Contacts of the helix formed by residues 140 - 153 (chain A) in PDB entry 2O0K
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 ARG 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLN* 4.4 10.2 + - - +
139A LEU* 1.3 77.0 - - - +
141A ASP* 1.3 66.6 + - - +
142A TYR* 3.6 29.6 - - + -
143A GLN* 2.6 37.0 + - - +
144A ARG* 3.1 12.6 + - - +
164A LEU 4.1 12.7 + - - -
165A GLY* 5.8 0.8 - - - -
317A SER 3.8 16.4 - - - +
318A VAL* 3.7 20.6 - - - +
319A LYS* 5.2 2.5 - - + +
320A GLU* 3.1 36.0 + - - -
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Residues in contact with ASP 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 4.4 8.8 - - - +
46A LYS* 2.7 39.0 + - - +
48A TYR* 4.6 5.7 + - - -
140A ARG* 1.3 73.0 - - - +
142A TYR* 1.3 63.8 + - - +
144A ARG* 2.6 48.2 + - - +
145A ASP* 3.1 21.0 + - - +
317A SER 5.7 0.2 + - - -
319A LYS* 5.2 13.5 - - - +
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Residues in contact with TYR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.2 34.2 - - + -
141A ASP* 1.3 80.2 - - - +
143A GLN* 1.3 79.2 + - + +
145A ASP* 3.3 5.2 - - - +
146A MET* 3.2 37.6 + - - +
160A LEU* 4.8 5.8 - - + -
164A LEU* 2.3 53.1 + - + +
165A GLY 3.6 11.6 + - - -
166A LYS* 3.8 4.2 + - + -
169A VAL* 5.5 0.4 - - + -
311A TYR* 3.4 18.6 + + - +
313A ALA* 4.0 17.5 - - + -
317A SER* 3.7 35.2 + - - +
318A VAL* 5.4 0.2 - - + -
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Residues in contact with GLN 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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137A VAL* 5.5 0.8 - - - +
138A GLN 4.0 2.8 - - - +
139A LEU* 3.2 27.0 - - + +
140A ARG* 2.6 49.0 + - - +
142A TYR* 1.3 105.6 + - + +
144A ARG* 1.3 63.9 + - - +
146A MET* 3.3 2.7 + - - +
147A LEU* 3.0 27.5 + - - +
165A GLY 3.7 21.0 + - - -
168A THR* 4.1 17.6 - - - +
169A VAL* 3.6 21.3 - - + +
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 6.2 2.6 - - - -
118A VAL* 4.2 19.7 - - + +
122A GLU* 2.8 32.0 + - - +
139A LEU* 3.3 50.5 + - + +
140A ARG 3.1 4.3 + - - +
141A ASP* 2.6 43.9 + - - +
143A GLN* 1.3 75.3 - - - +
145A ASP* 1.3 66.0 + - - +
147A LEU* 3.2 4.0 + - - +
148A LYS* 2.9 36.9 + - - +
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Residues in contact with ASP 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ASP* 3.1 14.3 + - - +
142A TYR* 3.3 4.8 - - - +
144A ARG* 1.3 77.6 - - - +
146A MET* 1.3 56.0 + - - +
148A LYS* 3.4 9.0 + - - +
149A ILE* 3.0 35.5 + - + +
311A TYR* 2.9 37.5 + - + +
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Residues in contact with MET 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 3.2 27.2 + - - +
143A GLN* 3.8 7.2 - - - +
144A ARG 3.2 0.2 - - - -
145A ASP* 1.3 75.7 - - - +
147A LEU* 1.3 62.2 + - - +
149A ILE* 4.4 5.4 - - + +
150A MET* 2.8 53.5 + - + +
158A CYS* 3.8 25.4 - - - -
160A LEU* 4.2 19.7 - - + -
166A LYS* 5.0 1.3 - - + -
169A VAL* 4.1 22.4 - - + -
170A VAL* 5.2 1.1 - - + -
285A THR* 4.2 16.4 - - + -
311A TYR* 3.6 32.3 - - + -
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.9 34.6 - - + +
118A VAL* 4.5 7.9 - - + -
121A ALA* 3.9 28.7 - - + -
139A LEU* 3.9 16.8 - - + -
143A GLN 3.0 19.2 + - - +
144A ARG* 3.6 7.6 - - - +
146A MET* 1.3 76.6 - - - +
148A LYS* 1.3 57.5 + - - +
150A MET* 4.1 4.3 - - + +
151A SER* 2.9 32.6 + - - -
169A VAL* 3.4 32.5 - - + +
172A ILE* 4.4 6.3 - - + -
173A PHE* 4.1 15.7 - - + +
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Residues in contact with LYS 148 (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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116A ASP* 5.2 3.6 + - - -
117A ILE* 4.9 3.6 - - + -
118A VAL* 3.7 32.5 - - + +
144A ARG* 2.9 27.1 + - + +
145A ASP* 3.7 7.6 - - - +
147A LEU* 1.3 74.0 - - - +
149A ILE* 1.3 66.5 + - + +
151A SER* 3.2 6.8 + - - -
152A SER* 2.8 28.2 + - - -
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Residues in contact with ILE 149 (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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145A ASP* 3.0 18.3 + - + +
146A MET* 3.8 4.0 - - + +
148A LYS* 1.3 75.3 - - + +
150A MET* 1.3 67.1 + - + +
151A SER 2.8 1.7 + - - -
152A SER* 2.9 18.5 + - - -
153A LYS* 2.9 17.7 + - + +
156A THR* 4.1 20.2 - - + +
309A GLU* 3.7 35.2 - - + +
310A PRO 5.3 1.3 - - - +
311A TYR* 3.1 42.6 - - + -
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Residues in contact with MET 150 (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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146A MET* 2.8 65.3 + - + +
147A LEU* 3.9 12.6 - - + +
149A ILE* 1.3 73.5 - - - +
151A SER* 1.3 60.8 + - - +
153A LYS 3.2 13.5 - - - +
156A THR* 3.9 25.6 - - + -
158A CYS* 5.3 0.7 - - - -
169A VAL* 4.2 18.4 - - + +
170A VAL* 5.1 6.5 - - - -
173A PHE* 3.7 26.7 - - + -
281A LYS* 3.4 15.2 + - - -
283A ILE* 3.9 36.7 - - + +
285A THR* 5.6 1.6 - - - -
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Residues in contact with SER 151 (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 ILE* 4.0 20.6 - - - +
147A LEU 2.9 22.1 + - - -
148A LYS* 3.3 6.5 - - - -
149A ILE 2.8 0.8 + - - -
150A MET* 1.3 79.7 - - - +
152A SER* 1.3 59.7 + - - -
173A PHE* 3.9 13.5 - - - -
176A HIS* 5.7 2.3 + - - -
281A LYS* 3.8 10.6 + - - +
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Residues in contact with SER 152 (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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148A LYS 2.8 17.3 + - - -
149A ILE* 2.9 13.5 + - - -
151A SER* 1.3 73.3 - - - +
153A LYS* 1.3 69.2 + - - +
154A ARG 4.1 0.9 + - - -
281A LYS* 4.9 0.4 + - - -
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Residues in contact with LYS 153 (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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149A ILE* 2.9 20.4 + - + +
150A MET 3.2 9.2 - - - +
152A SER* 1.3 84.8 - - - +
154A ARG* 1.3 62.7 + - - +
155A MET 4.1 4.0 - - - +
156A THR* 4.1 10.8 + - - +
281A LYS* 2.9 18.1 + - - -
283A ILE* 6.0 0.7 - - - +
309A GLU* 3.8 52.5 + - + -
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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