Contacts of the helix formed by residues 143 - 156 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ASP* 5.2 0.8 + - - -
137A TYR* 3.6 38.4 - - + -
138A ASP 4.9 1.1 - - - +
139A SER* 4.2 21.1 - - - +
142A GLY* 1.3 75.0 - - - +
144A SER* 1.3 57.5 + - - +
145A THR 3.3 2.5 - - - -
146A LEU* 3.7 23.6 - - + +
147A GLN* 3.0 43.1 + - + +
143B LEU* 4.7 21.8 - - + -
147B GLN* 4.2 18.2 - - - +
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Residues in contact with SER 144 (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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104A ASP* 3.3 36.8 + - - -
116A ASP* 5.5 2.4 + - - -
118A LYS* 5.5 3.7 - - - +
141A ARG 4.9 4.3 - - - -
142A GLY 3.0 6.2 - - - -
143A LEU* 1.3 77.5 - - - +
145A THR* 1.3 66.1 + - - +
147A GLN* 3.7 8.7 + - - +
148A ALA* 3.3 18.5 + - - +
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Residues in contact with THR 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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116A ASP* 5.3 1.8 - - - +
117A LEU* 5.3 7.2 - - + +
118A LYS* 4.5 25.6 - - + +
121A LEU* 5.1 10.8 - - + -
135A TYR* 3.0 10.7 + - - -
142A GLY 4.4 6.7 + - - +
144A SER* 1.3 77.3 - - - +
146A LEU* 1.3 66.3 + - - +
148A ALA* 3.2 9.8 + - - +
149A VAL* 3.1 26.9 + - - +
195A ASP* 2.7 30.7 + - - +
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Residues in contact with LEU 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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135A TYR* 3.5 36.3 - - + -
137A TYR* 3.7 30.1 - - + +
143A LEU* 3.3 37.5 + - + +
145A THR* 1.3 79.2 + - - +
147A GLN* 1.3 66.3 + - + +
149A VAL* 3.1 7.6 - - + +
150A LEU* 3.0 44.3 + - + +
162A ALA* 3.9 19.1 - - + -
143B LEU* 6.4 0.9 - - + -
146B LEU* 5.5 6.1 - - + -
147B GLN* 5.5 2.9 - - + -
150B LEU* 4.9 6.1 - - + -
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Residues in contact with GLN 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* 3.0 28.9 + - + +
144A SER* 3.9 7.4 - - - +
146A LEU* 1.3 76.8 - - + +
148A ALA* 1.3 57.7 + - - +
150A LEU* 4.3 6.3 - - + -
151A ASP* 2.8 45.0 + - - +
137B TYR* 3.9 17.0 - - + +
139B SER* 4.5 8.7 - - - -
143B LEU* 4.1 28.5 - - + +
146B LEU* 5.9 1.8 - - + -
164B ASN* 3.4 25.4 + - - +
167B ASN* 4.9 5.9 + - - -
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Residues in contact with ALA 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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118A LYS* 4.5 17.9 - - + -
122A LEU* 4.4 15.8 - - + +
144A SER 3.3 12.7 + - - +
145A THR* 3.2 15.4 + - - +
146A LEU 3.1 0.4 - - - -
147A GLN* 1.3 79.7 - - - +
149A VAL* 1.3 59.0 + - + +
151A ASP* 4.0 3.7 - - - +
152A SER* 3.0 33.5 + - - -
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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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121A LEU* 4.7 11.0 - - + -
122A LEU* 3.9 22.7 - - + -
125A ILE* 4.6 11.7 - - + -
133A PHE* 5.0 11.0 - - + -
135A TYR* 4.2 36.8 - - + -
145A THR 3.1 11.6 + - - +
146A LEU* 3.1 23.3 - - + +
148A ALA* 1.3 74.6 - - + +
150A LEU* 1.3 65.9 + - + +
152A SER* 3.8 1.7 - - - -
153A ALA* 2.9 28.8 + - - +
158A TRP* 4.1 5.1 - - + -
160A VAL* 4.3 6.8 - - + +
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Residues in contact with LEU 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 LEU* 3.0 41.1 + - + +
147A GLN* 3.8 5.4 - - + +
149A VAL* 1.3 77.6 - - + +
151A ASP* 1.3 68.2 + - - +
153A ALA* 3.2 17.4 + - + +
154A ALA* 3.5 5.9 + - - +
160A VAL* 4.4 28.3 - - + +
162A ALA* 4.7 6.7 - - + -
137B TYR* 4.7 5.6 - - - +
146B LEU* 4.6 9.9 - - + -
150B LEU* 4.0 27.8 - - + -
162B ALA* 3.9 35.1 - - + +
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Residues in contact with ASP 151 (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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147A GLN* 2.8 32.0 + - - +
148A ALA* 4.0 4.3 - - - +
150A LEU* 1.3 78.2 - - - +
152A SER* 1.3 61.2 - - - +
154A ALA* 3.2 20.8 + - - +
155A GLU* 3.6 6.4 + - - +
137B TYR* 4.0 8.8 + - - -
162B ALA 4.5 4.2 - - - +
163B ILE* 4.6 4.6 - - - +
164B ASN* 3.9 27.3 + - - +
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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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122A LEU* 3.5 22.1 - - - +
148A ALA 3.0 19.8 + - - -
149A VAL 4.0 0.9 - - - -
151A ASP* 1.3 71.5 - - - +
153A ALA* 1.3 60.6 + - - +
154A ALA 3.1 2.7 - - - -
155A GLU* 3.8 6.5 - - - +
156A LYS* 2.8 35.6 + - - +
158A TRP* 3.9 23.1 - - - -
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Residues in contact with ALA 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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149A VAL 2.9 18.9 + - - +
150A LEU* 3.3 13.5 - - + +
151A ASP 3.2 0.6 - - - -
152A SER* 1.3 77.1 - - - +
154A ALA* 1.3 56.3 + - - +
157A LYS* 3.1 8.2 - - - -
158A TRP* 2.8 46.0 + - + +
160A VAL* 3.8 23.6 - - + -
161B THR* 6.2 0.4 - - - -
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Residues in contact with ALA 154 (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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150A LEU 3.5 5.6 + - - +
151A ASP* 3.2 12.3 + - - +
152A SER 3.1 0.8 - - - -
153A ALA* 1.3 81.3 - - - +
155A GLU* 1.3 64.4 + - - +
157A LYS* 3.8 4.3 + - - -
161B THR* 4.8 12.3 - - + -
163B ILE* 4.5 23.3 - - + -
183B ASP* 4.0 32.2 - - + +
186B LEU* 4.2 10.0 - - - +
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASP 3.6 7.0 + - - +
152A SER* 3.3 8.4 + - - +
154A ALA* 1.3 79.8 - - - +
156A LYS* 1.3 59.2 + - - +
157A LYS* 3.0 11.3 + - - +
183B ASP* 4.2 12.3 + - - +
186B LEU* 4.8 6.2 - - - +
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Residues in contact with LYS 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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126A GLU* 4.8 9.0 - - - +
152A SER* 2.8 19.5 + - - +
155A GLU* 1.3 72.4 - - - +
157A LYS* 1.3 71.8 + - - +
158A TRP* 3.5 37.6 + - + +
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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