Contacts of the helix formed by residues 144 - 160 (chain A) in PDB entry 1G3K
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ARG* 4.8 3.4 - - - +
9A ASN* 5.4 5.8 - - - +
11A GLN* 5.0 11.2 - - - -
142A GLU 3.6 2.7 + - - -
143A LEU* 1.3 76.0 - - - +
145A ALA* 1.3 66.0 + - - +
146A HIS* 3.6 8.1 + - - +
147A GLU* 3.0 36.4 + - - +
148A ILE* 3.0 21.9 + - - +
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.5 40.8 - - + +
8A ARG* 4.0 25.1 + - + +
11A GLN* 4.1 10.9 + - + +
13A VAL* 3.8 13.0 - - + -
143A LEU 3.9 0.2 + - - -
144A SER* 1.3 73.0 - - - +
146A HIS* 1.3 57.8 + - - +
148A ILE* 3.3 2.2 + - - +
149A VAL* 2.9 34.3 + - - +
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Residues in contact with HIS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.7 10.6 - - + +
144A SER* 3.2 8.3 + - - +
145A ALA* 1.3 80.2 - - - +
147A GLU* 1.3 66.8 + - + +
149A VAL* 3.4 2.4 + - - +
150A GLU* 3.0 45.1 + - - +
169A ILE* 3.7 34.8 + - + +
171A GLU* 3.3 34.4 + - + +
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 3.7 28.9 - - + +
144A SER* 3.0 39.8 + - - +
146A HIS* 1.3 81.4 - - + +
148A ILE* 1.3 63.5 + - - +
150A GLU* 3.4 5.4 + - - +
151A LYS* 2.9 41.7 + - - +
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Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.9 13.9 - - + -
8A ARG* 3.6 18.2 - - - +
134A ALA* 3.7 35.2 - - + +
137A LEU* 3.9 19.1 - - + -
138A VAL* 3.7 26.5 - - + +
143A LEU* 3.6 33.2 - - + +
144A SER 3.0 17.4 + - - +
145A ALA* 3.7 4.9 - - - +
147A GLU* 1.3 76.6 - - - +
149A VAL* 1.3 56.2 + - - +
151A LYS* 3.8 0.9 - - - +
152A SER* 2.8 38.3 + - - +
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 3.7 20.4 - - + +
6A VAL* 3.6 33.2 - - + +
13A VAL* 3.7 22.7 - - + +
15A GLY* 3.9 17.3 - - - +
145A ALA 2.9 20.5 + - - +
146A HIS 3.9 3.6 - - - +
148A ILE* 1.3 76.0 - - - +
150A GLU* 1.3 57.7 + - - +
152A SER* 3.9 1.0 - - - -
153A LEU* 2.9 54.5 + - + +
169A ILE* 4.4 5.6 - - + -
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A HIS* 3.0 39.6 + - - +
147A GLU* 3.7 5.8 - - - +
149A VAL* 1.3 76.9 - - - +
151A LYS* 1.3 66.3 + - + +
153A LEU* 3.9 4.0 - - - +
154A ARG* 3.2 23.7 + - - +
167A PHE* 3.9 14.1 - - + -
169A ILE* 3.9 21.1 - - + +
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Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A LEU* 4.1 14.8 - - + -
143A LEU* 3.8 38.1 - - + -
147A GLU* 2.9 27.7 + - - +
148A ILE 3.9 3.1 - - - +
150A GLU* 1.3 78.8 - - + +
152A SER* 1.3 58.7 + - - +
154A ARG* 3.3 6.6 + - - +
155A ILE* 3.1 37.1 + - + +
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Residues in contact with SER 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 4.8 3.6 - - - -
130A ALA* 3.5 29.6 - - - -
133A ALA* 3.7 11.5 - - - +
134A ALA* 3.2 31.7 + - - +
137A LEU* 4.0 1.9 - - - +
148A ILE* 2.8 24.4 + - - +
149A VAL* 3.9 4.5 - - - -
151A LYS* 1.3 74.5 - - - +
153A LEU* 1.3 60.1 + - - +
155A ILE* 3.4 1.6 + - - +
156A ALA* 3.0 28.9 + - - +
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A THR* 3.8 30.1 - - + +
4A VAL* 3.7 19.7 - - + -
15A GLY* 3.6 31.9 - - - +
16A GLY* 3.8 7.6 - - - +
17A ASP* 4.5 2.0 - - + +
130A ALA* 4.9 0.2 - - - -
149A VAL* 2.9 33.8 + - + +
150A GLU 3.9 2.0 - - - +
152A SER* 1.3 74.8 - - - +
154A ARG* 1.3 60.7 + - - +
156A ALA* 3.8 3.5 - - - +
157A GLY* 2.8 26.9 + - - -
163A THR* 4.8 2.2 - - + +
164A ASN 4.7 0.2 - - - +
167A PHE* 3.6 40.2 - - + -
169A ILE* 4.2 5.8 - - + -
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Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A GLU* 3.2 14.3 + - - +
151A LYS* 3.5 10.1 - - - +
152A SER 3.2 0.4 - - - -
153A LEU* 1.3 79.2 - - - +
155A ILE* 1.3 61.0 + - + +
157A GLY* 3.2 1.6 + - - -
158A ASP* 3.0 43.2 + - - +
165A THR* 3.3 39.9 + - - +
167A PHE* 3.5 22.7 - - + -
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Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TYR 4.5 6.5 - - - +
133A ALA* 3.8 28.9 - - + -
137A LEU* 5.4 5.4 - - + -
151A LYS* 3.1 23.0 + - + +
152A SER 3.8 3.8 - - - +
153A LEU 3.3 0.2 - - - -
154A ARG* 1.3 80.2 - - + +
156A ALA* 1.3 62.5 + - - +
158A ASP* 3.3 13.7 + - - +
159A ILE* 3.3 30.7 + - + +
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A THR* 3.9 19.5 - - + +
126A GLY 3.6 24.5 - - - +
129A TYR* 3.8 11.9 - - + -
130A ALA 3.7 9.4 - - - +
152A SER 3.0 17.8 + - - +
153A LEU 3.8 3.6 - - - +
155A ILE* 1.3 80.0 - - - +
157A GLY* 1.3 57.0 + - - +
159A ILE* 3.1 1.0 + - - +
160A CYS* 2.8 34.0 + - - +
163A THR* 4.5 2.2 - - - -
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Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU 2.8 17.4 + - - -
154A ARG 3.2 2.2 + - - -
156A ALA* 1.3 78.1 - - - +
158A ASP* 1.3 62.4 + - - +
159A ILE 3.4 0.3 + - - -
160A CYS 3.5 0.2 - - - +
163A THR* 3.3 24.1 - - - +
164A ASN* 4.0 7.5 - - - -
165A THR* 4.4 6.9 - - - +
500A NA 2.3 29.8 - - - -
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Residues in contact with ASP 158 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ARG* 3.0 33.8 + - - +
155A ILE* 3.8 7.8 - - - +
156A ALA 3.2 0.4 - - - -
157A GLY* 1.3 79.9 - - - +
159A ILE* 1.3 61.1 + - + +
165A THR* 4.0 12.5 - - - +
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Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TYR* 3.9 41.1 - - + -
155A ILE* 3.3 30.9 + - + +
156A ALA 3.1 3.6 + - - +
158A ASP* 1.3 83.1 - - + +
160A CYS* 1.3 64.7 + - - +
161A VAL* 3.6 8.7 + - - +
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Residues in contact with CYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A SER* 3.1 33.2 - - - -
126A GLY* 3.9 9.0 - - - -
129A TYR* 4.0 19.1 - - + -
156A ALA 2.8 19.2 + - - +
157A GLY 3.5 0.2 - - - +
159A ILE* 1.3 72.7 - - - +
161A VAL* 1.3 58.4 + - - +
162A PHE* 3.2 17.4 + - - -
163A THR* 3.2 23.0 - - - +
500A NA 2.3 29.6 - - - -
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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