Contacts of the helix formed by residues 135 - 147 (chain A) in PDB entry 2LCK
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 GLN 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A VAL* 3.4 29.4 + - + +
132A ALA* 5.5 1.3 - - - +
134A ALA* 1.3 77.2 - - - +
136A PRO* 1.3 78.4 - - + +
137A THR* 3.1 4.2 - - - +
138A ASP* 2.9 28.7 + - + +
139A VAL* 3.1 14.9 + - + +
179A THR* 2.8 33.9 + - - +
182A ASN* 5.2 7.5 - - + +
183A VAL* 4.1 15.1 - - - +
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Residues in contact with PRO 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 ALA 6.0 0.2 - - - +
133A VAL 4.6 5.8 - - - +
134A ALA* 3.8 4.0 - - - -
135A GLN* 1.3 97.1 - - + +
137A THR* 1.3 62.5 + - - +
139A VAL* 3.3 11.2 - - + +
140A VAL* 3.0 34.2 + - + +
163A TYR* 6.2 5.4 - - + -
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Residues in contact with THR 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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88A ARG* 5.8 5.2 - - + -
91A SER* 5.7 10.3 - - - +
135A GLN 3.1 2.5 - - - +
136A PRO* 1.3 79.3 - - - +
138A ASP* 1.3 69.1 + - - +
140A VAL* 3.1 20.4 - - + +
141A LYS* 3.3 32.7 + - + +
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Residues in contact with ASP 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 ALA* 5.0 2.9 - - - +
135A GLN* 2.9 23.1 + - + +
137A THR* 1.3 84.0 - - - +
139A VAL* 1.3 63.4 + - - +
141A LYS* 3.6 9.6 + - - +
142A VAL* 3.8 10.9 + - - +
182A ASN* 5.9 4.3 - - - +
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Residues in contact with VAL 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 GLN* 3.1 10.0 + - + +
136A PRO* 3.3 21.8 - - + +
138A ASP* 1.3 79.9 - - - +
140A VAL* 1.3 73.8 + - + +
142A VAL* 3.3 13.5 - - + +
143A ARG* 3.2 45.7 - - - +
163A TYR* 5.9 0.7 - - + -
175A LEU* 3.6 34.5 - - + +
178A GLY* 5.2 4.0 - - - +
179A THR* 4.8 14.6 - - - +
182A ASN* 5.5 7.8 - - - +
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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 PRO* 3.0 23.3 - - + +
137A THR* 3.1 15.0 - - + +
139A VAL* 1.3 87.4 - - + +
141A LYS* 1.3 68.0 + - + +
143A ARG* 3.6 7.3 - - - +
144A PHE* 2.5 41.7 + - + +
159A THR* 4.9 14.4 - - - +
163A TYR* 4.5 25.8 - - + -
175A LEU* 5.6 0.9 - - + -
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Residues in contact with LYS 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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84A ALA* 4.3 19.0 + - - +
85A GLY* 5.8 0.6 - - - -
87A GLN* 5.9 2.1 - - - +
88A ARG* 3.8 41.8 - - + +
137A THR* 3.3 34.4 + - + +
138A ASP* 4.1 5.6 - - - +
139A VAL 3.4 0.6 - - - -
140A VAL* 1.3 89.2 - - + +
142A VAL* 1.3 61.8 + - - +
144A PHE* 3.6 14.7 - - + +
145A GLN* 3.2 31.3 + - + +
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Residues in contact with VAL 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 ASP 3.8 7.3 + - - +
139A VAL* 3.3 17.4 + - + +
141A LYS* 1.3 77.9 - - - +
143A ARG* 1.3 83.7 + - + +
145A GLN* 3.3 9.0 + - + +
146A ALA* 3.3 19.3 + - - +
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Residues in contact with ARG 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 VAL* 3.2 30.0 - - - +
140A VAL* 3.3 6.9 + - - +
142A VAL* 1.3 86.9 - - + +
144A PHE* 1.3 65.6 + - - +
146A ALA* 3.2 10.0 + - - +
147A GLN* 3.1 22.0 + - - +
166A ILE* 5.7 7.2 - - - +
170A GLU* 4.3 11.7 + - - -
174A GLY 2.5 37.5 + - - -
175A LEU* 2.8 39.1 + - - +
177A LYS* 3.3 18.1 - - - +
178A GLY* 3.9 4.9 - - - +
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Residues in contact with PHE 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* 2.5 25.8 + - + +
141A LYS* 3.6 17.9 - - + +
143A ARG* 1.3 69.4 - - - +
145A GLN* 1.3 85.3 - - - +
147A GLN* 3.2 41.0 + - + +
157A GLN* 6.2 1.8 - - + -
158A SER* 5.2 11.2 - - - -
159A THR* 5.4 5.2 - - - -
162A ALA* 4.8 19.3 - - + -
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Residues in contact with GLN 145 (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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32A PHE* 3.9 34.4 - - + -
35A ASP* 4.4 11.5 - - - +
141A LYS* 3.2 17.0 + - + +
142A VAL* 3.7 8.5 - - - +
143A ARG 3.3 0.2 - - - -
144A PHE* 1.3 99.8 - - - +
146A ALA* 1.3 63.5 + - - +
147A GLN 3.5 6.1 + - - +
148A ALA* 5.1 1.4 - - - +
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Residues in contact with ALA 146 (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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142A VAL 3.3 9.4 + - - +
143A ARG* 3.2 14.0 + - - +
145A GLN* 1.3 77.3 - - - +
147A GLN* 1.3 65.4 + - - +
148A ALA* 2.8 13.5 + - - +
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Residues in contact with GLN 147 (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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143A ARG 3.1 12.3 + - - +
144A PHE* 3.2 38.8 + - + +
145A GLN 3.5 7.8 - - - +
146A ALA* 1.3 73.5 - - - +
148A ALA* 1.3 68.2 + - - +
150A ALA 3.1 22.4 + - - +
151A GLY* 5.2 0.4 - - - -
157A GLN* 4.4 20.3 + - - +
162A ALA* 6.2 2.5 - - + -
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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