Contacts of the helix formed by residues 130 - 144 (chain A) in PDB entry 1LK9
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 VAL 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A GLY* 1.3 68.5 - - - -
131A GLY* 1.3 60.6 + - - +
134A GLN* 2.7 36.1 + - - +
259A ARG* 3.3 30.5 + - + +
284A GLY 4.5 1.3 - - - +
285A THR* 4.0 14.1 - - + -
286A PRO* 4.2 17.3 - - + -
130B VAL* 4.3 17.5 - - + -
282B THR* 3.6 38.3 - - + +
284B GLY 4.1 7.6 - - - +
286B PRO* 4.2 10.8 - - + -
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Residues in contact with GLY 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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129A GLY 2.9 13.1 + - - -
130A VAL* 1.3 74.7 - - - +
132A VAL* 1.3 67.5 + - - -
133A THR 3.0 1.6 - - - -
134A GLN 3.2 6.9 + - - -
135A LEU* 3.6 7.4 + - - +
259A ARG* 3.3 19.5 + - - -
260A PHE 4.0 0.4 - - - -
261A GLY* 3.8 15.0 - - - -
600A PLP 3.3 17.7 - - - -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLY* 1.3 72.7 - - - -
133A THR* 1.3 61.2 + - - +
135A LEU* 2.9 17.6 + - + -
136A ILE* 3.0 29.8 + - + +
225A ASP* 4.1 3.8 - - - +
227A VAL* 3.9 6.1 - - + -
246A LEU* 4.0 24.2 - - + -
247A PHE 3.2 40.2 - - - +
248A THR* 3.8 6.7 - - - -
261A GLY* 4.0 3.7 - - - -
262A TRP 4.6 0.7 - - - +
600A PLP 2.7 39.6 + - + +
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Residues in contact with THR 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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131A GLY 3.0 0.2 - - - -
132A VAL* 1.3 77.3 - - - +
134A GLN* 1.3 62.6 + - - +
136A ILE* 3.5 14.7 + - - +
165A TYR* 4.6 3.6 + - - -
167A VAL* 5.0 9.9 - - + +
171A GLN* 2.9 34.2 + - - +
259A ARG* 3.7 12.3 + - - -
600A PLP 2.6 31.6 + - - -
279B THR 4.3 2.5 - - - +
280B LYS 3.8 7.0 - - - +
281B ASN 3.6 18.4 - - - +
282B THR* 4.2 5.2 - - - +
283B GLU* 3.9 20.7 + - + +
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Residues in contact with GLN 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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129A GLY* 3.5 1.3 - - - -
130A VAL* 2.7 50.9 + - - +
131A GLY 3.2 5.9 + - - +
133A THR* 1.3 80.1 - - - +
135A LEU* 1.3 64.1 - - - +
136A ILE 3.4 0.3 + - - -
137A HIS* 3.5 1.6 + - - +
138A GLY 3.4 7.3 + - - -
171A GLN* 5.1 0.2 - - - +
277A TYR* 2.9 37.0 + - + +
278A MET* 3.2 26.2 - - - +
281A ASN* 3.0 22.9 + - - +
282A THR* 3.2 31.1 + - - +
281B ASN* 3.3 16.9 + - - +
282B THR* 4.1 2.4 - - + +
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Residues in contact with LEU 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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127A VAL* 4.2 3.6 - - + +
128A PHE 3.8 9.6 - - - +
129A GLY* 3.7 23.6 - - - +
131A GLY 3.9 5.2 - - - +
132A VAL* 2.9 9.9 + - - +
134A GLN* 1.3 75.8 - - - +
136A ILE* 1.3 60.4 + - - +
138A GLY* 3.3 2.4 + - - +
139A LEU* 2.9 38.0 + - + +
246A LEU* 3.8 18.8 - - + -
261A GLY 3.8 8.5 - - - +
262A TRP* 3.6 41.7 - - - +
263A ALA* 3.7 3.8 - - + +
274A LEU* 4.1 22.6 - - + +
278A MET* 4.2 11.4 - - - -
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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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132A VAL* 3.0 39.6 + - + +
133A THR* 3.8 8.5 - - - +
134A GLN 3.3 0.4 - - - -
135A LEU* 1.3 77.8 - - - +
137A HIS* 1.3 62.6 + - - +
139A LEU* 3.2 4.8 + - - +
140A VAL* 3.0 28.1 + - + +
165A TYR* 4.9 5.8 - - + -
167A VAL* 5.2 5.4 - - + -
168A PHE* 3.7 33.7 - - + -
171A GLN* 3.4 17.5 - - - +
172A THR* 5.5 4.5 - - - +
201A MET* 4.1 24.7 - - + -
223A ILE* 4.7 1.0 - - - +
225A ASP* 4.3 2.2 - - - +
246A LEU* 4.1 13.9 - - + -
600A PLP 4.8 5.2 - - + -
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Residues in contact with HIS 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 THR 3.9 0.6 + - - -
134A GLN* 3.5 3.6 + - - +
135A LEU 3.4 0.2 - - - -
136A ILE* 1.3 77.0 - - - +
138A GLY* 1.3 56.8 + - - +
140A VAL* 3.2 7.8 + - + +
141A ILE* 2.9 52.7 + - + +
171A GLN* 3.2 25.0 + - + +
172A THR* 5.6 4.0 - - + -
175A PHE* 3.3 45.3 - + + +
180A TYR* 2.7 34.5 + + - -
277A TYR* 3.9 18.6 + + - +
175B PHE* 4.9 3.1 - + - -
177B LYS* 4.0 10.8 - - - -
281B ASN* 5.7 0.7 - - - +
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Residues in contact with GLY 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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134A GLN 3.4 5.7 + - - -
135A LEU 3.3 2.6 + - - -
136A ILE 3.2 0.8 - - - -
137A HIS* 1.3 77.0 - - - +
139A LEU* 1.3 57.8 - - - +
141A ILE* 3.4 4.0 + - - +
142A SER* 2.8 30.7 + - - -
274A LEU* 3.5 10.2 - - - +
277A TYR* 3.4 40.8 - - - -
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Residues in contact with LEU 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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135A LEU* 2.9 22.3 + - + +
136A ILE* 3.8 1.8 - - - +
138A GLY* 1.3 75.5 - - - +
140A VAL* 1.3 63.9 + - - +
142A SER* 3.1 2.3 + - - -
143A LEU* 2.9 29.7 + - + +
223A ILE* 3.8 20.0 - - + -
244A ILE* 3.6 34.1 - - + -
246A LEU* 3.9 28.7 - - + -
263A ALA* 4.5 6.1 - - + -
265A ILE* 4.5 3.8 - - + -
270A VAL* 3.9 27.1 - - + -
274A LEU* 4.0 22.4 - - + -
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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 ILE* 3.0 28.1 + - + +
137A HIS* 3.2 12.1 + - + +
139A LEU* 1.3 76.4 - - - +
141A ILE* 1.3 63.2 + - - +
143A LEU 3.4 0.3 + - - -
144A SER* 2.8 28.6 + - - +
158A VAL* 3.8 33.4 - - + -
172A THR* 4.8 7.4 - - + +
180A TYR* 3.7 37.2 - - + -
199A ILE* 3.9 8.6 - - + +
201A MET* 4.7 2.7 - - - -
223A ILE* 4.3 13.7 - - + -
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Residues in contact with ILE 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 HIS* 2.9 52.0 + - + +
138A GLY 3.6 7.0 - - - +
140A VAL* 1.3 77.1 - - - +
142A SER* 1.3 63.5 + - - +
144A SER* 3.2 22.5 + - - +
177A LYS* 3.9 32.1 - - + -
180A TYR* 4.2 7.0 - - + -
277A TYR* 4.0 17.7 - - + -
174B TYR* 3.6 25.8 - - + +
175B PHE* 4.1 9.2 - - + -
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Residues in contact with SER 142 (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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138A GLY 2.8 24.1 + - - -
139A LEU* 3.1 9.4 + - - -
141A ILE* 1.3 79.1 - - - +
143A LEU* 1.3 61.7 + - - +
144A SER 4.3 2.4 - - - +
221A LYS* 5.2 0.5 + - - -
270A VAL* 4.4 17.9 - - - +
273A ASN* 3.3 56.6 + - - -
274A LEU* 3.4 7.8 + - - +
277A TYR* 5.0 0.7 - - - +
174B TYR* 5.4 0.2 + - - -
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Residues in contact with LEU 143 (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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139A LEU* 2.9 14.6 + - - +
140A VAL 3.4 0.2 + - - -
141A ILE 3.2 0.2 - - - -
142A SER* 1.3 79.0 - - - +
144A SER* 1.3 60.5 + - - +
145A PRO* 4.6 0.7 - - - +
156A SER* 4.0 6.2 + - - -
199A ILE* 3.8 21.9 - - + +
221A LYS* 2.9 58.1 + - + +
222A SER 4.7 1.8 - - - +
223A ILE* 3.7 37.7 - - + -
244A ILE* 3.9 23.6 - - + -
270A VAL* 4.1 21.5 - - + -
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Residues in contact with SER 144 (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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140A VAL 2.8 19.8 + - - -
141A ILE* 3.2 14.7 + - - +
142A SER 4.3 2.8 - - - +
143A LEU* 1.3 80.5 - - - +
145A PRO* 1.3 79.4 - - - +
146A ASN* 3.7 0.9 + - - +
156A SER* 3.4 6.2 - - - -
179A GLY* 3.3 17.9 - - - -
180A TYR* 3.5 13.1 - - - +
199A ILE* 3.2 17.0 - - - +
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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