Contacts of the helix formed by residues 121 - 136 (chain B) in PDB entry 1KKC
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 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B ILE* 4.3 0.4 - - - +
116B GLU* 3.6 16.0 + - - +
119B TRP* 3.2 5.4 + - - +
120B GLY* 1.3 82.5 - - - +
122B PHE* 1.3 63.3 + - - +
123B ASP* 3.4 8.6 + - - +
124B LYS* 3.0 33.1 + - - +
125B PHE* 3.1 21.7 + - - +
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Residues in contact with PHE 122 (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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105B ILE* 3.6 49.1 - - + -
112B LYS* 4.8 15.3 - - + -
115B ILE* 4.3 14.4 - - + -
116B GLU* 4.2 11.3 + - + +
121B SER* 1.3 74.0 - - - +
123B ASP* 1.3 63.1 + - - +
125B PHE* 3.2 20.1 + + - +
126B LYS* 3.0 55.5 + - + +
196B TRP* 4.6 4.7 - + + -
201B TRP* 3.6 33.4 - + - -
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Residues in contact with ASP 123 (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 SER* 3.2 8.2 + - - +
122B PHE* 1.3 81.0 - - - +
124B LYS* 1.3 64.8 + - - +
126B LYS* 3.2 21.6 + - - +
127B ASP* 3.1 35.7 + - - +
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Residues in contact with LYS 124 (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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119B TRP* 3.4 30.2 - - + +
120B GLY* 4.5 6.0 - - - -
121B SER* 3.0 25.5 + - - +
123B ASP* 1.3 77.4 - - - +
125B PHE* 1.3 66.3 + - - +
127B ASP* 3.4 12.2 + - - +
128B ALA* 3.1 22.0 + - - +
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Residues in contact with PHE 125 (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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115B ILE* 3.3 32.8 - - + -
119B TRP* 3.7 36.3 - + + +
121B SER 3.1 7.4 + - - +
122B PHE* 3.4 17.9 - + - +
123B ASP 3.2 0.2 - - - -
124B LYS* 1.3 79.1 - - - +
126B LYS* 1.3 60.1 + - - +
128B ALA* 3.1 3.5 + - - +
129B PHE* 2.8 38.6 + + - +
144B LEU* 3.9 18.8 - - + -
155B ILE* 3.8 26.0 - - + -
171B PHE* 3.8 25.1 - + - -
196B TRP* 3.7 24.2 - + - -
201B TRP* 4.3 7.6 - + - -
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Residues in contact with LYS 126 (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 PHE* 3.0 49.2 + - + +
123B ASP* 3.2 21.4 + - - +
125B PHE* 1.3 75.5 - - - +
127B ASP* 1.3 55.2 + - - +
129B PHE* 3.2 0.9 + - - +
130B ASN* 2.7 44.6 + - - +
196B TRP* 3.8 55.2 - - + +
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Residues in contact with ASP 127 (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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123B ASP* 3.1 29.0 + - - +
124B LYS* 3.6 14.5 - - - +
125B PHE 3.2 0.2 - - - -
126B LYS* 1.3 76.6 - - - +
128B ALA* 1.3 58.6 + - - +
130B ASN* 3.9 8.5 + - - +
131B THR* 2.8 37.1 + - - +
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Residues in contact with ALA 128 (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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119B TRP* 3.9 15.7 - - + +
124B LYS 3.1 11.5 + - - +
125B PHE 3.4 7.6 - - - +
127B ASP* 1.3 79.4 - - - +
129B PHE* 1.3 58.0 + - - +
131B THR* 3.5 5.9 + - - -
132B THR* 3.0 32.1 + - - -
155B ILE* 3.7 17.5 - - + -
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Residues in contact with PHE 129 (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 PHE* 2.8 33.4 + + + +
126B LYS 3.6 4.3 - - - +
128B ALA* 1.3 74.9 - - - +
130B ASN* 1.3 60.2 + - - +
132B THR* 3.1 5.1 + - + -
133B LEU* 2.7 66.4 + - + +
142B GLY* 3.7 23.6 - - - -
143B TRP* 3.6 28.3 - - - -
144B LEU* 3.9 3.6 - - + -
155B ILE* 3.8 16.4 - - + +
171B PHE* 3.6 22.0 - + - -
173B VAL* 3.7 17.7 - - + -
196B TRP* 3.7 25.8 - + + -
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Residues in contact with ASN 130 (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 LYS* 2.7 29.7 + - - +
127B ASP* 3.9 8.6 + - - +
129B PHE* 1.3 71.8 - - - +
131B THR* 1.3 64.8 + - - +
133B LEU* 3.1 10.0 + - - +
134B LEU* 2.9 34.8 + - + +
192B ALA* 3.7 21.4 - - + +
193B LYS* 4.9 6.7 - - - +
196B TRP* 2.8 35.5 + - - +
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Residues in contact with THR 131 (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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127B ASP* 2.8 25.6 + - - +
128B ALA* 3.6 7.2 - - - +
130B ASN* 1.3 75.8 - - - +
132B THR* 1.3 59.1 + - - +
134B LEU* 3.4 6.1 + - - +
135B GLY* 3.0 26.2 + - - -
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Residues in contact with THR 132 (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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128B ALA* 3.0 15.3 + - - +
129B PHE* 3.4 8.7 - - + +
131B THR* 1.3 78.3 - - - +
133B LEU* 1.3 63.8 + - + +
135B GLY* 3.1 11.5 + - - -
136B ILE* 3.4 12.1 + - - +
142B GLY* 5.2 3.6 - - - -
155B ILE* 3.6 28.5 - - + +
156B THR 4.6 1.1 - - - +
157B THR* 3.2 29.8 - - + +
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Residues in contact with LEU 133 (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 PHE* 2.7 49.5 + - + +
130B ASN* 3.1 9.6 + - - +
132B THR* 1.3 73.4 - - + +
134B LEU* 1.3 65.3 + - + +
135B GLY 3.2 0.7 + - - -
136B ILE* 3.3 15.4 + - - +
142B GLY* 3.6 32.8 - - - +
173B VAL* 3.9 28.7 - - + +
175B MET* 3.5 35.5 - - + +
188B LYS* 5.3 1.4 + - - +
192B ALA* 4.0 24.0 - - + +
195B ILE* 5.3 1.3 - - + -
196B TRP* 5.4 0.9 - - + -
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Residues in contact with LEU 134 (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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130B ASN* 2.9 24.5 + - + +
131B THR* 3.7 5.8 - - - +
133B LEU* 1.3 77.5 - - - +
135B GLY* 1.3 58.7 + - - +
136B ILE 3.3 0.4 - - - +
175B MET* 3.9 14.6 - - + -
188B LYS* 3.2 63.8 + - + +
189B ALA* 3.9 22.0 - - + -
192B ALA* 4.0 10.5 - - + -
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Residues in contact with GLY 135 (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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131B THR 3.0 14.5 + - - -
132B THR* 3.1 7.0 + - - -
134B LEU* 1.3 77.4 - - - +
136B ILE* 1.3 63.7 + - - +
137B GLN* 3.3 14.6 + - - +
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Residues in contact with ILE 136 (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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132B THR 3.4 10.7 + - - +
133B LEU* 3.3 21.1 + - - +
134B LEU 4.1 5.2 - - - +
135B GLY* 1.3 77.6 - - - +
137B GLN* 1.3 66.8 + - - +
138B GLY 3.8 19.7 + - - +
139B SER 4.7 0.4 - - - +
140B GLY* 4.0 17.9 - - - +
141B TRP 3.7 34.5 - - - +
142B GLY* 3.9 2.0 - - - +
157B THR* 4.0 18.2 - - + +
158B THR 5.4 0.7 - - - +
159B HIS* 5.3 2.5 - - - +
175B MET* 3.8 21.3 - - + -
188B LYS* 4.2 10.4 + - - -
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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