Contacts of the helix formed by residues 150 - 171 (chain A) in PDB entry 3DAE
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 150 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LYS 4.1 0.8 + - - -
149A MET* 1.3 75.1 - - - +
151A GLU* 1.3 57.6 + - - +
152A GLN* 3.8 10.9 + - - +
153A GLU* 2.7 46.5 + - - +
154A ALA* 3.0 11.1 + - - +
246A LEU* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A MET 3.5 3.0 + - - -
150A SER* 1.3 70.0 - - - +
152A GLN* 1.3 59.0 + - + +
154A ALA* 3.3 1.6 + - - +
155A ARG* 2.9 40.5 + - - +
246A LEU* 4.0 18.7 - - + +
276A SER* 2.5 43.8 + - - -
279A ALA* 4.0 6.8 - - - +
305A TRP* 3.3 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A SER* 3.1 11.9 + - - +
151A GLU* 1.3 78.8 - - + +
153A GLU* 1.3 61.8 + - - +
155A ARG* 3.6 21.3 + - - +
156A ARG* 3.1 21.5 + - - +
309A ASP* 5.2 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 2.9 41.3 + - - -
146A ARG* 4.5 9.6 + - - -
149A MET* 3.8 24.0 - - + +
150A SER* 2.7 26.6 + - - +
152A GLN* 1.3 72.6 - - - +
154A ALA* 1.3 63.2 + - - +
156A ARG* 3.2 20.5 + - + +
157A PHE* 3.2 28.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A MET* 4.2 8.3 - - - -
150A SER 3.0 7.3 + - - +
151A GLU 4.0 0.4 - - - +
153A GLU* 1.3 73.4 - - - +
155A ARG* 1.3 62.9 + - - +
158A PHE* 2.7 33.6 + - - +
242A LEU* 4.4 6.1 - - + -
245A MET* 3.7 33.2 - - + +
246A LEU* 3.6 31.9 - - + -
305A TRP* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLU* 2.9 27.4 + - - +
152A GLN* 4.0 22.9 + - - +
154A ALA* 1.3 77.3 - - - +
156A ARG* 1.3 63.0 + - - +
158A PHE* 4.0 5.4 - - + -
159A GLN* 3.0 41.6 + - + +
305A TRP* 2.6 86.6 + - + +
306A PHE* 3.6 3.8 - - + +
308A VAL* 3.3 46.5 + - - +
309A ASP* 5.1 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLN 3.1 14.5 + - - +
153A GLU* 3.4 14.8 - - - +
154A ALA 3.1 1.0 - - - -
155A ARG* 1.3 78.3 - - - +
157A PHE* 1.3 77.3 + - - +
159A GLN* 3.9 11.5 - - - +
160A GLN* 3.3 38.6 + - - +
188A HIS 3.6 12.3 + - - -
189A LEU* 3.0 31.7 + - - +
190A ASN* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.0 15.9 - - + -
142A TYR* 3.7 35.4 - + - -
149A MET* 4.0 17.0 - - + -
153A GLU* 3.2 29.4 + - + -
154A ALA 4.0 0.9 - - - +
156A ARG* 1.3 90.6 - - + +
158A PHE* 1.3 66.2 + - - +
160A GLN* 3.1 10.9 + - - +
161A ILE* 3.0 27.3 + - + +
185A LEU* 3.6 14.6 - - + -
189A LEU* 3.1 31.6 - - + -
191A VAL* 3.6 20.7 - - + +
245A MET* 3.9 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ALA 2.7 21.7 + - - +
155A ARG* 3.7 4.5 - - - +
157A PHE* 1.3 76.4 - - - +
159A GLN* 1.3 64.4 + - - +
161A ILE* 2.9 15.6 + - + +
162A ILE* 2.8 47.5 + - + +
238A CYS* 3.3 28.5 - - + -
241A ILE* 5.4 0.2 - - + -
242A LEU* 3.6 35.2 - - + -
245A MET* 4.3 8.5 - - + +
282A LEU* 3.8 16.4 - - + -
286A MET* 3.8 18.6 - - - -
300A ILE* 4.7 1.8 - - + -
305A TRP* 4.1 11.9 - + - -
306A PHE* 3.7 20.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ARG* 3.0 30.8 + - + +
156A ARG* 3.9 10.4 - - - +
158A PHE* 1.3 79.0 - - - +
160A GLN* 1.3 58.1 + - - +
162A ILE* 4.2 0.5 - - - +
163A SER* 3.0 29.6 + - - -
301A MET* 6.0 0.2 - - - +
306A PHE* 2.8 44.3 + - + +
308A VAL 2.8 30.1 + - - -
309A ASP 3.6 3.1 - - - +
310A LEU* 3.5 20.6 - - + +
311A PRO* 3.5 18.4 - - - +
314A LEU* 3.7 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A HIS* 3.3 43.4 - - + +
156A ARG* 3.3 40.3 + - + +
157A PHE* 3.1 10.6 + - - +
158A PHE 3.0 0.8 - - - -
159A GLN* 1.3 74.6 - - - +
161A ILE* 1.3 65.1 + - - +
163A SER* 3.5 3.9 - - - -
164A ALA* 3.2 16.8 + - - +
190A ASN* 3.0 21.6 + - - -
191A VAL* 3.0 36.6 + - + +
313A TYR* 3.8 10.0 + - - +
314A LEU* 4.2 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.3 11.7 - - + -
157A PHE* 3.0 26.7 + - + +
158A PHE* 2.9 14.7 + - + +
160A GLN* 1.3 72.2 - - - +
162A ILE* 1.3 68.8 + - + +
164A ALA* 3.0 9.4 + - - +
165A VAL* 2.9 28.6 + - + +
178A LEU* 5.2 1.8 - - + -
183A LEU* 4.2 24.7 - - + -
191A VAL* 3.8 22.9 - - + -
193A ILE* 5.2 2.9 - - + -
238A CYS* 3.7 27.1 - - + -
241A ILE* 4.0 27.4 - - + -
245A MET* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 2.8 54.1 + - + +
159A GLN 4.2 0.2 - - - +
161A ILE* 1.3 73.5 - - - +
163A SER* 1.3 65.3 + - - +
165A VAL* 3.1 5.1 + - - +
166A GLU* 2.8 22.0 + - - +
238A CYS* 4.1 19.7 - - + -
297A ILE* 4.0 21.5 - - + -
300A ILE* 4.0 27.1 - - + -
301A MET* 4.3 14.8 - - - -
306A PHE* 4.0 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A HIS* 3.7 17.5 + - - -
159A GLN 3.0 21.6 + - - -
160A GLN 3.5 5.6 - - - -
161A ILE 3.1 0.2 - - - -
162A ILE* 1.3 78.9 - - - +
164A ALA* 1.3 65.6 + - - +
166A GLU* 3.1 18.4 + - - +
167A TYR* 3.1 9.7 + - - +
301A MET* 5.3 6.5 - - - -
306A PHE* 5.5 0.2 - - - -
314A LEU* 3.2 45.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
112A HIS* 3.5 14.1 - - - -
114A HIS* 3.3 28.5 - - + +
115A ILE* 3.7 9.9 - - + +
160A GLN 3.2 8.3 + - - +
161A ILE* 3.0 9.5 + - - +
163A SER* 1.3 77.1 - - - +
165A VAL* 1.3 61.6 + - - +
167A TYR* 3.0 6.2 + - - +
168A CYS* 3.0 24.7 + - - -
193A ILE* 3.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 2.9 25.5 + - + +
162A ILE* 3.6 7.9 - - - +
164A ALA* 1.3 71.8 - - - +
166A GLU* 1.3 63.9 + - - +
168A CYS* 3.0 10.2 + - + +
169A HIS* 3.0 52.8 + - + +
175A HIS* 6.1 0.4 - - + -
178A LEU* 3.8 23.3 - - + -
193A ILE* 4.1 9.4 - - + -
234A ASP* 3.8 15.9 - - + +
238A CYS* 4.1 13.2 - - - -
297A ILE* 4.2 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A HIS* 5.8 0.3 + - - -
162A ILE 2.8 13.0 + - - +
163A SER* 3.5 12.3 + - - +
165A VAL* 1.3 73.5 - - - +
167A TYR* 1.3 62.5 + - - +
169A HIS* 3.8 5.6 - - - +
170A ARG* 3.1 52.9 + - - +
297A ILE* 3.4 34.0 - - + +
298A HIS* 5.6 1.6 - - - +
301A MET* 4.3 18.2 - - - +
315A LEU 5.6 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU 3.9 5.9 + - - -
110A LEU* 3.6 37.9 - - + -
111A ARG* 3.7 29.1 + - - +
112A HIS* 3.3 27.8 - + + +
115A ILE* 4.1 11.7 - - + -
163A SER 3.1 5.6 + - - +
164A ALA 3.0 10.4 + - - +
166A GLU* 1.3 77.4 + - - +
168A CYS* 1.3 64.7 + - - +
170A ARG* 3.0 44.7 + - - +
171A HIS* 3.2 47.5 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 4.4 12.6 - - - -
115A ILE* 3.8 15.7 - - - -
164A ALA 3.0 19.5 + - - -
165A VAL* 3.0 11.0 + - + +
167A TYR* 1.3 76.0 - - - +
169A HIS* 1.3 65.0 + - + +
171A HIS* 3.0 10.0 + - - -
173A ILE* 2.8 42.5 + - + +
174A VAL* 5.4 0.2 - - - -
175A HIS* 5.4 6.3 - - + +
193A ILE* 5.1 6.1 - - - -
196A PHE* 3.6 30.1 - - - -
234A ASP* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A VAL* 3.0 35.7 + - + +
166A GLU* 3.8 5.8 - - - +
168A CYS* 1.3 72.3 - - + +
170A ARG* 1.3 60.7 + - - +
172A LYS* 2.7 29.2 + - - +
173A ILE 3.7 15.9 - - - +
174A VAL* 4.3 5.8 - - + +
231A PRO* 3.3 51.3 - - + +
234A ASP* 2.9 26.0 + - + -
297A ILE* 3.8 21.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
166A GLU* 3.1 49.8 + - - +
167A TYR* 3.0 49.2 - - - +
169A HIS* 1.3 79.4 - - - +
171A HIS* 1.3 67.6 + - + +
172A LYS* 3.3 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 4.1 33.1 - - + +
110A LEU* 4.1 15.9 - - + -
167A TYR* 3.2 60.5 + + - +
168A CYS 3.0 9.0 + - - +
170A ARG* 1.3 90.3 + - + +
172A LYS* 1.3 69.5 + - - +
173A ILE* 3.1 12.6 + - + +
----------------------------------------------------------
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