Contacts of the helix formed by residues 122 - 128 (chain D) in PDB entry 3GBA
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 122 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ARG* 6.0 3.6 - - - -
112D ILE* 3.9 7.4 - - - +
120D ILE* 4.0 6.2 - - - +
121D ASP* 1.3 81.4 - - - +
123D ALA* 1.3 64.2 + - - +
124D ASP* 3.4 12.0 + - - +
125D ASP* 3.1 35.7 + - - +
126D LEU* 3.3 10.4 + - - +
207D ILE* 3.5 5.5 - - - +
208D GLY* 4.9 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ASN* 5.1 2.9 - - - +
112D ILE* 3.7 20.4 - - + +
122D SER* 1.3 69.8 - - - +
124D ASP* 1.3 54.6 + - - +
126D LEU* 3.0 7.8 + - - +
127D ALA* 2.6 37.9 + - - +
153D THR* 4.3 1.6 - - + -
154D TYR* 4.2 18.6 - - + +
157D MET* 3.9 22.0 - - + +
188D LEU* 5.8 0.9 - - + -
211D ILE* 5.0 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ARG* 5.9 2.3 - - - +
253B GLY* 5.3 6.8 - - - -
254B ASN* 2.9 24.0 + - - +
122D SER* 3.2 10.2 + - - +
123D ALA* 1.3 77.3 - - - +
125D ASP* 1.3 60.3 + - - +
127D ALA* 3.7 6.2 - - - +
128D LYS* 2.9 35.4 + - + +
153D THR* 2.9 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D PRO 3.8 6.2 - - - +
120D ILE* 4.0 13.2 - - + +
121D ASP* 2.9 35.1 + - - +
122D SER* 3.1 23.6 + - - +
124D ASP* 1.3 77.6 - - - +
126D LEU* 1.3 56.5 + - - +
128D LYS* 2.6 46.5 + - - +
129D GLN* 3.1 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ILE* 3.8 38.4 - - + -
114D TYR* 5.9 0.9 - - + -
120D ILE* 4.0 18.4 - - + -
122D SER 3.3 7.2 + - - +
123D ALA* 3.0 8.4 + - - +
125D ASP* 1.3 77.3 - - - +
127D ALA* 1.3 65.8 + - - +
128D LYS 3.2 0.4 - - - -
129D GLN* 3.0 39.9 + - - +
132D ILE* 4.4 16.4 - - + -
134D TYR* 3.6 31.0 - - + -
157D MET* 4.5 7.2 - - + -
186D ALA* 4.2 18.8 - - + -
188D LEU* 4.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ALA 2.6 12.9 + - - +
124D ASP* 3.1 4.7 + - - +
126D LEU* 1.3 73.8 - - - +
128D LYS* 1.3 59.0 + - + +
129D GLN 3.1 5.6 + - - +
134D TYR* 4.1 4.1 + - - -
153D THR* 3.3 40.4 - - + +
156D LYS* 2.9 34.9 + - + +
157D MET* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ILE* 4.1 10.3 - - - +
124D ASP* 2.9 12.6 + - + +
125D ASP* 2.6 51.3 + - - +
126D LEU 3.2 0.4 - - - -
127D ALA* 1.3 75.5 - - + +
129D GLN* 1.3 68.2 + - - +
156D LYS* 3.4 17.6 + - - +
----------------------------------------------------------
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