Contacts of the helix formed by residues 142 - 151 (chain A) in PDB entry 2C6U
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 ASN 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A ASP* 1.3 82.0 - - - +
143A ARG* 1.3 59.8 + - - +
144A ASN* 2.9 13.9 + - - +
145A ILE* 2.8 45.4 + - - +
146A VAL* 3.1 10.9 + - - +
182A MET* 3.6 14.0 - - - -
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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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142A ASN* 1.3 71.8 - - - +
144A ASN* 1.3 60.8 + - - +
146A VAL* 3.2 4.0 + - - +
147A GLU* 2.9 57.2 + - + +
182A MET* 4.3 3.0 - - - -
185A PHE* 3.9 33.6 - - + -
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Residues in contact with ASN 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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109A TYR* 2.6 38.1 + - - -
142A ASN* 2.9 14.3 + - - +
143A ARG* 1.3 79.1 - - - +
145A ILE* 1.3 57.4 + - - +
147A GLU* 3.3 20.1 + - - +
148A TYR* 2.9 26.9 + - - +
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Residues in contact with ILE 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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109A TYR* 4.6 8.2 - - + -
114A TYR* 3.2 41.3 - - + +
138A LEU* 5.8 0.2 - - + -
139A LYS 4.5 9.6 - - - +
140A ILE* 3.4 17.5 - - + -
141A ASP 3.5 6.7 - - - +
142A ASN* 2.8 53.4 + - - +
144A ASN* 1.3 71.0 - - - +
146A VAL* 1.3 65.1 + - - +
148A TYR* 3.2 10.9 + - + -
149A ILE* 2.9 44.4 + - + +
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Residues in contact with VAL 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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140A ILE* 3.5 20.6 - - + -
142A ASN 3.1 16.2 + - - +
143A ARG* 3.3 11.7 - - - +
145A ILE* 1.3 76.4 - - - +
147A GLU* 1.3 66.2 + - + +
149A ILE* 3.5 0.4 + - - -
150A LYS* 3.1 24.3 + - + +
182A MET* 3.8 13.9 - - + -
185A PHE* 4.0 23.6 - - + -
198A PHE* 3.5 14.5 - - + -
201A GLY* 3.4 35.9 - - - +
203A MET* 6.1 0.7 - - + -
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Residues in contact with GLU 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* 2.9 56.8 + - + +
144A ASN* 3.6 25.6 + - - +
146A VAL* 1.3 74.8 - - + +
148A TYR* 1.3 66.6 + - - +
150A LYS* 3.5 24.8 + - - +
151A ALA* 3.1 24.1 + - - +
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Residues in contact with TYR 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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107A ARG* 3.3 28.2 - - + +
108A TYR 3.9 8.7 + - - -
109A TYR* 3.3 61.7 - + + -
114A TYR* 3.8 16.2 - + + -
116A PHE* 5.0 1.1 - + - -
144A ASN 2.9 17.1 + - - +
145A ILE* 3.2 9.4 + - + +
147A GLU* 1.3 76.4 - - - +
149A ILE* 1.3 79.9 + - + +
151A ALA* 3.1 15.9 + - + +
152A ARG* 3.1 53.5 + - + +
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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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114A TYR* 4.3 6.7 - - + -
116A PHE* 4.2 14.4 - - + -
138A LEU* 3.5 28.0 - - + -
140A ILE* 5.1 5.4 - - + -
145A ILE* 2.9 41.7 + - + +
146A VAL 4.0 0.4 - - - +
148A TYR* 1.3 85.9 - - + +
150A LYS* 1.3 58.2 + - - +
152A ARG* 2.9 18.9 + - - +
153A THR* 3.0 18.1 + - + +
198A PHE* 3.5 26.0 - - + -
215A MET* 3.6 28.3 - - + -
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Residues in contact with LYS 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 VAL* 3.1 16.9 + - - +
147A GLU* 3.5 32.8 + - - +
149A ILE* 1.3 76.3 - - - +
151A ALA* 1.3 59.0 + - - +
152A ARG 3.2 0.4 - - - -
153A THR 3.2 20.2 + - - +
154A HIS* 5.0 4.7 - - - +
198A PHE* 3.9 5.3 - - + -
200A ASN* 3.9 14.9 + - - +
201A GLY* 3.7 37.2 - - - +
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Residues in contact with ALA 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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147A GLU 3.1 17.1 + - - +
148A TYR* 3.1 9.7 + - + +
150A LYS* 1.3 78.2 - - + +
152A ARG* 1.3 67.3 + - + +
153A THR 3.7 0.4 - - - -
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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