Contacts of the helix formed by residues 153 - 166 (chain A) in PDB entry 3ARE
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 153 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP* 5.1 2.3 - - - +
149A VAL 4.1 0.2 + - - -
150A LEU* 3.4 21.0 + - + +
151A ASN 2.9 5.5 - - - -
152A ALA* 1.3 77.9 - - - +
154A GLN* 1.3 62.1 + - - +
155A GLY 3.5 0.7 + - - -
156A THR* 3.0 22.0 + - - +
157A SER* 3.1 22.2 + - - -
601A 4GH 2.6 47.3 + - - +
95C ARG* 5.0 3.1 - - - -
96C GLY 3.5 13.9 - - - +
97C SER* 4.0 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASN 4.9 5.8 - - - +
152A ALA* 3.7 6.3 + - - +
153A ASP* 1.3 73.6 + - - +
155A GLY* 1.3 52.9 + - - +
157A SER* 3.3 6.5 + - - -
158A ALA* 2.7 37.4 + - - +
96C GLY 4.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASP* 3.3 3.2 + - - -
154A GLN* 1.3 75.8 - - - +
156A THR* 1.3 55.1 + - - +
158A ALA* 3.4 5.9 + - - +
159A THR* 2.7 38.2 + - - -
601A 4GH 3.2 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TRP* 4.8 7.9 - - + +
150A LEU* 5.6 3.1 - - + +
153A ASP* 3.0 28.2 + - - -
155A GLY* 1.3 73.5 - - - +
157A SER* 1.3 58.7 + - - +
159A THR* 3.2 2.4 + - - -
160A VAL* 2.9 35.6 + - + +
601A 4GH 2.9 83.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 3.5 20.0 - - - -
131A THR 2.7 28.0 + - - -
132A SER* 4.0 2.9 - - - -
133A TRP* 5.3 6.9 + - - +
150A LEU 5.4 2.2 - - - -
151A ASN* 5.2 7.0 + - - -
153A ASP 3.1 18.4 + - - -
154A GLN* 3.6 8.1 - - - -
156A THR* 1.3 78.8 - - - +
158A ALA* 1.3 59.2 + - - +
160A VAL* 4.9 0.2 - - - -
161A GLN* 3.1 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLN 2.7 21.0 + - - +
155A GLY* 3.7 7.9 - - - +
157A SER* 1.3 72.7 - - - +
159A THR* 1.3 64.6 + - - +
161A GLN* 3.4 13.1 + - - +
162A MET* 3.0 23.7 + - - +
501A NAG 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MET* 3.8 31.4 - - + -
155A GLY 2.7 21.9 + - - -
156A THR* 3.2 5.0 + - - -
158A ALA* 1.3 76.2 - - - +
160A VAL* 1.3 56.8 + - - +
162A MET* 3.2 14.7 + - - +
163A LEU* 2.9 36.0 + - + +
601A 4GH 3.9 27.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
116A LEU* 3.9 20.6 - - + -
128A PHE* 3.6 39.7 - - + -
133A TRP* 4.3 20.0 - - + -
156A THR* 2.9 22.7 + - + +
157A SER 4.1 0.2 - - - +
159A THR* 1.3 75.7 - - - +
161A GLN* 1.3 56.8 + - - +
163A LEU* 3.0 9.7 + - + +
164A LEU* 2.9 33.8 + - + +
601A 4GH 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 3.6 9.6 - - + -
130A GLY 3.3 22.3 - - - +
131A THR* 3.4 36.1 + - - +
157A SER* 3.1 29.0 + - - +
158A ALA* 3.6 10.4 - - - +
159A THR 3.4 0.2 - - - -
160A VAL* 1.3 77.5 - - - +
162A MET* 1.3 57.5 + - - +
164A LEU* 4.8 1.6 - - - -
165A ASN* 2.9 40.2 + - - +
501A NAG 3.2 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ALA 3.0 13.9 + - - +
159A THR* 3.4 17.5 - - - +
160A VAL 3.2 0.2 - - - -
161A GLN* 1.3 75.0 - - - +
163A LEU* 1.3 62.3 + - - +
165A ASN* 5.2 0.2 - - - -
166A ASP* 2.9 40.3 + - + +
167A THR* 3.0 19.9 + - - +
501A NAG 5.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.9 18.2 - - + -
69A MET* 3.8 33.7 - - + -
70A PHE* 4.6 9.2 - - + -
159A THR* 2.9 33.3 + - + +
160A VAL* 3.6 7.6 - - - +
162A MET* 1.3 80.8 - - + +
164A LEU* 1.3 58.4 + - + +
167A THR* 3.4 17.9 - - + +
168A CYS* 2.9 32.6 + - - +
601A 4GH 3.5 46.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY 4.7 1.3 - - - +
114A SER* 2.7 38.7 + - - -
115A PHE* 3.7 25.1 - - - +
116A LEU* 4.2 20.9 - - + -
128A PHE* 3.7 35.2 - - + +
160A VAL* 2.9 22.8 + - + +
161A GLN* 4.2 0.9 - - - +
163A LEU* 1.3 77.2 - - + +
165A ASN* 1.3 71.4 + - - +
166A ASP 3.5 0.2 - - - -
168A CYS* 4.1 1.5 - - + +
169A PRO* 3.7 10.9 - - - +
601A 4GH 4.0 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 5.5 2.0 - - - -
130A GLY 5.4 0.2 - - - +
161A GLN* 2.9 18.9 + - - +
162A MET* 5.2 0.2 - - - -
164A LEU* 1.3 86.2 - - - +
166A ASP* 1.3 70.0 + - - +
169A PRO* 3.8 12.5 - - - +
501A NAG 1.4 75.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A MET* 2.9 24.8 + - + +
164A LEU 3.5 0.2 - - - -
165A ASN* 1.3 90.1 - - - +
167A THR* 1.3 65.4 + - - +
168A CYS 3.6 1.3 - - - -
169A PRO* 3.4 2.9 - - - +
170A LEU* 3.3 25.4 + - - +
501A NAG 5.5 2.1 - - - +
----------------------------------------------------------
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