Contacts of the helix formed by residues 155 - 160 (chain D) in PDB entry 3V81
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 155 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE* 3.4 24.1 - - - -
88D TRP* 4.4 0.8 - - - -
153D TRP* 3.3 29.8 - - - +
154D LYS* 1.3 78.1 - - - +
156D SER* 1.3 64.4 + - - +
158D ALA* 2.8 15.6 + - - +
159D ILE* 3.0 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D TYR* 2.9 34.9 - - - -
149D LEU* 3.6 13.7 - - - +
150D PRO* 2.7 43.8 + - - +
152D GLY 5.4 1.1 - - - -
153D TRP* 3.3 14.5 - - - +
155D GLY* 1.3 75.0 - - - +
157D PRO* 1.3 66.9 - - - +
159D ILE 3.7 0.2 + - - -
160D PHE* 3.3 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D TYR* 2.9 28.9 - - + +
153D TRP 3.1 19.5 - - - +
154D LYS* 3.4 16.2 - - + +
156D SER* 1.3 93.0 - - - +
158D ALA* 1.3 59.1 + - - +
160D PHE* 4.1 1.3 - - + -
161D GLN* 3.4 21.7 + - - +
182D GLN* 3.8 16.9 + - + +
184D MET* 4.3 27.6 - - - +
185D ASP* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE* 3.5 25.1 - - + -
88D TRP* 4.9 6.1 - - + -
92D LEU* 4.0 29.9 - - + +
154D LYS 4.4 4.5 - - - +
155D GLY 2.8 11.4 + - - +
157D PRO* 1.3 78.1 - - - +
159D ILE* 1.3 65.1 + - - +
161D GLN* 3.1 22.6 - - - +
162D SER 4.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 4.2 39.9 - - + +
10D VAL* 4.2 15.0 - - + -
87D PHE* 3.7 26.9 - - + -
118D VAL* 3.9 17.9 - - + +
119D PRO 5.2 1.3 - - - +
120D LEU* 5.2 2.2 - - + -
121D ASP 6.0 0.7 - - - +
149D LEU* 3.9 37.0 - - + -
153D TRP* 4.4 4.5 - - + -
155D GLY 3.0 9.3 + - - +
158D ALA* 1.3 79.5 - - - +
160D PHE* 1.3 56.9 + - - +
161D GLN 3.1 0.7 + - - -
162D SER* 3.3 19.2 + - - -
163D SER* 4.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D VAL* 6.4 0.7 - - + -
114D ALA* 3.2 49.8 - - + -
115D TYR* 4.6 15.7 - + + -
117D SER* 4.8 6.1 - - - -
118D VAL* 3.5 24.0 - - + -
149D LEU* 4.3 7.9 - - + -
156D SER 3.3 16.7 + - - +
157D PRO 4.1 2.7 - - - +
158D ALA 3.2 0.8 - - - -
159D ILE* 1.3 78.0 - - - +
161D GLN* 1.3 58.8 + - - +
162D SER 3.3 1.3 - - - -
163D SER* 3.3 26.4 + - - -
164D MET* 2.9 44.0 + - + +
167D ILE* 5.6 3.6 - - + -
182D GLN* 5.5 3.1 - - - -
209D LEU* 6.1 1.6 - - + -
212D TRP* 6.0 4.7 - + - -
----------------------------------------------------------
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