Contacts of the helix formed by residues 144 - 158 (chain J) in PDB entry 1G3I
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 144 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ARG* 5.2 0.2 - - - +
142J GLU 4.0 1.0 + - - -
143J LEU* 1.3 75.8 - - - +
145J ALA* 1.3 67.3 + - - +
146J HIS* 3.4 15.2 + - - +
147J GLU* 3.1 38.4 + - - +
148J ILE* 2.8 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J VAL* 4.3 22.2 - - + +
7J ARG* 4.6 0.7 - - - -
8J ARG* 4.0 42.1 + - + +
11J GLN* 4.2 14.8 - - + -
13J VAL* 4.4 6.3 - - + -
143J LEU 3.5 2.4 + - - -
144J SER* 1.3 72.2 + - - +
146J HIS* 1.3 65.7 + - - +
148J ILE* 3.0 16.8 + - - +
149J VAL* 3.2 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 146 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J VAL* 3.8 14.4 - - + +
144J SER* 3.4 8.4 + - - +
145J ALA* 1.3 77.9 - - - +
147J GLU* 1.3 73.5 + - + +
149J VAL* 3.2 6.4 + - - +
150J GLU* 3.1 37.3 + - + -
169J ILE* 4.3 28.3 - - + +
171J GLU* 3.7 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J LEU* 3.9 21.9 - - + +
144J SER* 3.1 38.0 + - - +
146J HIS* 1.3 85.8 - - - +
148J ILE* 1.3 62.5 + - - +
150J GLU* 3.1 7.4 + - - +
151J LYS* 2.8 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J VAL* 4.0 12.6 - - + -
8J ARG* 4.0 14.4 - - - +
134J ALA* 3.5 36.6 - - + -
137J LEU* 3.6 32.1 - - + +
138J VAL* 3.2 28.3 - - + -
143J LEU* 4.1 11.2 - - + +
144J SER 2.8 22.8 + - - +
145J ALA 3.0 6.2 + - - +
147J GLU* 1.3 70.5 - - - +
149J VAL* 1.3 54.4 + - - +
151J LYS* 3.2 7.4 + - - +
152J SER* 2.8 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J VAL* 4.0 15.5 - - + +
6J VAL* 4.0 24.2 - - + +
13J VAL* 3.9 25.8 - - + +
15J GLY* 3.9 25.4 - - - +
145J ALA 3.6 12.6 - - - +
146J HIS 3.2 6.9 + - - +
148J ILE* 1.3 79.2 - - - +
150J GLU* 1.3 66.4 + - - +
152J SER* 3.8 1.3 - - - -
153J LEU* 2.9 32.6 + - + +
169J ILE* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J HIS* 3.1 22.2 + - + +
147J GLU* 3.3 12.6 - - - +
149J VAL* 1.3 80.6 - - - +
151J LYS* 1.3 69.6 + - - +
153J LEU* 4.8 1.3 - - - -
154J ARG* 3.4 42.3 + - - +
167J PHE* 3.5 20.7 - - - -
169J ILE* 4.0 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 151 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J LEU* 3.6 23.3 - - + -
143J LEU* 6.1 1.3 - - + -
147J GLU 2.8 16.2 + - - +
148J ILE* 3.3 8.1 - - - +
150J GLU* 1.3 75.6 + - - +
152J SER* 1.3 63.3 - - - +
154J ARG* 3.1 17.6 + - - +
155J ILE* 3.1 19.2 + - + +
140P ASN* 4.9 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 152 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J VAL* 4.7 5.2 - - - -
130J ALA* 3.1 30.6 - - - -
133J ALA* 3.2 14.3 - - - +
134J ALA* 2.9 30.8 + - - +
137J LEU* 4.2 1.9 - - - +
148J ILE* 2.8 22.2 + - - +
149J VAL* 4.0 2.0 - - - -
151J LYS* 1.3 70.1 - - - +
153J LEU* 1.3 67.3 + - - +
155J ILE* 3.4 2.1 + - - +
156J ALA* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J THR* 4.0 22.4 - - + +
4J VAL* 3.4 25.4 - - + +
15J GLY 3.7 14.8 - - - +
16J GLY* 3.8 18.8 - - - +
17J ASP* 4.8 0.4 - - + +
130J ALA* 4.7 0.2 - - - -
149J VAL* 2.9 29.4 + - + +
152J SER* 1.3 76.9 - - - +
154J ARG* 1.3 53.5 + - - +
156J ALA* 3.4 4.3 - - - +
157J GLY* 2.6 34.5 + - - -
163J THR* 5.0 2.7 - - + +
167J PHE* 3.2 49.0 - - + -
169J ILE* 4.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 154 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150J GLU* 3.4 33.5 + - - +
151J LYS* 3.1 11.5 + - - +
153J LEU* 1.3 78.9 - - - +
155J ILE* 1.3 66.9 + - + +
157J GLY* 2.8 15.2 + - - +
158J ASP* 2.8 29.9 + - - +
165J THR* 3.8 32.1 + - + +
167J PHE* 3.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J TYR 5.2 0.7 - - - +
133J ALA* 3.5 24.5 - - + -
137J LEU* 5.3 3.8 - - + -
151J LYS* 3.1 15.1 + - + +
152J SER* 3.4 7.4 + - - +
154J ARG* 1.3 78.7 - - + +
156J ALA* 1.3 63.8 + - - +
158J ASP* 3.5 9.0 + - - +
159J ILE* 3.3 23.0 + - + +
132P SER* 3.6 37.0 - - - +
135P ARG* 4.5 14.3 + - + +
136P ALA* 3.6 31.2 - - + +
139P GLU* 5.0 10.1 - - - +
140P ASN* 5.7 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J THR* 4.0 9.0 - - + +
126J GLY 3.4 15.5 - - - +
129J TYR* 3.7 12.3 - - + -
130J ALA* 3.4 26.2 - - + +
152J SER 2.9 17.6 + - - +
153J LEU 3.4 3.4 - - - +
154J ARG 2.9 0.4 + - - -
155J ILE* 1.3 74.2 - - - +
157J GLY* 1.3 54.4 + - - +
158J ASP 3.0 4.5 - - - -
159J ILE* 2.6 26.3 + - - +
160J CYS* 2.9 14.5 + - - +
163J THR* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 157 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153J LEU 2.6 18.6 + - - -
154J ARG* 2.8 6.0 + - - -
156J ALA* 1.3 71.3 - - - +
158J ASP* 1.3 58.3 + - - +
160J CYS 3.1 10.4 - - - +
163J THR* 3.0 44.6 - - - +
164J ASN* 4.1 7.3 - - - -
165J THR* 5.2 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 158 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J ARG* 2.8 31.3 + - - +
155J ILE* 3.7 8.5 + - - +
157J GLY* 1.3 78.8 - - - +
159J ILE* 1.3 61.6 + - - +
165J THR* 4.2 14.6 - - - +
26O VAL* 3.6 24.3 - - - +
135P ARG* 4.5 14.4 + - - +
----------------------------------------------------------
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