Contacts of the helix formed by residues 141 - 150 (chain A) in PDB entry 2C6N
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 PRO 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A SER* 3.9 5.2 - - - +
140A ASP* 1.3 98.3 - - - +
142A ASP* 1.3 82.8 + - - +
143A LEU 3.4 1.8 - - - -
144A THR* 3.0 16.0 + - - -
145A ASN* 3.0 30.5 + - - +
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Residues in contact with ASP 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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136A CYS 4.4 1.9 - - - +
137A TRP* 3.5 34.2 - - + +
138A SER* 2.8 33.1 + - - +
141A PRO* 1.3 89.2 - - - +
143A LEU* 1.3 66.1 + - - +
145A ASN* 3.1 6.8 + - - +
146A ILE* 3.0 28.6 + - + +
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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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126A LYS 5.9 0.2 - - - -
127A VAL* 3.9 17.3 - - + -
137A TRP* 3.9 28.7 - - + +
138A SER* 2.9 18.9 + - - +
139A LEU* 3.6 19.7 - - + +
142A ASP* 1.3 76.2 - - - +
144A THR* 1.3 66.2 + - - +
146A ILE* 3.1 9.1 + - + +
147A LEU* 3.1 22.2 + - - +
159A ALA* 3.8 23.8 - - + -
163A TRP* 3.6 47.3 - - + -
256A MET* 4.4 7.6 - - + -
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Residues in contact with THR 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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139A LEU* 2.9 25.2 + - - +
140A ASP* 4.7 6.5 - - - +
141A PRO* 3.0 11.2 + - + +
143A LEU* 1.3 74.3 - - - +
145A ASN* 1.3 75.8 + - - +
147A LEU* 2.9 9.8 + - - +
148A ALA* 2.8 26.4 + - + +
256A MET* 6.1 3.1 - - - +
257A TRP* 5.8 3.8 - - - -
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Residues in contact with ASN 145 (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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141A PRO* 3.0 32.2 + - - +
142A ASP* 3.7 6.9 - - - +
144A THR* 1.3 84.2 - - - +
146A ILE* 1.3 57.3 + - + +
148A ALA* 3.6 7.3 - - - +
149A SER* 2.8 40.2 + - - +
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Residues in contact with ILE 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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137A TRP* 3.6 49.1 - - + -
142A ASP* 3.0 21.7 + - + +
143A LEU* 3.1 11.2 + - + +
145A ASN* 1.3 76.6 - - + +
147A LEU* 1.3 58.2 + - - +
150A SER* 2.8 35.2 + - - -
155A MET* 3.6 43.1 - - + +
156A LEU* 3.0 12.2 - - + +
159A ALA* 4.6 8.1 - - + -
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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
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143A LEU 3.1 8.1 + - - +
144A THR* 2.9 10.6 + - - +
146A ILE* 1.3 78.2 - - - +
148A ALA* 1.3 67.5 + - - +
149A SER 3.2 0.7 + - - -
150A SER 4.2 4.0 + - - +
151A ARG* 4.5 2.6 + - - -
156A LEU* 3.8 35.7 - - + +
159A ALA* 4.4 9.2 - - + -
160A TRP* 4.8 6.5 - - + +
251A HIS* 4.5 14.1 - - + +
254A GLY* 3.3 22.0 - - - +
255A ASP* 3.1 8.7 - - - +
256A MET* 2.6 69.5 - - + +
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Residues in contact with ALA 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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144A THR* 2.8 21.6 + - + +
145A ASN* 3.6 10.5 - - - +
147A LEU* 1.3 77.9 - - - +
149A SER* 1.3 61.6 + - - +
151A ARG* 4.1 2.5 + - - -
254A GLY* 3.3 13.3 + - - +
263A ASN* 3.2 52.0 - - - +
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Residues in contact with SER 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 ASN* 2.8 21.5 + - - +
148A ALA* 1.3 79.1 - - - +
150A SER* 1.3 63.0 + - - +
151A ARG* 3.6 22.0 + - - +
263A ASN* 5.6 0.7 - - - -
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Residues in contact with SER 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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145A ASN 4.1 0.2 + - - -
146A ILE* 2.8 36.7 + - - -
147A LEU 4.4 0.2 - - - +
149A SER* 1.3 79.1 + - - +
151A ARG* 1.3 73.1 + - - +
152A SER* 3.4 15.6 + - - -
155A MET* 3.6 22.9 - - - +
156A LEU* 3.3 24.2 - - - +
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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