Contacts of the helix formed by residues 149 - 155 (chain D) in PDB entry 2VRF
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 LEU 149 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D GLN* 5.0 2.0 - - + -
123D ALA* 3.7 24.9 - - + +
124D GLY* 4.2 15.9 - - - -
127D GLY* 3.8 20.6 - - - -
146D PHE* 3.2 34.2 + - + +
147D PRO 3.1 9.1 + - - +
148D GLY* 1.3 83.7 - - - +
150D ALA* 1.3 61.5 + - - +
151D ALA 3.4 1.8 - - - -
152D ASP 3.1 4.5 + - - -
153D GLN* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D VAL* 3.8 14.8 - - + +
119D VAL 3.2 26.6 + - - +
120D LYS* 4.1 0.2 - - - -
121D GLN* 3.8 22.6 - - + +
125D GLY 3.4 24.2 + - - +
126D LEU 3.5 5.1 + - - +
127D GLY* 4.5 0.4 - - - -
149D LEU* 1.3 74.4 - - - +
151D ALA* 1.3 63.2 + - - +
153D GLN* 3.4 4.7 + - - +
154D SER* 3.2 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D VAL* 4.0 9.6 - - + -
126D LEU* 2.9 22.7 + - + +
127D GLY* 4.2 1.3 - - - +
128D ILE* 3.3 26.0 - - + -
145D ILE* 4.0 9.4 - - + -
149D LEU 3.4 0.4 - - - -
150D ALA* 1.3 74.0 - - - +
152D ASP* 1.3 62.9 + - - +
154D SER* 2.6 25.5 + - - -
155D ARG* 3.3 4.0 + - - -
156D ALA 4.3 0.7 + - - -
157D LEU* 3.7 21.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLN* 4.5 10.9 + - - +
122B GLU* 5.7 0.5 - - - +
127D GLY 5.2 0.2 + - - -
145D ILE* 3.7 17.7 - - + +
146D PHE 3.5 17.0 + - - +
147D PRO* 3.6 9.5 - - - +
148D GLY* 2.9 22.4 + - - +
149D LEU 3.1 9.7 + - - +
151D ALA* 1.3 79.1 - - - +
153D GLN* 1.3 62.1 + - - +
155D ARG* 3.0 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D GLN* 2.8 34.7 + - - +
148D GLY* 3.1 25.6 + - - +
149D LEU 2.9 14.3 + - - +
150D ALA* 3.6 8.1 - - - +
151D ALA 3.3 0.2 - - - -
152D ASP* 1.3 77.7 - - - +
154D SER* 1.3 60.8 + - - +
155D ARG* 3.3 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLY* 4.8 0.7 - - - +
153B GLN* 5.0 0.5 + - - -
117D ARG 3.9 20.9 - - - -
118D VAL* 4.4 9.9 - - - +
150D ALA 3.2 9.1 + - - -
151D ALA* 2.6 23.3 + - - -
153D GLN* 1.3 79.6 - - - +
155D ARG* 1.3 63.9 + - - +
156D ALA* 3.0 27.3 + - - +
157D LEU* 4.0 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLN* 3.5 24.7 + - - +
147B PRO 5.6 1.0 + - - -
148B GLY* 3.2 29.1 - - - +
149B LEU* 3.4 26.2 - - - +
153B GLN* 2.8 22.3 + - - +
151D ALA 3.3 2.5 + - - -
152D ASP* 3.0 36.2 + - - -
153D GLN* 3.5 14.6 - - - +
154D SER* 1.3 81.3 + - - +
156D ALA* 1.3 54.3 + - - +
157D LEU 3.5 2.5 - - - -
158D ARG* 2.8 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