Contacts of the helix formed by residues 121 - 136 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115Y ILE* 4.8 0.4 - - - -
116Y GLU* 3.7 14.5 + - - +
119Y TRP* 3.2 5.4 + - - +
120Y GLY* 1.3 79.5 - - - +
122Y PHE* 1.3 65.6 + - - +
123Y ASP* 3.7 7.7 + - - +
124Y LYS* 3.2 39.2 + - - +
125Y PHE* 3.1 20.8 + - - +
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Residues in contact with PHE 122 (chain Y).
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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103Y GLY 5.9 1.6 - - - -
105Y ILE* 3.6 39.9 - - + -
112Y LYS* 5.0 16.8 - - + -
115Y ILE* 4.3 14.4 - - + -
116Y GLU* 4.2 7.6 + - + +
121Y SER* 1.3 72.8 - - - +
123Y ASP* 1.3 67.4 + - - +
125Y PHE* 3.0 15.4 + + - +
126Y LYS* 2.9 68.8 + - + +
196Y TRP* 4.5 2.9 - + + -
201Y TRP* 3.5 43.5 - + - -
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Residues in contact with ASP 123 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121Y SER* 3.3 8.1 + - - +
122Y PHE* 1.3 82.7 - - - +
124Y LYS* 1.3 57.3 + - + +
126Y LYS* 3.3 27.7 + - - +
127Y ASP* 3.0 27.5 + - - +
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Residues in contact with LYS 124 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119Y TRP* 3.2 31.2 - - + +
120Y GLY* 4.3 4.7 - - - -
121Y SER* 3.2 26.1 + - - +
123Y ASP* 1.3 75.0 - - + +
125Y PHE* 1.3 64.6 - - - +
127Y ASP* 3.3 8.5 + - - +
128Y ALA* 3.1 22.3 + - - +
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Residues in contact with PHE 125 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115Y ILE* 3.5 32.3 - - + -
119Y TRP* 3.5 37.6 - + + +
121Y SER 3.1 6.6 + - - +
122Y PHE* 3.0 18.9 + + - +
124Y LYS* 1.3 78.7 - - - +
126Y LYS* 1.3 59.3 + - + +
128Y ALA* 3.2 2.3 + - - +
129Y PHE* 2.8 44.3 + + - +
144Y LEU* 3.6 28.0 - - + -
155Y ILE* 3.6 27.6 - - + -
171Y PHE* 3.7 11.7 - + - -
196Y TRP* 3.7 20.9 - + - -
201Y TRP* 4.1 7.0 - + - -
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Residues in contact with LYS 126 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122Y PHE* 2.9 61.1 + - + +
123Y ASP* 3.5 24.7 + - - +
125Y PHE* 1.3 72.9 - - + +
127Y ASP* 1.3 61.6 + - - +
129Y PHE* 3.2 0.7 + - - +
130Y ASN* 2.8 40.0 + - - +
196Y TRP* 4.0 50.6 - - + +
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Residues in contact with ASP 127 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123Y ASP 3.0 13.6 + - - +
124Y LYS* 3.5 12.3 - - - +
126Y LYS* 1.3 77.7 - - - +
128Y ALA* 1.3 58.7 + - - +
130Y ASN* 3.4 7.2 + - - +
131Y THR* 2.9 41.2 + - - -
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Residues in contact with ALA 128 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119Y TRP* 4.3 15.0 - - + +
124Y LYS 3.1 10.6 + - - +
125Y PHE 3.2 8.0 + - - +
127Y ASP* 1.3 81.6 + - - +
129Y PHE* 1.3 62.0 + - - +
131Y THR* 3.4 7.3 + - - -
132Y THR* 3.0 26.9 + - - -
155Y ILE* 3.9 15.7 - - + -
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Residues in contact with PHE 129 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125Y PHE* 2.8 35.8 + + + +
128Y ALA* 1.3 73.8 - - - +
130Y ASN* 1.3 53.7 + - - +
132Y THR* 3.0 6.4 + - - -
133Y LEU* 2.8 55.9 + - + +
142Y GLY* 3.7 24.0 - - - -
143Y TRP* 3.5 27.8 - - - -
144Y LEU* 3.7 5.6 - - + -
155Y ILE* 3.8 15.6 - - + +
171Y PHE* 3.6 22.0 - + - -
173Y VAL* 3.7 24.7 - - + -
196Y TRP* 3.5 31.0 - + + -
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Residues in contact with ASN 130 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126Y LYS* 2.8 27.6 + - - +
127Y ASP* 3.8 6.3 - - - +
129Y PHE* 1.3 71.7 - - - +
131Y THR* 1.3 58.3 + - - +
133Y LEU* 3.2 9.5 + - - +
134Y LEU* 2.8 43.8 + - + +
192Y ALA* 3.9 18.6 - - + +
193Y LYS* 4.7 9.7 - - - +
196Y TRP* 2.7 36.1 + - - +
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Residues in contact with THR 131 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Y ASP* 2.9 33.1 + - - -
128Y ALA* 3.6 8.5 - - - +
130Y ASN* 1.3 76.2 - - - +
132Y THR* 1.3 64.4 + - - +
134Y LEU* 3.5 6.0 + - - +
135Y GLY* 3.0 20.6 + - - -
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Residues in contact with THR 132 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128Y ALA 3.0 14.0 + - - -
129Y PHE* 3.0 8.8 + - + -
131Y THR* 1.3 79.8 - - - +
133Y LEU* 1.3 64.5 + - + +
135Y GLY* 3.1 11.4 + - - -
136Y ILE* 3.4 11.4 + - - +
142Y GLY* 5.2 2.7 - - - -
155Y ILE* 3.6 29.1 - - + +
156Y THR* 4.5 1.3 - - - +
157Y THR* 3.2 32.8 - - + -
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Residues in contact with LEU 133 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Y PHE* 2.8 43.4 + - + +
130Y ASN* 3.5 19.3 - - - +
132Y THR* 1.3 74.8 - - + +
134Y LEU* 1.3 64.4 + - + +
135Y GLY 3.1 1.0 + - - -
136Y ILE* 3.2 25.0 + - - +
142Y GLY* 3.6 28.0 - - - -
173Y VAL* 3.8 27.8 - - + -
175Y MET* 3.5 38.7 - - + +
188Y LYS* 5.4 0.3 + - - -
192Y ALA* 4.3 15.7 - - + +
195Y ILE* 5.5 0.4 - - + -
196Y TRP* 5.2 1.3 - - + +
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Residues in contact with LEU 134 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Y ASN* 2.8 31.8 + - + +
131Y THR* 4.1 6.3 - - - +
133Y LEU* 1.3 72.7 - - - +
135Y GLY* 1.3 58.8 + - - +
136Y ILE 3.3 0.6 - - - +
175Y MET* 4.5 2.7 - - + -
188Y LYS* 3.3 60.1 + - + +
189Y ALA* 3.8 29.8 - - + -
192Y ALA* 4.2 11.0 - - + -
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Residues in contact with GLY 135 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Y THR 3.0 14.5 + - - -
132Y THR* 3.1 6.5 + - - -
133Y LEU 3.1 1.0 - - - -
134Y LEU* 1.3 78.0 - - - +
136Y ILE* 1.3 63.0 + - - +
137Y GLN* 3.4 12.6 + - - +
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Residues in contact with ILE 136 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132Y THR 3.4 7.8 + - - +
133Y LEU* 3.2 22.1 + - - +
134Y LEU 4.2 4.9 - - - +
135Y GLY* 1.3 78.2 - - - +
137Y GLN* 1.3 67.4 + - - +
138Y GLY 3.8 18.4 + - - +
139Y SER 4.4 1.1 - - - +
140Y GLY* 4.1 17.9 - - - +
141Y TRP 3.6 35.7 - - - +
142Y GLY* 4.0 1.8 - - - +
157Y THR* 4.0 19.5 - - + -
158Y THR 5.3 0.9 - - - +
159Y HIS* 5.1 3.1 - - - +
175Y MET* 3.9 20.2 - - + -
188Y LYS* 4.3 10.0 + - - -
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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