Contacts of the helix formed by residues 143 - 156 (chain B) in PDB entry 3KG2
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 LEU 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LEU* 4.7 23.3 - - + -
146A LEU* 6.4 0.9 - - + -
147A GLN* 4.1 18.8 - - + +
104B ASP* 5.2 1.4 + - - -
137B TYR* 3.6 38.8 - - + -
138B ASP 4.9 0.9 - - - +
139B SER* 4.2 20.6 - - - +
142B GLY* 1.3 75.5 - - - +
144B SER* 1.3 57.9 + - - +
145B THR* 3.3 2.9 - - - -
146B LEU* 3.7 22.7 - - + +
147B GLN* 3.0 43.3 + - + +
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Residues in contact with SER 144 (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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104B ASP* 3.3 36.8 + - - +
116B ASP* 5.5 2.4 + - - -
118B LYS* 5.5 1.5 - - - +
141B ARG 4.9 4.9 - - - -
142B GLY* 3.0 7.1 - - - -
143B LEU* 1.3 77.8 - - - +
145B THR* 1.3 64.7 + - - +
147B GLN* 3.8 9.2 + - - +
148B ALA* 3.3 18.5 + - - +
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Residues in contact with THR 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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116B ASP* 5.3 2.5 - - - +
117B LEU* 5.3 7.4 - - + +
118B LYS* 4.5 25.6 - - + +
121B LEU* 5.1 10.8 - - + -
135B TYR* 3.0 10.5 + - - -
142B GLY 4.4 6.0 + - - -
143B LEU* 5.4 0.2 - - - -
144B SER* 1.3 79.2 - - - +
146B LEU* 1.3 65.6 + - - +
148B ALA* 3.2 8.8 + - - +
149B VAL* 3.1 27.2 + - - +
195B ASP* 2.7 30.3 + - - +
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Residues in contact with LEU 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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146A LEU* 5.5 5.8 - - + -
147A GLN* 5.9 2.0 - - + -
150A LEU* 4.6 10.3 - - + -
135B TYR* 3.5 36.3 - - + +
137B TYR* 3.7 30.7 - - + +
143B LEU* 3.3 36.0 + - + +
145B THR* 1.3 79.0 + - - +
147B GLN* 1.3 66.7 + - + +
149B VAL* 3.1 8.0 - - + +
150B LEU* 3.0 40.8 + - + +
162B ALA* 3.9 18.4 - - + -
195B ASP* 5.8 0.2 - - - +
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Residues in contact with GLN 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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137A TYR* 3.3 30.5 - - + +
139A SER* 4.5 6.1 - - - -
143A LEU* 4.2 22.4 - - - +
146A LEU* 5.5 3.4 - - + -
164A ASN* 3.0 28.8 + - - +
167A ASN* 5.0 4.0 + - - -
143B LEU* 3.0 28.0 + - + +
144B SER* 4.0 8.1 - - - +
146B LEU* 1.3 77.9 - - + +
148B ALA* 1.3 56.8 + - - +
150B LEU* 4.3 4.0 - - + -
151B ASP* 2.8 44.0 + - - +
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Residues in contact with ALA 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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118B LYS* 4.5 17.7 - - + +
122B LEU* 4.4 15.7 - - + -
144B SER 3.3 12.7 + - - +
145B THR* 3.2 14.8 + - - +
146B LEU 3.1 0.4 - - - -
147B GLN* 1.3 79.6 - - - +
149B VAL* 1.3 58.8 + - + +
151B ASP* 4.0 3.8 - - - +
152B SER* 3.0 34.3 + - - -
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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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121B LEU* 4.7 10.1 - - + -
122B LEU* 3.9 24.2 - - + -
125B ILE* 4.6 11.7 - - + -
133B PHE* 5.0 10.8 - - + -
135B TYR* 4.2 35.4 - - + -
145B THR 3.1 12.3 + - - +
146B LEU* 3.1 23.3 - - + +
148B ALA* 1.3 75.2 - - + +
150B LEU* 1.3 64.3 + - + +
152B SER* 3.8 1.9 - - - -
153B ALA* 2.9 29.1 + - - +
158B TRP* 4.1 4.5 - - + -
160B VAL* 4.3 6.9 - - + +
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Residues in contact with LEU 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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137A TYR* 4.9 5.8 - - - +
146A LEU* 4.9 4.5 - - + -
150A LEU* 4.0 25.1 - - + -
160A VAL 5.9 2.5 - - - +
161A THR* 5.7 1.0 - - - +
162A ALA* 3.7 42.7 + - + +
146B LEU* 3.0 40.0 + - + +
147B GLN* 3.8 7.0 - - - +
149B VAL* 1.3 77.2 - - + +
151B ASP* 1.3 66.2 + - - +
153B ALA* 3.2 17.5 + - + +
154B ALA* 3.5 6.6 + - - +
160B VAL* 4.4 28.0 - - + +
162B ALA* 4.7 6.3 - - + -
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Residues in contact with ASP 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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137A TYR* 4.0 5.5 + - - -
162A ALA 3.9 2.8 - - - +
163A ILE* 3.9 12.6 - - + -
164A ASN* 3.5 34.6 + - - +
183A ASP* 4.9 1.0 - - - +
147B GLN* 2.8 28.5 + - - +
148B ALA* 4.0 4.3 - - - +
150B LEU* 1.3 77.3 - - - +
152B SER* 1.3 62.3 + - - +
154B ALA* 3.2 20.2 + - - +
155B GLU* 3.6 5.9 + - - +
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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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122B LEU* 3.5 22.4 - - - +
148B ALA 3.0 19.1 + - - -
149B VAL 4.0 0.7 - - - -
151B ASP* 1.3 72.6 - - - +
153B ALA* 1.3 60.6 + - - +
154B ALA 3.1 2.2 - - - -
155B GLU* 3.8 6.7 - - - +
156B LYS* 2.8 35.9 + - - +
158B TRP* 3.9 22.7 - - - -
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Residues in contact with ALA 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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161A THR* 5.8 0.7 - - - -
149B VAL 2.9 19.1 + - - +
150B LEU* 3.3 13.9 - - + +
151B ASP 3.2 0.4 - - - -
152B SER* 1.3 78.7 - - - +
154B ALA* 1.3 56.4 + - - +
157B LYS* 3.1 8.2 - - - -
158B TRP* 2.8 45.8 + - + +
160B VAL* 3.8 23.3 - - + +
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Residues in contact with ALA 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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161A THR* 4.2 16.4 - - + +
163A ILE* 4.1 22.9 - - + -
183A ASP* 3.6 29.0 - - + +
186A LEU* 3.5 18.2 - - - +
150B LEU 3.5 4.9 + - - +
151B ASP 3.2 12.1 + - - +
152B SER 3.1 0.6 - - - -
153B ALA* 1.3 81.2 - - - +
155B GLU* 1.3 63.0 + - - +
157B LYS* 3.8 3.1 + - - -
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Residues in contact with GLU 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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183A ASP* 3.6 20.3 + - - +
186A LEU* 3.8 12.3 - - - +
151B ASP 3.6 6.3 + - - +
152B SER* 3.3 8.6 + - - +
154B ALA* 1.3 78.6 - - - +
156B LYS* 1.3 58.1 + - - +
157B LYS* 3.0 8.4 + - - +
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Residues in contact with LYS 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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126B GLU* 4.8 9.4 - - + +
152B SER* 2.8 18.6 + - - +
155B GLU* 1.3 73.1 - - + +
157B LYS* 1.3 72.5 + - - +
158B TRP* 3.5 36.9 + - + +
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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