Contacts of the helix formed by residues 154 - 162 (chain B) in PDB entry 3GNI
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 SER 154 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ATP 3.9 5.6 + - - -
153B GLY* 1.3 75.0 - - - -
155B ALA* 1.3 63.6 + - - +
156B LYS* 3.2 7.1 + - - +
157B ASP* 2.7 37.1 + - - +
158B LEU* 3.0 25.9 + - - +
198B ALA 3.7 1.8 - - - -
199B SER* 3.6 23.6 - - - -
201B ILE 3.0 13.5 - - - -
202B LEU* 3.7 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 1.3 71.0 - - - +
156B LYS* 1.3 56.3 + - - +
158B LEU* 3.5 7.2 + - - +
159B ILE* 3.1 25.2 + - - +
167B MET* 3.2 21.8 - - + +
175B ILE* 4.8 7.4 - - + -
198B ALA* 3.3 16.5 + - + +
201B ILE* 2.9 24.0 + - + +
203B ILE* 4.7 2.9 - - + +
272B LEU* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 3.1 9.2 + - - +
155B ALA* 1.3 76.5 - - - +
157B ASP* 1.3 67.6 + - - +
159B ILE* 3.2 13.8 + - + +
160B CYS* 2.9 43.1 + - - -
198B ALA* 3.4 6.5 + - + +
199B SER* 3.8 26.7 - - - +
243B TRP* 5.1 4.5 - - - -
271B GLU* 3.0 33.7 + - - +
275B GLY 4.3 13.3 + - - -
276B HIS* 4.8 0.8 - - - +
277B VAL* 4.7 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ATP 2.6 29.5 + - - -
75B ILE 5.1 4.4 - - - +
152B TYR 4.6 2.0 - - - +
153B GLY* 3.6 9.8 - - - -
154B SER* 2.7 31.8 + - - +
156B LYS* 1.3 75.4 - - - +
158B LEU* 1.3 57.8 + - + +
160B CYS* 3.2 7.5 + - - +
161B THR* 2.9 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 3.6 33.9 - - + +
154B SER 3.0 14.3 + - - +
155B ALA* 3.6 10.5 - - - +
156B LYS 3.2 0.2 - - - -
157B ASP* 1.3 72.3 - - - +
159B ILE* 1.3 67.2 + - - +
161B THR* 3.5 5.6 - - + +
162B HIS 3.2 9.7 + - - -
163B PHE* 3.1 25.0 + - + -
167B MET* 3.7 9.2 - - + -
203B ILE* 3.7 29.8 - - + -
394B LEU* 4.1 23.6 - - + -
397B VAL* 3.9 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ALA 3.1 20.8 + - - +
156B LYS* 3.4 20.9 - - + +
158B LEU* 1.3 75.4 - - - +
160B CYS* 1.3 67.7 + - - +
163B PHE* 3.1 25.5 + - - +
164B MET* 2.9 34.5 + - + +
167B MET* 3.8 14.1 - - + +
198B ALA* 4.7 4.7 - - + -
271B GLU* 3.8 24.9 - - + +
272B LEU* 4.2 22.0 - - + +
275B GLY* 3.8 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LYS* 2.9 38.4 + - - +
157B ASP* 3.2 7.2 + - - +
159B ILE* 1.3 81.4 - - - +
161B THR* 1.3 59.9 + - - +
164B MET* 3.1 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ASP 2.9 16.3 + - - +
158B LEU* 3.5 17.5 - - + +
160B CYS* 1.3 77.7 - - - +
162B HIS* 1.3 72.2 + - + +
164B MET* 5.3 1.6 - - - -
397B VAL* 4.2 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU 3.2 2.4 + - - +
160B CYS 3.4 1.6 + - - -
161B THR* 1.3 84.5 - - + +
163B PHE* 1.3 80.8 + + + +
164B MET* 2.9 18.7 + - - +
395B ARG 4.6 0.2 - - - -
396B PRO* 3.2 40.9 - - + +
397B VAL* 3.8 26.5 - - + -
----------------------------------------------------------
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