A THR* 4.4 3.6 - - - +
167A ILE* 1.3 77.7 - - + +
169A THR* 1.3 62.2 + - - +
171A GLU* 3.5 11.4 + - - +
172A SER* 3.3 19.4 + - - -
197A ASP 5.6 0.5 - - - +
200A VAL* 5.0 5.4 - - + -
201A ILE* 4.2 16.5 - - + +
225A ARG* 3.8 37.7 - - + +
228A LYS* 4.0 31.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A THR* 2.6 26.6 + - + +
166A GLY* 3.6 8.3 + - - -
168A TYR* 1.3 76.1 - - - +
170A PHE* 1.3 60.5 + - - +
172A SER* 3.2 6.6 + - - +
173A LEU* 3.0 35.1 + - - +
201A ILE* 3.7 27.8 - - + -
205A TYR* 3.1 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 5.9 1.1 - - + -
133A PHE* 4.4 16.4 - + - -
136A PHE* 6.2 3.6 - + - -
166A GLY 3.6 15.9 + - - +
167A ILE* 3.5 8.0 + - + +
168A TYR 3.4 0.4 - - - -
169A THR* 1.3 81.0 + - - +
171A GLU* 1.3 59.9 + - - +
173A LEU* 3.7 15.7 - - + +
174A ILE* 2.9 59.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE* 4.0 19.7 - - + -
137A ILE* 3.4 32.1 - - + +
167A ILE 3.2 11.8 + - - +
168A TYR* 3.7 12.6 - - - +
169A THR 3.2 0.2 - - - -
170A PHE* 1.3 78.9 - - - +
172A SER* 1.3 61.9 + - - +
174A ILE* 3.3 7.4 - - - +
175A LYS* 3.2 43.5 + - + +
197A ASP* 5.1 6.2 - - - +
228A LYS* 3.0 33.0 + - - -
231A THR* 5.7 0.5 + - - -
232A VAL* 5.4 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR 3.3 10.0 + - - -
169A THR 3.2 9.2 + - - -
171A GLU* 1.3 78.7 - - - +
173A LEU* 1.3 64.3 + - - +
175A LYS* 3.5 5.6 + - - +
176A ILE* 3.2 39.1 + - - +
188A PHE* 4.5 13.7 - - - -
197A ASP* 5.3 7.5 + - - -
198A PHE* 5.1 4.5 - - - -
201A ILE* 3.8 26.3 - - - +
----------------------------------------------------------
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 THR* 3.0 21.6 + - - +
170A PHE* 3.8 17.5 - - + +
172A SER* 1.3 77.0 - - - +
174A ILE* 1.3 62.1 + - - +
175A LYS 3.1 2.0 - - - -
176A ILE* 4.7 5.8 - - + +
177A LEU* 3.2 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ALA* 4.4 20.4 - - + +
127A VAL* 3.7 32.8 - - + -
128A LEU* 4.6 7.1 - - + +
133A PHE* 3.7 30.1 - - + -
170A PHE* 2.9 47.6 + - + +
171A GLU 3.3 14.6 - - - +
173A LEU* 1.3 76.6 - - - +
175A LYS* 1.3 62.1 + - + +
177A LEU* 4.9 3.4 - - - -
178A ALA* 3.2 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.7 29.6 - - + +
171A GLU* 3.2 40.0 + - + +
172A SER* 4.0 3.1 - - - +
173A LEU 3.1 0.4 - - - -
174A ILE* 1.3 81.4 - - + +
176A ILE* 1.3 65.3 + - - +
177A LEU 3.4 0.4 - - - -
178A ALA* 4.0 2.4 - - - +
179A ARG* 3.1 46.3 + - - +
188A PHE* 3.1 41.3 - - + -
194A ASN* 3.3 20.5 + - - +
197A ASP* 5.3 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A SER* 3.2 29.5 + - - +
173A LEU* 4.5 6.1 - - + +
175A LYS* 1.3 76.1 - - - +
177A LEU* 1.3 70.5 + - + +
178A ALA 3.3 0.5 + - - -
180A GLY 3.1 12.0 + - - +
181A PHE 4.9 5.6 - - - +
182A CYS* 6.3 0.7 - - - -
184A ASP* 3.1 27.3 - - - +
185A ASP* 3.5 34.1 - - + +
188A PHE* 3.7 28.7 - - + -
189A LEU* 5.9 0.2 - - + -
198A PHE* 6.0 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A VAL* 5.5 11.4 - - + -
121A ARG* 3.5 25.9 - - - +
124A ALA* 4.6 11.9 - - + -
173A LEU* 3.2 45.8 + - + +
174A ILE* 4.9 1.3 - - - -
176A ILE* 1.3 84.5 - - + +
178A ALA* 1.3 59.0 + - - +
180A GLY 3.9 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 3.8 6.2 + - - +
124A ALA* 4.0 18.8 - - + +
125A ILE* 3.4 40.4 - - + +
128A LEU* 4.0 16.6 - - + -
174A ILE 3.2 20.9 + - - +
175A LYS 3.5 4.4 + - - +
176A ILE 3.2 1.0 - - - -
177A LEU* 1.3 80.2 - - - +
179A ARG* 1.3 64.5 + - - +
180A GLY 3.3 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 3.4 13.0 + - - -
128A LEU* 4.6 19.6 - - + +
175A LYS* 3.1 32.2 + - - +
176A ILE 3.5 0.2 + - - -
178A ALA* 1.3 80.0 - - + +
180A GLY* 1.3 55.8 + - - +
184A ASP* 3.0 30.9 - - - +
187A THR 6.1 0.9 - - - -
188A PHE* 4.9 15.8 - - + +
191A ASP* 5.6 4.0 + - - -
194A ASN* 5.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 3.4 30.0 - - - -
176A ILE* 3.1 13.9 + - - +
177A LEU* 3.9 9.5 - - - +
178A ALA 3.3 2.2 - - - -
179A ARG* 1.3 80.3 - - - +
181A PHE* 1.3 63.5 + - - +
184A ASP* 3.1 10.0 + - - -
----------------------------------------------------------
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