Contacts of the helix formed by residues 157 - 174 (chain A) in PDB entry 3HYW
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 157 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ALA* 3.5 23.8 - - + -
154A VAL* 3.3 34.1 - - + -
155A SER* 4.0 4.3 - - - -
156A CSS 1.3 75.8 - - - -
158A GLY* 1.3 68.7 + - - +
159A PRO* 3.3 3.1 - - - -
160A ALA* 2.9 20.9 + - + +
161A TYR* 3.3 26.0 - - + -
184A PHE* 6.1 0.9 - + - -
186A THR* 3.6 1.3 - - - -
187A SER* 3.4 18.8 - - - -
188A GLU* 3.5 29.2 - - + -
194A PHE* 3.5 29.8 - - - -
195A GLY* 3.8 17.7 - - - -
251A MET* 5.0 0.2 - - - -
308A THR* 3.5 20.4 - - + -
800A PS9 3.7 3.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 1.3 77.0 - - - +
159A PRO* 1.3 61.4 - - - +
161A TYR* 3.1 12.5 + - - +
162A GLU* 2.9 30.0 + - - +
194A PHE* 4.5 0.6 - - - -
349A ALA* 4.9 1.3 - - - +
800A PS9 3.1 44.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 4.5 0.6 - - + +
123A ILE* 3.7 9.8 - - + +
156A CSS 4.0 14.8 - - - +
157A PHE 3.4 4.5 - - - -
158A GLY* 1.3 89.6 - - - +
160A ALA* 1.3 55.0 + - - +
162A GLU* 3.6 13.0 - - - +
163A PHE* 2.9 31.2 + - - +
251A MET* 4.1 13.9 - - + -
441A FAD 3.4 50.7 - - + -
800A PS9 3.7 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ILE* 3.7 8.2 - - + +
149A GLY 4.1 12.1 - - - +
150A ALA* 5.5 1.1 - - + -
157A PHE* 2.9 13.2 + - + +
159A PRO* 1.3 74.0 - - - +
161A TYR* 1.3 61.4 + - - +
163A PHE* 3.5 0.3 + - - +
164A ALA* 3.0 30.0 + - - +
184A PHE* 3.6 21.7 - - + -
249A MET* 4.1 11.9 - - + -
251A MET* 3.8 24.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 3.3 25.9 + - + -
158A GLY* 3.1 7.3 + - - +
160A ALA* 1.3 74.2 - - - +
162A GLU* 1.3 65.0 + - - +
164A ALA* 3.5 2.3 + - - +
165A LEU* 3.1 36.1 + - + +
184A PHE* 3.5 27.4 - + - -
188A GLU* 2.6 32.4 + - - -
191A LEU* 3.5 7.8 - - + +
192A GLY 3.1 20.4 + - - -
194A PHE* 3.6 29.8 - + + -
206A VAL* 3.5 29.8 - - + -
210A PHE* 3.6 21.5 - + - -
349A ALA* 5.3 4.0 - - + -
351A PHE* 5.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 3.7 20.1 - - + +
47A HIS* 5.0 0.4 - - - -
158A GLY 2.9 14.6 + - - +
159A PRO* 3.6 16.7 - - - +
161A TYR* 1.3 75.5 - - - +
163A PHE* 1.3 57.1 + - - +
165A LEU* 3.3 1.7 + - - -
166A MET* 2.8 45.2 + - + +
348A ILE 4.2 0.2 - - - -
349A ALA* 3.6 13.2 - - + +
350A ASP* 2.8 46.5 + - - +
351A PHE* 4.8 3.1 - - - -
382A LYS* 3.0 31.3 + - - -
441A FAD 4.4 7.7 + - - -
800A PS9 4.6 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 4.4 6.5 - - + -
49A ALA* 3.9 12.8 - - + -
50A MET* 3.8 21.3 - - - -
123A ILE* 3.9 22.7 - - + -
132A THR* 3.8 31.0 - - + -
136A LEU* 3.8 15.0 - - + -
148A ILE* 3.8 17.9 - - + -
159A PRO 2.9 18.5 + - - +
160A ALA 3.9 3.1 - - - +
162A GLU* 1.3 75.1 - - - +
164A ALA* 1.3 57.4 + - - +
166A MET* 3.7 7.0 - - - +
167A LEU* 2.9 37.7 + - + +
247A PHE* 3.7 15.7 - + - -
249A MET* 3.6 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ILE* 3.7 22.7 - - + -
160A ALA 3.0 18.1 + - - +
161A TYR 3.8 4.0 - - - +
163A PHE* 1.3 79.4 - - - +
165A LEU* 1.3 59.8 + - + +
168A HIS* 3.1 23.7 + - - +
182A MET* 3.2 17.0 - - + +
184A PHE* 4.1 20.2 - - + -
210A PHE* 4.9 7.9 - - + -
215A ILE* 4.8 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 3.1 17.8 + - + +
162A GLU 4.0 0.2 - - - +
164A ALA* 1.3 74.3 - - - +
166A MET* 1.3 60.5 + - - +
168A HIS* 3.5 7.8 + - + +
169A TYR* 3.0 22.9 + - - +
206A VAL* 6.1 0.2 - - + -
209A LEU* 3.3 23.1 - - + -
210A PHE* 4.0 28.9 - - + -
213A ARG* 3.6 33.4 - - + +
215A ILE* 4.5 11.0 - - + -
351A PHE* 3.2 54.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 4.0 23.1 - - + +
47A HIS* 3.2 42.2 - - + +
50A MET* 4.0 19.1 - - + -
52A TRP* 3.6 31.3 - - + -
162A GLU* 2.8 30.8 + - + +
163A PHE* 3.7 4.7 - - - +
165A LEU* 1.3 73.9 - - - +
167A LEU* 1.3 59.1 + - - +
169A TYR* 3.3 3.6 + - - +
170A GLU* 2.9 28.4 + - - +
350A ASP* 3.4 31.0 - - + +
351A PHE 3.7 9.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 4.0 12.3 - - + -
136A LEU* 3.6 34.3 - - + -
139A LEU* 4.3 3.4 - - + -
140A TYR* 3.9 23.8 - - + +
146A VAL* 3.9 35.7 - - + -
148A ILE* 4.0 10.5 - - + -
163A PHE* 2.9 23.5 + - + +
164A ALA 3.7 3.8 - - - +
166A MET* 1.3 74.7 - - - +
168A HIS* 1.3 59.6 + - - +
170A GLU* 3.2 2.3 + - - +
171A LEU* 2.9 46.4 + - + +
182A MET* 4.4 3.8 - - + -
247A PHE* 4.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA 3.1 15.3 + - - +
165A LEU* 3.5 13.0 - - + +
167A LEU* 1.3 76.0 - - - +
169A TYR* 1.3 66.6 + - + +
171A LEU* 3.4 1.4 + - - +
172A LYS* 3.0 48.0 + - + +
177A ARG* 3.1 39.0 + - + +
182A MET* 4.0 16.0 - - - -
213A ARG* 3.4 56.2 + - + +
215A ILE* 4.2 4.5 - - + -
367C ARG 5.1 1.3 - - - -
368C GLU 4.9 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TRP* 3.6 27.4 - + - -
165A LEU 3.0 15.1 + - - +
166A MET* 3.4 7.2 - - - +
167A LEU 3.2 0.2 - - - -
168A HIS* 1.3 80.7 - - + +
170A GLU* 1.3 60.3 + - - +
172A LYS* 3.3 7.0 + - + +
173A LYS* 2.9 49.5 + - + +
351A PHE 3.8 9.0 - - - +
352A GLY* 4.1 7.9 - - - -
353A GLU* 3.7 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 3.5 23.8 - - + -
52A TRP* 3.0 28.0 + - + -
140A TYR* 3.4 30.5 - - + +
166A MET 2.9 6.9 + - - +
167A LEU* 3.2 6.2 + - + +
169A TYR* 1.3 77.3 - - - +
171A LEU* 1.3 58.3 + - - +
173A LYS* 3.1 25.4 + - - +
174A ARG* 2.8 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.5 5.4 - - + -
140A TYR* 3.7 31.9 - - + -
167A LEU* 2.9 42.4 + - + +
168A HIS 3.8 3.1 - - - +
170A GLU* 1.3 72.1 - - - +
172A LYS* 1.3 57.6 + - - +
174A ARG* 3.3 2.2 + - - -
175A GLY 2.9 8.0 + - - -
176A ILE* 2.9 45.7 + - + -
177A ARG* 3.9 18.4 - - + -
180A VAL* 3.7 37.5 - - + -
182A MET* 4.1 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A HIS* 3.0 39.6 + - + +
169A TYR* 3.6 7.4 - - + +
171A LEU* 1.3 74.2 - - - +
173A LYS* 1.3 64.8 + - - +
175A GLY* 3.3 8.5 + - - -
177A ARG* 3.9 5.8 - - + +
213A ARG* 6.1 0.6 - - - +
435A SO4 2.9 48.9 + - - -
368C GLU* 3.1 47.8 + - + +
369C ARG* 4.0 14.9 + - - +
370C VAL 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TYR* 2.9 35.4 + - + +
170A GLU* 3.2 31.4 - - - +
172A LYS* 1.3 77.9 - - - +
174A ARG* 1.3 61.2 + - + +
175A GLY 3.2 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLN* 3.6 18.6 + - - +
140A TYR* 3.4 59.5 - - - +
170A GLU* 2.8 42.6 + - - +
171A LEU 3.8 4.0 - - - +
173A LYS* 1.3 77.7 - - + +
175A GLY* 1.3 62.1 + - - +
176A ILE* 3.4 20.2 + - + +
----------------------------------------------------------
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