Contacts of the helix formed by residues 160 - 169 (chain A) in PDB entry 3EBV
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 GLY 160 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE 5.3 2.0 - - - -
154A ASP* 3.6 20.6 - - - -
157A SER* 3.0 15.6 + - - +
159A GLN* 1.3 79.2 - - - +
161A GLY* 1.3 61.2 + - - -
162A TYR 3.4 2.5 - - - -
163A PHE* 3.0 2.8 + - - -
164A GLN* 2.8 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 3.9 24.0 - - - -
126A PRO* 3.9 14.3 - - - +
154A ASP* 4.3 3.8 + - - +
159A GLN 3.6 2.3 + - - -
160A GLY* 1.3 68.8 - - - +
162A TYR* 1.3 61.7 + - - +
164A GLN* 3.5 1.8 + - - +
165A THR* 2.8 30.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
118A ILE* 3.5 30.6 + - + +
119A ASP* 3.5 4.2 - - - -
120A LEU* 2.7 46.6 + - - +
123A GLY 5.6 0.4 - - - -
124A LEU* 3.8 30.0 - - + +
148A MSE 3.6 22.4 - - + +
149A ALA 4.6 1.1 + - - -
150A PRO* 3.7 28.5 - - + -
154A ASP* 3.6 36.6 + - + +
155A MSE 3.8 16.4 - - - -
160A GLY 3.4 0.4 - - - -
161A GLY* 1.3 74.0 - - - +
163A PHE* 1.3 58.1 + - - +
165A THR* 3.3 2.5 + - - -
166A ALA* 2.8 31.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
154A ASP 3.6 3.9 + - - +
155A MSE 3.5 38.3 - - + -
157A SER 3.1 32.8 - - - +
158A THR* 3.7 11.0 - - + +
160A GLY 3.0 5.7 + - - +
162A TYR* 1.3 79.0 - - - +
164A GLN* 1.3 64.2 + - - +
166A ALA* 3.2 2.5 + - + +
167A LEU* 2.9 39.2 + - + +
208A ILE* 3.8 28.3 - - + -
209A GLN* 3.8 27.1 - - + -
212A GLY 3.6 25.6 - - - -
214A LEU* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PRO* 4.0 18.2 - - + -
158A THR 3.7 16.7 + - - +
159A GLN* 4.3 19.5 + - - +
160A GLY 2.8 16.3 + - - +
161A GLY* 3.9 3.4 - - - +
163A PHE* 1.3 76.4 - - - +
165A THR* 1.3 58.0 + - - +
167A LEU* 3.4 12.1 + - - +
168A ASN* 2.9 64.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
124A LEU* 3.2 13.7 - - - +
126A PRO* 3.3 13.3 - - - +
129A MSE 3.8 19.5 - - + -
130A THR* 3.9 20.6 - - - +
133A LEU* 4.0 12.6 - - + -
148A MSE 3.8 22.9 - - + -
161A GLY 2.8 21.7 + - - -
162A TYR 3.7 3.4 - - - -
164A GLN* 1.3 77.8 - - - +
166A ALA* 1.3 64.1 + - - +
168A ASN* 3.0 3.5 + - - +
169A VAL* 2.9 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MSE 4.0 19.9 - - - -
155A MSE 5.0 1.8 - - + -
162A TYR 2.8 20.9 + - - +
163A PHE* 3.5 7.9 - - - +
165A THR* 1.3 73.3 - - - +
167A LEU* 1.3 56.8 + - - +
169A VAL* 3.3 5.7 + - - -
170A LYS* 3.0 29.3 + - - +
173A LEU* 3.8 20.1 - - + +
176A VAL* 4.1 11.4 - - + -
214A LEU* 4.2 11.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
158A THR* 4.1 19.1 - - + +
163A PHE* 2.9 40.9 + - + +
164A GLN* 3.7 13.5 - - - +
166A ALA* 1.3 72.4 - - - +
168A ASN* 1.3 67.9 + - - +
170A LYS* 3.2 22.1 + - + +
212A GLY 3.7 11.0 - - - +
213A GLY* 3.6 35.9 - - - +
214A LEU* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PRO* 4.3 5.7 + - - +
127A THR* 6.0 0.2 - - - +
130A THR* 3.0 38.3 + - + +
134A ARG* 2.9 19.6 + - - -
164A GLN* 2.9 48.8 + - - +
165A THR 3.0 7.6 + - - +
167A LEU* 1.3 77.7 - - - +
169A VAL* 1.3 59.8 + - - +
170A LYS 3.5 0.7 + - - -
171A ASP* 4.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 4.1 21.8 - - + +
133A LEU* 4.2 29.4 - - + -
134A ARG* 3.6 16.6 - - - +
146A LEU* 4.0 20.4 - - + -
148A MSE 5.3 1.6 - - - -
165A THR* 2.9 20.6 + - + +
166A ALA* 3.9 7.9 - - - +
168A ASN* 1.3 81.4 - - - +
170A LYS* 1.3 63.7 + - - +
171A ASP* 3.2 4.0 - - - -
172A ILE* 2.9 27.0 + - + -
173A LEU* 3.1 15.6 + - + -
----------------------------------------------------------
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