Contacts of the helix formed by residues 148 - 154 (chain D) in PDB entry 2GVG
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 ILE 148 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ILE* 3.8 29.2 - - + -
70D LEU* 4.3 16.8 - - + -
112D LEU* 4.5 9.6 - - + -
114D ILE* 3.4 32.1 - - + -
116D ILE* 5.0 0.9 - - + -
134D VAL* 4.1 7.0 - - + -
144D LEU* 3.6 10.8 - - + +
145D THR 3.3 14.8 - - - +
147D TRP* 1.3 85.6 - - + +
149D GLU* 1.3 63.1 + - - +
150D THR 3.3 2.7 - - - -
151D ILE* 3.3 14.4 - - + +
152D LEU* 3.0 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LYS* 2.9 22.2 + - - +
145D THR 4.0 0.8 + - - -
146D ASN* 3.5 24.6 + - - +
147D TRP 3.3 2.2 - - - -
148D ILE* 1.3 78.1 - - - +
150D THR* 1.3 56.5 + - - +
152D LEU* 3.1 1.7 + - - +
153D VAL* 2.7 46.9 + - + +
399D PHE* 3.2 64.0 - - + +
400D LYS* 4.8 1.0 + - - -
610D PO4 4.4 2.4 + - - -
196E ARG* 3.4 27.0 + - - +
246E GLU* 3.9 4.0 - - - +
609E PO4 4.9 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ALA 4.4 1.3 - - - +
15D THR* 3.4 15.2 + - - -
16D ASP* 2.7 42.2 + - - +
19D LYS* 3.5 5.4 - - - +
147D TRP 4.8 0.4 - - - -
148D ILE 3.3 0.4 - - - -
149D GLU* 1.3 82.9 - - - +
151D ILE* 1.3 61.3 + - - +
153D VAL* 3.4 9.4 + - - +
154D GLN* 3.5 16.0 + - - +
195E TYR* 3.6 41.1 - - + -
196E ARG* 3.7 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE* 3.6 20.9 - - + -
11D ILE* 5.1 3.4 - - + -
14D ALA* 4.3 14.5 + - + +
65D ILE* 3.7 23.6 - - + +
69D TYR* 3.5 39.7 - - + -
70D LEU* 4.0 22.4 - - + -
148D ILE* 3.3 21.5 + - + +
150D THR* 1.3 79.4 - - - +
152D LEU* 1.3 70.0 + - + +
154D GLN* 3.5 19.6 + - - +
195E TYR* 6.4 0.2 - - - -
201E GLN* 3.8 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LEU* 3.7 30.3 - - + -
65D ILE* 4.3 8.0 - - + +
70D LEU* 3.9 20.2 - - + -
116D ILE* 4.1 9.2 - - + -
132D PHE* 4.0 17.6 - - + -
134D VAL* 3.7 29.8 - - + -
148D ILE* 3.0 38.5 + - + +
149D GLU 3.7 2.7 - - - +
151D ILE* 1.3 86.7 - - + +
153D VAL* 1.3 60.0 + - - +
155D SER* 2.9 29.3 + - - -
399D PHE* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 4.2 14.7 - - + -
149D GLU* 2.7 33.6 + - + +
150D THR 3.8 5.2 - - - +
151D ILE 3.3 0.6 - - - -
152D LEU* 1.3 68.6 - - - +
154D GLN* 1.3 57.3 + - - +
155D SER* 2.8 11.8 + - - -
156D TRP* 2.9 19.6 + - - +
392D ARG* 3.6 33.2 - - + +
397D CYS 4.8 1.1 - - - +
399D PHE* 3.4 36.6 - - + +
196E ARG* 3.8 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ILE* 4.3 5.7 - - + +
69D TYR* 5.7 1.9 - - - -
150D THR 3.6 13.9 - - - +
151D ILE* 3.7 12.9 - - - +
152D LEU 3.2 1.8 - - - -
153D VAL* 1.3 73.3 - - - +
155D SER* 1.3 59.9 + - - +
156D TRP* 2.8 15.7 + - - -
157D TYR* 3.2 14.9 + - - +
158D PRO* 3.3 7.6 - - - +
195E TYR* 3.0 33.3 + - - +
196E ARG 3.9 11.7 - - - +
198E VAL* 3.7 11.3 - - - +
199E SER 4.6 5.5 - - - +
200E SER* 3.5 25.3 + - - -
201E GLN* 3.2 28.5 + - - +
----------------------------------------------------------
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