Contacts of the helix formed by residues 144 - 160 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B ARG* 4.9 2.5 - - - +
9B ASN* 5.7 4.3 - - - +
142B GLU 3.7 1.4 + - - -
143B LEU* 1.3 76.0 - - - +
145B ALA* 1.3 66.1 + - - +
146B HIS* 3.6 9.1 + - - +
147B GLU* 2.8 41.5 + - - +
148B ILE* 2.9 21.8 + - - +
171B GLU* 6.1 0.4 - - - -
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.6 35.7 - - - +
8B ARG* 3.9 33.1 + - + +
11B GLN* 4.0 9.5 - - + +
13B VAL* 3.8 13.5 - - + -
143B LEU 4.0 0.2 + - - -
144B SER* 1.3 73.8 - - - +
146B HIS* 1.3 57.6 + - - +
148B ILE* 3.3 2.8 + - - +
149B VAL* 2.9 33.4 + - - +
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Residues in contact with HIS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B VAL* 3.6 13.3 - - + +
144B SER* 3.1 8.8 + - - +
145B ALA* 1.3 79.7 - - - +
147B GLU* 1.3 67.2 + - + +
149B VAL* 3.3 3.6 + - - +
150B GLU* 3.0 25.3 + - + +
169B ILE* 3.5 41.3 - - + +
171B GLU* 3.4 33.1 + - + +
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 3.4 28.9 - - + +
144B SER* 2.8 47.0 + - - +
146B HIS* 1.3 80.9 - - + +
148B ILE* 1.3 58.5 + - - +
150B GLU* 3.4 5.1 + - - +
151B LYS* 3.0 44.0 + - - +
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.9 18.2 - - + -
8B ARG* 3.7 13.7 - - - +
134B ALA* 3.8 29.2 - - + +
137B LEU* 3.9 19.5 - - + +
138B VAL* 3.5 31.2 - - + +
143B LEU* 3.6 31.6 - - + +
144B SER 2.9 17.7 + - - +
145B ALA 3.7 4.3 - - - +
147B GLU* 1.3 73.1 - - - +
149B VAL* 1.3 67.7 + - - +
151B LYS* 3.4 1.1 + - - +
152B SER* 2.8 31.7 + - - +
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 3.8 22.4 - - + +
6B VAL* 3.6 27.4 - - + +
13B VAL* 3.7 26.7 - - + -
15B GLY* 3.8 16.8 - - - +
145B ALA 2.9 19.7 + - - +
146B HIS 3.3 5.1 + - - +
148B ILE* 1.3 77.6 - - - +
150B GLU* 1.3 62.8 + - - +
152B SER* 3.4 1.3 + - - -
153B LEU* 3.0 46.0 + - + +
169B ILE* 4.3 5.6 - - + -
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B HIS* 3.0 21.2 + - + +
147B GLU* 3.8 7.4 - - - +
149B VAL* 1.3 77.3 - - - +
151B LYS* 1.3 64.4 + - + +
153B LEU* 3.5 4.3 + - - +
154B ARG* 3.2 22.3 + - - +
167B PHE* 4.1 9.3 - - + -
169B ILE* 4.2 20.6 - - + +
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Residues in contact with LYS 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 4.0 19.1 - - + -
143B LEU* 3.9 38.4 - - + -
147B GLU* 3.0 27.1 + - - +
150B GLU* 1.3 78.1 - - + +
152B SER* 1.3 58.6 + - - +
154B ARG* 3.4 6.6 + - - +
155B ILE* 3.1 36.6 + - + +
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Residues in contact with SER 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 4.6 3.4 - - - -
130B ALA* 3.5 30.1 - - - -
133B ALA* 3.7 12.2 - - - +
134B ALA* 3.2 30.0 + - - +
137B LEU* 4.1 1.9 - - - +
148B ILE* 2.8 22.7 + - - +
149B VAL* 3.8 4.9 - - - -
151B LYS* 1.3 74.8 - - - +
153B LEU* 1.3 62.2 + - - +
155B ILE* 3.3 1.6 + - - +
156B ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B THR* 3.6 40.8 - - + +
4B VAL* 3.7 14.6 - - + -
15B GLY* 3.6 25.8 - - - +
16B GLY* 3.7 8.7 - - - +
17B ASP* 4.3 1.8 - - + +
130B ALA* 4.8 0.2 - - - -
149B VAL* 3.0 31.3 + - + +
150B GLU 3.9 2.0 - - - +
152B SER* 1.3 76.6 - - - +
154B ARG* 1.3 58.1 + - - +
156B ALA* 3.3 4.6 + - - +
157B GLY* 2.8 27.0 + - - -
163B THR* 4.8 1.6 - - + +
164B ASN 4.7 0.3 - - - +
167B PHE* 3.5 39.9 - - + -
169B ILE* 4.3 6.1 - - + -
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLU 3.2 11.5 + - - +
151B LYS* 3.6 10.8 - - - +
152B SER 3.2 0.2 - - - -
153B LEU* 1.3 80.8 - - - +
155B ILE* 1.3 65.8 + - + +
157B GLY* 3.2 1.7 + - - -
158B ASP* 3.0 40.8 + - - +
165B THR* 3.5 41.1 + - - +
167B PHE* 3.6 17.7 - - + -
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Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B TYR 4.5 7.0 - - - +
133B ALA* 3.7 29.6 - - + -
137B LEU* 5.4 5.2 - - + -
151B LYS* 3.1 26.4 + - + +
152B SER 3.3 3.8 + - - +
154B ARG* 1.3 79.4 - - + +
156B ALA* 1.3 63.9 + - - +
158B ASP* 3.3 13.7 + - - +
159B ILE* 3.4 30.7 + - + +
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B THR* 3.8 20.4 - - + +
126B GLY 3.6 24.5 - - - +
129B TYR* 3.8 12.1 - - + +
130B ALA 3.7 8.7 - - - +
152B SER 2.9 17.2 + - - +
153B LEU 3.7 4.0 - - - +
155B ILE* 1.3 78.2 - - - +
157B GLY* 1.3 58.0 + - - +
159B ILE* 3.0 1.9 + - - +
160B CYS* 2.9 33.3 + - - +
163B THR* 4.4 2.2 - - - -
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Residues in contact with GLY 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LEU 2.8 17.1 + - - -
154B ARG 3.2 2.4 + - - -
156B ALA* 1.3 78.5 - - - +
158B ASP* 1.3 61.5 - - - +
159B ILE 3.4 0.2 + - - -
163B THR* 3.4 22.6 - - - +
164B ASN* 3.9 8.0 - - - -
165B THR* 4.3 7.2 - - - +
500B NA 2.3 29.3 - - - -
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Residues in contact with ASP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ARG* 3.0 36.1 + - - +
155B ILE* 3.9 7.1 - - - +
156B ALA 3.2 0.6 - - - -
157B GLY* 1.3 79.0 - - - +
159B ILE* 1.3 62.6 + - + +
165B THR* 3.9 13.5 - - - +
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B TYR* 3.9 39.9 - - + -
155B ILE* 3.5 26.5 - - + +
156B ALA 3.0 5.9 + - - +
158B ASP* 1.3 85.7 - - + +
160B CYS* 1.3 63.5 + - - +
161B VAL* 3.5 8.5 + - - +
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Residues in contact with CYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B SER* 3.2 31.9 - - - -
126B GLY* 3.9 18.2 - - - -
129B TYR* 3.9 11.2 - - + -
156B ALA 2.9 15.2 + - - +
157B GLY 3.6 0.5 - - - +
159B ILE* 1.3 72.5 - - - +
161B VAL* 1.3 55.7 + - - +
162B PHE* 3.0 20.3 + - - -
163B THR* 3.2 24.8 - - - +
500B NA 2.4 28.7 - - - -
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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