Contacts of the helix formed by residues 128 - 141 (chain A) in PDB entry 1KNY
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 ALA 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A VAL 3.7 1.8 + - - -
127A GLU* 1.3 74.6 - - - +
129A GLN* 1.3 64.7 + - - +
131A PHE* 3.1 26.3 + - - +
132A HIS* 3.4 5.8 + - - +
182A ARG* 3.5 27.7 + - - +
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Residues in contact with GLN 129 (chain A).
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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127A GLU* 3.2 8.6 - - + +
128A ALA* 1.3 78.2 - - - +
130A THR* 1.3 57.2 + - - +
132A HIS* 2.7 45.4 + - - +
133A ASP* 2.7 45.1 + - - +
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Residues in contact with THR 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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90A SER 5.4 2.0 - - - +
92A VAL* 3.2 27.0 - - + +
126A VAL* 3.0 32.0 - - + +
127A GLU* 3.1 18.2 + - - +
129A GLN* 1.3 79.6 - - - +
131A PHE* 1.4 54.0 - - + +
133A ASP* 3.6 11.1 - - - +
134A ALA* 3.2 27.0 + - - +
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Residues in contact with PHE 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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92A VAL* 3.9 17.3 - - + -
96A TRP* 3.9 33.2 - + - -
126A VAL* 3.0 47.6 - - + -
127A GLU 3.0 20.9 - - - -
128A ALA* 3.1 10.9 + - - +
130A THR* 1.4 72.8 - - + +
132A HIS* 1.3 60.4 - - - +
134A ALA* 3.8 7.2 - - - +
135A ILE* 3.1 34.2 + - + +
179A LEU* 3.4 30.9 - - + +
182A ARG* 3.4 37.0 - - + +
243A TYR* 5.6 0.2 - - - -
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Residues in contact with HIS 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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128A ALA 3.4 5.7 + - - +
129A GLN* 2.7 39.3 + - - +
131A PHE* 1.3 70.3 - - - +
133A ASP* 1.3 60.9 + - - +
134A ALA 3.0 1.3 - - - -
135A ILE* 2.7 23.4 + - - +
136A CYS* 2.8 34.4 + - - -
241A HIS 5.4 0.7 - - - -
242A GLY* 2.8 29.5 + - - -
243A TYR* 3.4 30.7 - + + -
244A ILE 4.7 3.1 - - - -
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Residues in contact with ASP 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 GLN* 2.7 47.9 + - - +
130A THR* 3.6 12.1 - - - +
132A HIS* 1.3 78.2 + - - +
134A ALA* 1.3 51.8 + - - +
136A CYS* 3.3 7.0 + - - +
137A ALA* 2.8 34.7 + - - +
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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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92A VAL* 3.8 28.3 - - + +
93A GLU* 4.6 5.2 - - - -
94A SER* 4.9 3.6 + - - +
130A THR 3.2 14.9 + - - +
131A PHE 3.9 2.5 - - - +
132A HIS 3.0 0.8 - - - -
133A ASP* 1.3 77.6 - - - +
135A ILE* 1.3 66.0 + - - +
137A ALA* 4.1 5.2 - - - +
138A LEU* 3.1 22.2 + - - +
179A LEU* 3.7 22.2 - - + +
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Residues in contact with ILE 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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131A PHE* 3.1 23.8 + - + +
132A HIS 2.7 6.5 + - - +
134A ALA* 1.3 76.4 - - - +
136A CYS* 1.3 66.6 + - - +
138A LEU* 3.1 8.4 + - - +
139A ILE* 3.1 30.4 + - + +
176A LEU* 3.6 28.5 - - + +
179A LEU* 3.8 17.7 - - + -
180A HIS* 3.8 24.2 - - + +
237A TRP* 4.5 0.7 - - + -
243A TYR* 3.4 55.2 - - + -
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Residues in contact with CYS 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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132A HIS* 2.8 41.2 + - - -
133A ASP* 3.7 8.5 - - - +
135A ILE* 1.3 73.5 - - - +
137A ALA* 1.3 64.2 + - - +
139A ILE* 3.0 15.9 + - - +
140A VAL* 3.3 11.2 + - - +
243A TYR* 4.1 18.8 - - - -
244A ILE 4.2 13.2 - - - -
245A VAL* 3.8 22.5 - - + +
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Residues in contact with ALA 137 (chain A).
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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94A SER* 5.4 3.4 - - - +
133A ASP 2.8 19.6 + - - +
134A ALA* 4.1 6.5 - - - +
136A CYS* 1.3 73.1 - - - +
138A LEU* 1.3 62.4 + - - +
139A ILE 3.0 0.5 + - - -
140A VAL* 3.1 4.6 + - - +
141A GLU* 2.8 52.7 + - - +
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Residues in contact with LEU 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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94A SER* 3.9 30.6 + - - +
134A ALA 3.1 10.5 + - - +
135A ILE* 3.1 11.1 + - - +
137A ALA* 1.3 78.7 - - - +
139A ILE* 1.3 58.3 + - - +
141A GLU* 4.8 0.4 + - - -
142A GLU* 2.8 50.5 + - + +
143A LEU* 3.1 33.6 + - + -
172A ALA* 4.0 22.0 - - + +
175A MET* 4.0 7.0 - - + -
176A LEU* 4.2 20.0 - - + +
179A LEU* 4.6 5.6 - - + -
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Residues in contact with ILE 139 (chain A).
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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135A ILE* 3.1 36.7 + - + +
136A CYS* 3.0 12.4 + - - +
137A ALA 3.0 0.2 + - - -
138A LEU* 1.3 82.3 - - + +
140A VAL* 1.3 68.9 + - + +
143A LEU* 4.4 14.6 - - + -
144A PHE* 2.9 30.0 + - + +
176A LEU* 4.9 3.8 - - + -
231A TRP* 4.7 17.3 - - + -
234A ILE* 5.5 4.9 - - + -
235A GLN* 5.2 7.2 - - - +
238A THR* 4.2 22.4 - - + -
243A TYR 4.6 4.9 - - - +
245A VAL* 4.2 17.7 - - + -
1B MET* 4.9 13.2 - - - -
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Residues in contact with VAL 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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136A CYS 3.3 8.5 + - - +
137A ALA* 3.1 6.8 + - - +
139A ILE* 1.3 79.2 - - + +
141A GLU* 1.3 68.2 + - + +
144A PHE* 3.2 10.2 - - - +
245A VAL* 3.3 34.8 - - + -
67B GLU* 3.9 11.9 - - + +
68B TRP* 3.9 31.4 - - - +
69B THR* 3.8 15.9 - - + +
74B LYS* 2.8 28.2 - - - +
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Residues in contact with GLU 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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94A SER* 4.6 4.0 + - - -
137A ALA* 2.8 42.8 + - - +
138A LEU 4.8 0.2 + - - -
140A VAL* 1.3 78.3 - - + +
142A GLU* 1.3 67.3 + - + +
145A GLU* 3.7 18.4 - - - +
558A KAN 2.8 53.3 + - - +
67B GLU* 4.0 30.7 - - + +
74B LYS* 4.1 2.2 - - - +
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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