Contacts of the helix formed by residues 165 - 175 (chain L) in PDB entry 2A3W
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 PRO 165 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163L VAL 3.5 7.8 - - - +
164L LEU* 1.3 88.9 - - + +
166L PRO* 1.3 77.8 - - + +
167L GLU* 3.2 21.8 - - - +
168L ASN* 3.0 43.6 + - - +
169L ILE* 3.2 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 166 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202K VAL* 4.0 21.1 - - + -
106L GLU* 6.0 1.1 - - - +
108L TRP* 3.7 36.5 - - + -
164L LEU 4.5 1.1 - - - +
165L PRO* 1.3 87.3 - - + +
167L GLU* 1.3 62.9 + - - +
169L ILE* 3.3 5.5 + - + +
170L LEU* 2.9 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165L PRO* 3.7 25.7 - - + +
166L PRO* 1.3 82.2 - - - +
168L ASN* 1.3 70.7 + - - +
170L LEU* 3.5 11.8 + - - +
171L SER* 2.9 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 168 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160L TRP* 5.7 0.3 - - - -
164L LEU* 3.6 29.0 - - + +
165L PRO* 3.0 34.0 + - - +
167L GLU* 1.3 83.6 - - - +
169L ILE* 1.3 64.8 + - - +
171L SER* 3.3 8.9 + - - -
172L ALA* 3.0 22.7 + - - +
177L PRO* 5.3 0.5 - - - +
178L LEU* 3.4 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L THR* 3.7 30.1 - - + -
93L HIS* 4.5 1.3 - - + +
95L CYS* 3.8 24.7 - - + -
96L VAL 6.2 0.2 - - - -
97L SER* 5.8 1.8 - - - -
108L TRP* 3.6 54.7 - - + +
111L GLY* 5.1 5.8 - - - +
164L LEU* 3.8 20.2 - - + +
165L PRO 3.2 13.9 + - - +
166L PRO* 3.5 8.5 - - + +
168L ASN* 1.3 73.5 - - - +
170L LEU* 1.3 67.9 + - + +
172L ALA* 3.1 6.4 + - - +
173L TYR* 2.9 20.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108L TRP* 4.9 7.4 - - + -
111L GLY* 3.5 33.9 - - - +
166L PRO* 2.9 22.1 + - + +
167L GLU* 3.6 10.3 - - - +
169L ILE* 1.3 75.3 - - - +
171L SER* 1.3 51.6 + - - +
173L TYR* 3.1 10.8 + - + +
174L GLN* 2.7 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 171 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167L GLU 2.9 17.6 + - - -
168L ASN* 3.3 15.5 + - - -
170L LEU* 1.3 75.6 - - - +
172L ALA* 1.3 61.4 + - - +
174L GLN* 3.2 8.1 + - - -
175L GLY 3.1 5.2 + - - -
176L THR* 2.9 50.2 + - - -
177L PRO* 4.8 0.2 - - - -
178L LEU* 4.5 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L CYS* 4.1 27.8 - - + -
38L ARG* 3.3 12.6 + - - -
93L HIS* 3.6 9.7 + - - +
156L ASP* 5.9 0.5 - - - +
158L TYR* 5.9 0.9 - - + -
160L TRP* 4.4 5.4 - - + -
168L ASN 3.0 12.4 + - - +
169L ILE 3.1 7.8 + - - +
171L SER* 1.3 75.0 - - - +
173L TYR* 1.3 63.3 + - - +
175L GLY* 3.2 10.9 + - - -
177L PRO* 3.9 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 173 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L ARG* 3.3 19.8 + - - -
93L HIS* 3.4 41.4 - - + +
110L ASN* 3.4 48.2 + - + +
111L GLY* 3.9 13.9 - - - +
169L ILE* 2.9 11.9 + - + +
170L LEU* 3.1 15.7 + - + +
172L ALA* 1.3 75.7 - - - +
174L GLN* 1.3 70.5 + - + +
175L GLY 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 174 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L ARG* 4.8 0.4 - - - -
170L LEU* 2.7 42.7 + - - +
171L SER* 3.2 9.2 + - - +
173L TYR* 1.3 83.5 - - + +
175L GLY* 1.3 58.2 + - - +
176L THR* 3.6 8.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 175 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L ARG* 4.1 10.3 - - - -
156L ASP* 5.9 0.9 - - - -
171L SER 3.1 2.0 + - - -
172L ALA 3.2 7.8 + - - -
173L TYR 3.2 3.8 - - - -
174L GLN* 1.3 78.9 - - - +
176L THR* 1.3 66.3 + - - +
177L PRO* 3.3 12.3 - - - +
----------------------------------------------------------
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