Contacts of the helix formed by residues 150 - 159 (chain A) in PDB entry 2CMG
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 ASP 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A GLU 3.9 2.4 + - - -
149A PRO* 1.3 77.3 - - - +
151A ILE* 1.3 65.9 + - + +
152A HIS* 3.0 20.4 + - + +
153A ARG* 2.6 37.9 + - - +
154A ILE* 3.0 18.9 + - - +
187A ASN* 5.4 2.2 - - - -
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Residues in contact with ILE 151 (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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150A ASP* 1.3 75.7 - - + +
152A HIS* 1.3 92.1 + - + +
154A ILE* 3.2 11.8 + - - +
155A ASP* 3.0 24.3 + - - +
187A ASN* 4.0 31.6 + - + +
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Residues in contact with HIS 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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150A ASP* 3.0 14.5 + - + +
151A ILE* 1.3 97.1 - - + +
153A ARG* 1.3 68.8 + - - +
155A ASP* 3.5 6.0 + - - +
156A GLY* 3.3 16.3 + - - -
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Residues in contact with ARG 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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79A VAL* 2.7 37.2 - - - +
80A ASP* 3.0 25.3 + - - +
100A VAL* 5.6 1.4 - - - +
132A LEU* 4.2 22.3 - - - +
145A CYS* 4.7 0.2 - - - -
149A PRO* 3.7 21.8 - - + -
150A ASP* 2.6 27.7 + - - +
152A HIS* 1.3 75.0 - - - +
154A ILE* 1.3 62.7 + - - +
156A GLY* 3.4 1.0 + - - -
157A LEU* 3.2 42.8 + - + +
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Residues in contact with ILE 154 (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 PRO* 3.7 29.4 - - + +
150A ASP 3.0 23.9 + - - +
151A ILE* 3.3 9.4 - - - +
152A HIS 3.2 0.2 - - - -
153A ARG* 1.3 74.3 - - - +
155A ASP* 1.3 68.2 + - - +
157A LEU* 4.0 2.1 - - - +
158A LYS* 2.9 25.3 + - - +
167A PHE* 5.0 7.2 - - + -
184A ALA 5.7 0.2 - - - +
187A ASN* 3.6 37.7 - - + +
188A MET* 4.4 13.0 - - + +
191A VAL* 4.4 18.6 - - + -
192A PHE* 4.2 23.6 - - + -
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Residues in contact with ASP 155 (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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151A ILE 3.0 15.5 + - - +
152A HIS* 3.9 5.8 - - - +
154A ILE* 1.3 76.6 - - - +
156A GLY* 1.3 68.6 + - - +
158A LYS* 3.2 22.0 - - - +
159A ARG* 3.1 34.4 + - - +
191A VAL* 5.5 6.0 - - + +
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Residues in contact with GLY 156 (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 LEU* 6.1 1.1 - - - -
152A HIS 3.3 10.6 + - - -
153A ARG 3.8 2.7 - - - -
154A ILE 3.3 0.6 - - - -
155A ASP* 1.3 82.5 + - - +
157A LEU* 1.3 63.4 + - - +
159A ARG* 3.1 21.5 + - - +
160A MET* 3.9 12.2 - - - +
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Residues in contact with LEU 157 (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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77A LEU* 4.4 14.6 - - + -
79A VAL* 4.2 26.9 - - + -
132A LEU* 4.1 25.1 - - + -
143A ILE* 3.3 31.8 - - + +
145A CYS* 4.4 4.5 - - + -
149A PRO* 5.1 0.4 - - + -
153A ARG* 3.2 39.5 + - + +
154A ILE 4.1 2.2 - - - +
156A GLY* 1.3 74.0 - - - +
158A LYS* 1.3 57.3 + - - +
160A MET* 2.9 24.4 + - - +
167A PHE* 3.6 32.1 - - + -
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Residues in contact with LYS 158 (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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154A ILE 2.9 19.4 + - - +
155A ASP* 3.2 23.3 - - - +
157A LEU* 1.3 77.4 - - - +
159A ARG* 1.3 78.1 + - + +
160A MET 3.0 5.5 + - - -
161A LEU* 3.4 12.3 + - - +
167A PHE* 5.8 0.2 - - - -
191A VAL* 3.3 33.2 - - + -
192A PHE* 4.0 20.4 - - + -
215A PHE* 3.8 32.9 - - + -
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Residues in contact with ARG 159 (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 LYS* 4.8 8.0 - - - +
155A ASP* 3.4 27.6 - - - +
156A GLY* 3.1 11.5 + - - +
158A LYS* 1.3 96.5 - - + +
160A MET* 1.3 63.3 + - + +
161A LEU 3.7 1.3 - - - -
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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