Contacts of the helix formed by residues 144 - 154 (chain A) in PDB entry 2GRA
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 GLU 144 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 5.6 0.2 + - - -
142A GLN* 2.5 39.9 + - - +
143A VAL* 1.3 91.2 + - - +
145A ASP* 1.3 62.1 + - - +
147A ARG* 3.6 32.7 + - - +
148A LEU* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 3.8 27.5 - - + +
116A ARG* 2.5 37.1 + - - +
118A ILE* 5.8 6.3 - - + -
137A THR* 6.3 0.2 - - + -
140A HIS 4.9 0.5 - - - +
141A ALA* 4.6 3.6 - - + -
142A GLN* 2.6 41.2 + - - +
144A GLU* 1.3 82.1 - - - +
146A GLY* 1.3 54.3 + - - +
147A ARG 2.8 5.1 + - - -
148A LEU* 3.0 6.6 + - - +
149A MET* 2.6 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE* 5.7 1.1 - - - +
135A TYR* 3.2 11.8 + - - -
137A THR* 4.1 25.5 - - - +
141A ALA* 6.3 0.2 - - - +
142A GLN 3.9 4.0 + - - -
143A VAL* 4.0 6.0 + - - +
145A ASP* 1.3 79.6 - - - +
147A ARG* 1.3 55.2 + - - +
149A MET* 4.3 5.2 - - - -
150A GLU* 3.0 30.3 + - - +
161A GLU* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A VAL* 3.8 19.1 + - - +
144A GLU* 3.6 41.3 + - - +
145A ASP 2.8 0.4 - - - -
146A GLY* 1.3 76.1 - - - +
148A LEU* 1.3 57.3 + - - +
149A MET 3.1 0.2 + - - -
150A GLU* 3.2 4.9 + - - +
151A GLN* 2.7 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.0 33.0 - - + -
65A VAL* 4.5 5.4 - - + -
91A ILE* 4.1 22.4 - - + -
144A GLU 3.3 11.4 + - - +
145A ASP* 3.0 8.2 + - - +
147A ARG* 1.3 78.8 - - - +
149A MET* 1.3 52.4 + - - +
151A GLN* 3.1 14.1 + - - +
152A LEU* 2.5 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 5.9 1.1 - - + -
67A PHE* 4.5 8.1 - - + -
91A ILE* 5.9 1.5 - - + +
93A VAL* 4.0 15.5 - - + -
118A ILE* 3.3 35.0 - - + -
135A TYR* 3.5 27.8 - - + -
145A ASP 2.6 20.4 + - - +
146A GLY* 3.9 6.5 - - - +
148A LEU* 1.3 71.2 - - - +
150A GLU* 1.3 55.6 + - - +
151A GLN 2.6 2.3 + - - -
152A LEU* 2.6 42.1 + - + -
153A LEU* 2.9 54.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TYR* 2.6 37.6 + - + +
146A GLY 3.0 14.1 + - - +
147A ARG* 3.6 4.7 - - - +
149A MET* 1.3 79.9 - - - +
151A GLN* 1.3 49.3 + - - +
154A SER* 2.5 45.2 + - - -
159A CYS* 3.8 23.2 - - - +
160A THR* 3.6 16.5 - - - -
161A GLU* 4.2 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ARG* 2.7 29.8 + - + +
148A LEU* 3.4 13.4 - - - +
149A MET 2.6 4.6 + - - -
150A GLU* 1.3 71.2 - - - +
152A LEU* 1.3 66.2 + - - +
153A LEU 3.4 0.3 + - - -
154A SER* 3.4 11.4 + - - -
155A SER* 3.5 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.2 27.4 - - + -
3A VAL* 4.9 4.7 - - + -
19A PHE* 3.7 35.7 - - + -
24A VAL* 4.1 25.8 - - + -
25A LEU* 6.3 1.3 - - + -
65A VAL* 5.0 7.9 - - + -
67A PHE* 4.5 10.5 - - + -
148A LEU* 2.5 32.8 + - + +
149A MET* 2.6 20.9 + - + +
151A GLN* 1.3 71.8 - - - +
153A LEU* 1.3 54.6 + - - +
155A SER* 2.5 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.5 12.1 - - + -
19A PHE* 3.4 33.7 - - + -
67A PHE* 4.4 6.5 - - + -
120A CYS* 4.7 12.1 - - + -
122A THR* 4.6 4.0 - - - +
126A VAL* 5.5 2.3 - - + +
133A THR* 3.4 35.4 + - + +
135A TYR* 5.2 1.6 - - + -
149A MET* 2.9 40.4 + - + +
152A LEU* 1.3 71.3 - - - +
154A SER* 1.1 55.4 + - - +
155A SER 2.4 17.0 + - - -
156A VAL* 2.7 19.4 + - + +
157A GLY* 3.6 7.3 + - - +
158A PHE 5.0 1.2 - - - +
159A CYS* 3.4 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A GLU* 2.5 30.6 + - - -
151A GLN* 3.9 6.1 - - - -
152A LEU 3.3 0.8 - - - -
153A LEU* 1.1 79.4 - - - +
155A SER* 1.3 54.7 - - - +
157A GLY 3.2 10.9 + - - +
159A CYS* 3.4 24.9 + - - +
1300A NAP 2.6 30.6 + - - -
1301A GLU 5.0 3.6 + - - -
----------------------------------------------------------
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