Contacts of the helix formed by residues 115 - 128 (chain B) in PDB entry 1K86
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 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B ASP 4.2 0.4 + - - -
114B CYS* 1.3 77.2 - - - +
116B CYS* 1.3 65.9 + - - +
117B ALA* 3.6 7.5 + - - +
118B LYS* 3.0 25.1 + - - +
119B MET* 3.0 23.0 + - - +
152B GLY* 4.2 0.2 - - - -
153B LYS* 3.7 8.5 - - - +
154B ASP* 3.6 24.5 - - - -
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Residues in contact with CYS 116 (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 SER* 1.3 70.3 - - - +
117B ALA* 1.3 62.1 + - - +
119B MET* 3.2 12.9 + - - +
120B GLN* 3.0 28.0 + - + +
152B GLY* 3.8 7.4 - - - -
154B ASP* 2.9 21.8 + - - +
155B GLY* 3.3 37.9 - - - -
156B VAL 3.4 7.4 - - - +
157B THR* 3.0 23.2 + - - +
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Residues in contact with ALA 117 (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 SER* 3.2 7.5 + - - +
116B CYS* 1.3 80.8 - - - +
118B LYS* 1.3 56.5 + - - +
120B GLN* 3.4 7.6 + - - +
121B ASP* 2.9 30.9 + - - +
154B ASP* 4.9 3.2 + - - +
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Residues in contact with LYS 118 (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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111B TYR* 4.2 28.4 - - - -
114B CYS* 4.0 14.8 - - + -
115B SER* 3.0 29.2 + - - +
117B ALA* 1.3 73.8 - - - +
119B MET* 1.3 67.8 + - - +
121B ASP* 4.4 14.3 + - + +
122B LEU* 2.9 39.6 + - + +
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Residues in contact with MET 119 (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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73B ILE* 4.1 21.8 - - + -
75B ASN* 3.6 22.7 - - - -
114B CYS* 3.7 15.0 - - + -
115B SER 3.0 8.3 + - - +
116B CYS* 3.5 17.5 - - - +
118B LYS* 1.3 75.5 - - - +
120B GLN* 1.3 63.9 + - - +
122B LEU* 3.7 8.4 - - - +
123B LEU* 3.1 30.8 + - - +
141B LEU* 5.5 0.4 - - - -
150B ILE* 4.5 16.4 - - + +
151B TYR 3.8 4.7 - - - +
152B GLY* 3.4 31.9 - - - +
157B THR* 3.8 15.7 - - - +
162B LEU* 4.1 16.4 - - + -
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Residues in contact with GLN 120 (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 CYS 3.0 17.7 + - - +
117B ALA* 3.6 10.1 - - - +
118B LYS 3.2 0.2 - - - -
119B MET* 1.3 78.0 - - - +
121B ASP* 1.3 56.6 + - - +
124B LYS* 2.9 31.6 + - - +
157B THR* 3.9 18.4 - - + +
161B ASP* 3.5 22.9 + - - +
162B LEU* 3.4 22.7 - - + +
165B HIS* 3.0 33.6 + - + +
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Residues in contact with ASP 121 (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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117B ALA 2.9 18.2 + - - +
118B LYS* 3.8 17.5 + - + +
120B GLN* 1.3 76.4 - - - +
122B LEU* 1.3 62.8 + - - +
124B LYS* 3.2 14.5 + - - +
125B LYS* 2.7 70.4 + - - +
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Residues in contact with LEU 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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71B ILE* 3.7 35.1 - - + +
73B ILE* 4.4 6.5 - - + -
111B TYR* 3.7 46.2 - - + +
114B CYS* 4.3 6.5 - - - -
118B LYS* 2.9 45.2 + - + +
119B MET* 3.7 8.3 - - - +
121B ASP* 1.3 75.7 - - - +
123B LEU* 1.3 73.4 + - + +
125B LYS* 3.4 6.1 + - - +
126B ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 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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71B ILE* 4.4 13.0 - - + -
73B ILE* 4.7 9.2 - - + -
119B MET 3.1 24.3 + - - +
120B GLN 3.9 2.0 - - - +
122B LEU* 1.3 89.9 - - + +
124B LYS* 1.3 63.5 + - - +
126B ALA* 3.2 2.4 + - - -
127B SER* 3.0 18.7 + - - -
137B PHE* 4.9 1.1 - - + -
139B CYS* 4.3 25.6 - - - -
141B LEU* 5.1 0.9 - - + -
162B LEU* 3.5 53.8 - - + +
163B THR* 6.0 0.2 - - + -
165B HIS* 4.1 4.7 - - + -
166B PHE* 3.4 27.1 - - + -
181B PHE* 5.5 1.6 - - + -
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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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120B GLN 2.9 19.6 + - - +
121B ASP* 3.6 16.1 + - - +
123B LEU* 1.3 77.6 - - - +
125B LYS* 1.3 66.9 + - - +
127B SER* 2.4 26.6 + - - +
128B GLU* 2.9 47.6 + - + +
165B HIS* 3.8 26.6 - - + +
170B ARG* 5.2 5.2 - - - +
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Residues in contact with LYS 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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121B ASP* 2.7 53.6 + - - +
122B LEU* 3.9 5.8 - - - +
124B LYS* 1.3 82.0 - - - +
126B ALA* 1.3 61.7 + - - +
128B GLU* 3.2 25.9 + - - +
129B GLU* 3.4 20.1 + - - +
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Residues in contact with ALA 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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69B LYS* 4.8 4.9 - - + +
71B ILE* 3.6 28.3 - - + -
122B LEU 2.9 17.9 + - - +
123B LEU 3.5 6.1 - - - +
125B LYS* 1.3 76.7 - - - +
127B SER* 1.3 55.5 + - - +
129B GLU* 3.2 19.9 + - - +
131B HIS* 2.6 33.6 + - + -
137B PHE* 4.8 3.6 - - + -
166B PHE* 4.2 10.8 - - + -
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Residues in contact with SER 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 LEU 3.0 11.1 + - - -
124B LYS* 2.4 24.3 + - - +
126B ALA* 1.3 76.3 - - - +
128B GLU* 1.3 62.7 + - - +
129B GLU 3.3 5.1 + - - +
165B HIS* 3.1 40.7 + - - +
166B PHE* 3.7 18.1 - - - -
170B ARG* 4.1 6.2 + - - +
171B CYS* 3.4 25.2 - - - +
173B THR* 5.7 0.2 + - - -
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Residues in contact with GLU 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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124B LYS* 2.9 56.2 + - + +
125B LYS* 3.2 18.6 + - - +
126B ALA 3.1 0.8 - - - -
127B SER* 1.3 81.6 - - - +
129B GLU* 1.3 62.6 + - - +
170B ARG 5.7 2.0 - - - +
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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