Contacts of the helix formed by residues 144 - 158 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8P ARG* 4.7 0.9 - - - +
9P ASN* 6.5 1.1 - - - -
11P GLN* 6.4 1.6 - - - -
142P GLU 4.3 0.4 + - - -
143P LEU* 1.3 73.5 - - - +
145P ALA* 1.3 65.9 + - - +
146P HIS* 2.8 10.3 + - - +
147P GLU* 2.8 48.6 + - - +
148P ILE* 2.9 18.9 + - - +
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Residues in contact with ALA 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P VAL* 3.5 32.8 - - - +
8P ARG* 3.7 34.5 + - + +
11P GLN* 3.8 12.0 - - + +
13P VAL* 3.4 11.5 - - + +
143P LEU 3.4 4.3 + - - -
144P SER* 1.3 70.5 - - - +
146P HIS* 1.3 60.2 + - - +
148P ILE* 4.1 1.3 - - - -
149P VAL* 3.3 29.6 + - - +
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Residues in contact with HIS 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P GLN* 5.7 0.6 - - - +
13P VAL* 3.4 21.4 - - + +
144P SER* 2.8 8.3 + - - +
145P ALA* 1.3 77.8 - - - +
147P GLU* 1.3 75.0 + - - +
148P ILE 3.1 0.5 + - - -
149P VAL* 3.1 4.3 + - - +
150P GLU* 2.8 28.8 + - + +
169P ILE* 4.0 32.5 + - + +
171P GLU* 3.9 39.0 - - + +
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Residues in contact with GLU 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143P LEU* 3.3 31.3 - - + +
144P SER* 2.8 31.0 + - - +
146P HIS* 1.3 80.0 - - - +
148P ILE* 1.3 57.0 + - - +
150P GLU* 3.5 5.3 - - - +
151P LYS* 2.8 31.9 + - - +
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Residues in contact with ILE 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P VAL* 3.5 25.1 - - + -
8P ARG* 4.4 2.7 - - - +
134P ALA* 4.0 9.6 - - + -
137P LEU* 3.6 18.4 - - + -
138P VAL* 3.1 45.8 - - + +
143P LEU* 3.7 28.7 - - + +
144P SER 2.9 17.6 + - - +
145P ALA 4.0 4.5 - - - +
147P GLU* 1.3 74.4 - - - +
149P VAL* 1.3 58.4 + - - +
150P GLU 2.8 1.0 + - - -
151P LYS* 2.9 2.1 + - - +
152P SER* 2.6 46.3 + - - +
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Residues in contact with VAL 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P VAL* 3.6 15.1 - - + +
5P SER* 3.9 6.1 - - - -
6P VAL* 3.2 39.7 - - + +
13P VAL* 4.0 9.4 - - + +
14P VAL 4.3 0.2 - - - -
15P GLY* 3.4 35.0 - - - +
145P ALA 3.3 16.1 + - - +
146P HIS 3.1 3.9 + - - +
148P ILE* 1.3 80.0 - - - +
150P GLU* 1.3 60.2 + - - +
152P SER* 4.0 1.6 - - - -
153P LEU* 3.1 23.3 + - + +
169P ILE* 3.9 12.1 - - + -
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Residues in contact with GLU 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146P HIS* 2.8 21.7 + - + +
147P GLU* 3.5 12.3 - - - +
149P VAL* 1.3 74.5 - - - +
151P LYS* 1.3 75.4 + - - +
153P LEU* 2.9 18.0 + - - +
154P ARG* 3.3 25.0 + - - -
167P PHE* 4.0 21.2 - - + -
169P ILE* 3.7 26.9 - - + +
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Residues in contact with LYS 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J ASN* 4.5 12.1 - - - +
137P LEU* 3.9 18.6 - - + -
143P LEU* 5.8 1.8 - - + -
147P GLU 2.8 20.8 + - - +
148P ILE 2.9 2.4 + - - +
150P GLU* 1.3 83.3 + - - +
152P SER* 1.3 61.8 + - - +
154P ARG* 3.2 11.8 + - - +
155P ILE* 3.0 26.8 + - + +
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Residues in contact with SER 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P VAL* 4.4 7.6 - - - -
130P ALA* 3.6 30.4 - - - -
133P ALA* 3.4 11.2 - - - +
134P ALA* 2.9 34.1 + - - +
137P LEU* 4.1 3.0 - - - +
148P ILE* 2.6 23.4 + - - +
149P VAL* 4.3 3.8 - - - -
151P LYS* 1.3 69.7 - - - +
153P LEU* 1.3 67.8 + - - +
155P ILE* 3.5 4.7 + - - +
156P ALA 3.3 14.6 + - - -
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Residues in contact with LEU 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P THR* 3.6 31.4 - - + +
4P VAL* 3.3 25.8 - - + -
15P GLY* 3.6 8.5 - - - +
16P GLY* 3.3 26.7 - - - +
17P ASP* 4.9 0.7 - - + +
130P ALA* 4.7 0.2 - - + -
149P VAL 3.1 17.0 + - - +
150P GLU 2.9 7.6 + - - +
152P SER* 1.3 78.2 - - - +
154P ARG* 1.3 62.9 + - - +
156P ALA* 3.1 7.4 + - - +
157P GLY* 2.9 19.4 + - - -
163P THR* 4.8 2.4 - - - +
167P PHE* 3.2 45.5 - - + -
169P ILE* 4.8 5.4 - - + -
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Residues in contact with ARG 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J GLU* 6.0 1.8 - - - -
150P GLU* 3.3 21.3 + - - +
151P LYS* 3.2 13.1 + - - +
153P LEU* 1.3 77.2 - - - +
155P ILE* 1.3 72.0 + - + +
157P GLY* 2.7 15.1 + - - +
158P ASP* 3.1 25.9 + - - +
165P THR* 3.5 34.7 + - + +
167P PHE* 3.6 25.6 - - + -
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Residues in contact with ILE 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J SER* 3.7 45.1 - - - +
135J ARG* 4.6 17.6 + - + +
136J ALA* 4.7 8.7 - - + +
139J GLU* 4.0 20.4 - - - +
140J ASN* 5.8 2.0 - - - +
129P TYR 4.7 1.6 - - - +
133P ALA* 4.1 17.9 - - + -
137P LEU* 6.4 1.1 - - + -
151P LYS* 3.0 23.3 + - + +
152P SER* 3.7 7.6 - - - +
154P ARG* 1.3 80.3 - - + +
156P ALA* 1.3 63.8 + - - +
158P ASP* 3.3 17.7 + - - +
159P ILE* 3.6 15.1 - - + +
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Residues in contact with ALA 156 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P THR* 3.6 31.2 - - + +
126P GLY 3.8 4.9 - - - +
129P TYR* 4.0 11.4 - - + -
130P ALA* 3.8 18.2 - - + +
152P SER 3.3 6.1 + - - +
153P LEU 3.1 8.9 + - - +
154P ARG 3.0 0.4 - - - -
155P ILE* 1.3 78.3 - - - +
157P GLY* 1.3 60.6 + - - +
159P ILE* 3.1 2.4 + - - +
160P CYS* 2.9 32.1 + - - +
163P THR* 4.2 2.0 - - - -
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Residues in contact with GLY 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153P LEU 2.9 9.3 + - - -
154P ARG* 2.7 11.5 + - - -
156P ALA* 1.3 72.7 - - - +
158P ASP* 1.3 60.7 + - - +
159P ILE 3.1 1.7 + - - -
160P CYS 3.3 9.9 - - - +
163P THR* 3.2 41.7 - - - +
164P ASN* 4.4 8.1 - - - -
165P THR* 5.5 3.6 - - - -
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Residues in contact with ASP 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J ARG* 4.3 13.9 + - - +
26K VAL* 4.2 16.7 - - - +
154P ARG* 3.1 26.5 + - - +
155P ILE* 3.6 12.5 - - - +
156P ALA 3.1 0.6 - - - -
157P GLY* 1.3 78.4 - - - +
159P ILE* 1.3 65.3 + - + +
165P THR* 4.3 15.4 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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