Contacts of the helix formed by residues 128 - 141 (chain A) in PDB entry 2KK0
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 ASN 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A VAL* 4.1 0.2 - - - +
117A TYR* 3.0 7.9 + - - -
121A CYS* 4.6 6.6 - - - -
125A GLY 5.4 4.5 + - - +
126A LEU 5.0 2.4 + - - -
127A SER* 1.3 75.3 - - - +
129A PRO* 1.3 72.6 - - + +
130A ASN* 3.1 15.7 - - + +
131A GLU* 2.8 50.9 + - + +
132A LEU* 3.0 6.4 + - - +
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Residues in contact with PRO 129 (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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117A TYR* 3.1 20.4 - - + +
121A CYS* 4.8 8.1 - - - -
127A SER 4.4 1.3 - - - +
128A ASN* 1.3 85.4 - - + +
130A ASN* 1.3 70.6 + - - +
132A LEU* 3.3 22.8 - - + +
133A GLN* 3.5 9.0 + - - +
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Residues in contact with ASN 130 (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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128A ASN* 3.1 10.9 - - + +
129A PRO* 1.3 83.6 - - - +
131A GLU* 1.3 66.4 + - - +
132A LEU 3.1 1.4 + - - -
133A GLN* 3.2 15.9 + - - +
134A ALA* 3.6 8.1 + - - +
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Residues in contact with GLU 131 (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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80A VAL* 3.3 30.3 - - + +
81A GLU 5.1 0.5 + - - -
126A LEU 4.1 4.0 - - - +
127A SER* 3.6 10.0 + - - -
128A ASN* 2.8 55.4 + - + +
130A ASN* 1.3 77.3 - - - +
132A LEU* 1.3 62.3 + - - +
134A ALA* 3.3 9.3 + - - +
135A ALA* 3.0 22.9 + - - +
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Residues in contact with LEU 132 (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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79A LEU* 3.6 20.4 - - + -
80A VAL* 3.4 24.2 - - + -
83A ILE* 3.7 18.6 - - + -
113A MET* 3.9 29.8 - - + -
117A TYR* 4.3 18.2 - - + +
128A ASN 3.0 14.4 + - - +
129A PRO* 3.3 17.5 - - + +
130A ASN 3.1 0.2 - - - -
131A GLU* 1.3 76.6 - - - +
133A GLN* 1.3 64.4 + - - +
135A ALA* 3.1 4.2 + - - +
136A ILE* 3.0 38.8 + - + +
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Residues in contact with GLN 133 (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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129A PRO 3.5 6.8 + - - +
130A ASN* 3.2 10.7 + - - +
132A LEU* 1.3 77.7 - - - +
134A ALA* 1.3 57.1 + - - +
136A ILE* 3.3 17.8 + - - +
137A ASP* 2.9 28.8 + - + +
140A ARG* 3.7 27.4 + - - +
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Residues in contact with ALA 134 (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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130A ASN 3.6 5.6 + - - +
131A GLU* 3.3 13.1 + - - +
133A GLN* 1.3 78.3 - - - +
135A ALA* 1.3 61.6 + - - +
137A ASP* 3.9 5.0 - - - +
138A SER* 2.9 31.5 + - - +
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Residues in contact with ALA 135 (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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80A VAL* 3.7 13.9 - - + -
83A ILE* 3.6 20.6 - - + -
84A ASN* 3.3 27.1 - - - +
131A GLU 3.0 13.1 + - - +
132A LEU* 3.3 9.9 - - - +
134A ALA* 1.3 76.3 - - - +
136A ILE* 1.3 62.8 + - - +
138A SER* 3.2 6.5 + - - -
139A ASN* 2.9 28.4 + - - -
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Residues in contact with ILE 136 (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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83A ILE* 4.2 18.4 - - + -
106A PHE* 5.4 9.6 - - + -
109A ARG* 4.9 9.4 - - - +
113A MET* 3.4 32.1 - - + -
132A LEU* 3.0 27.5 + - + +
133A GLN* 3.7 14.6 - - - +
135A ALA* 1.3 73.8 - - - +
137A ASP* 1.3 58.3 + - - +
139A ASN* 3.0 10.1 + - + +
140A ARG* 2.8 62.7 + - + +
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Residues in contact with ASP 137 (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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133A GLN* 2.9 25.0 + - + +
134A ALA* 3.9 5.8 - - - +
136A ILE* 1.3 76.2 - - - +
138A SER* 1.3 63.3 + - - +
140A ARG* 3.0 26.4 + - - +
141A ARG* 3.0 26.3 + - - +
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Residues in contact with SER 138 (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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84A ASN* 5.7 1.1 - - - -
134A ALA* 2.9 23.8 + - - +
135A ALA* 3.3 8.7 - - - -
137A ASP* 1.3 78.6 + - - +
139A ASN* 1.3 63.5 + - - +
141A ARG* 3.8 11.5 + - - +
142A GLU* 3.8 18.9 + - - +
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Residues in contact with ASN 139 (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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83A ILE* 3.2 30.7 + - - +
84A ASN* 5.2 1.6 + - - +
86A LYS* 3.3 29.5 - - - +
109A ARG* 3.0 43.0 + - - +
135A ALA* 2.9 17.0 + - - +
136A ILE 3.0 9.9 + - - +
138A SER* 1.3 79.3 - - - +
140A ARG* 1.3 65.2 - - + +
142A GLU* 3.2 21.8 + - - +
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Residues in contact with ARG 140 (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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106A PHE* 5.7 10.3 - - + -
133A GLN* 3.7 22.4 + - - +
136A ILE* 2.8 42.8 + - + +
137A ASP* 3.0 23.5 + - - +
139A ASN* 1.3 77.2 - - + +
141A ARG* 1.3 61.5 + - - +
142A GLU 3.1 7.7 + - - +
143A GLY* 4.1 3.5 + - - -
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Residues in contact with ARG 141 (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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137A ASP* 3.0 17.2 + - - +
138A SER* 4.1 8.5 - - - +
139A ASN 3.3 0.2 - - - -
140A ARG* 1.3 75.6 - - - +
142A GLU* 1.3 57.3 + - + +
143A GLY 3.1 7.3 + - - -
144A ARG* 3.8 14.9 + - - +
145A ARG 5.8 4.0 + - - +
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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