Contacts of the helix formed by residues 146 - 155 (chain A) in PDB entry 3D0G
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 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LEU* 5.2 4.9 - - + -
144A LEU 3.4 4.5 - - - -
145A GLU* 1.3 102.4 - - + +
147A GLY* 1.3 66.5 + - - +
149A ASN* 4.1 0.2 - - - +
150A GLU* 3.1 26.2 + - + +
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Residues in contact with GLY 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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142A LEU* 4.1 25.8 - - - +
143A LEU 3.4 11.4 + - - +
144A LEU 3.2 3.8 + - - -
145A GLU 3.3 2.4 - - - -
146A PRO* 1.3 82.8 - - - +
148A LEU* 1.3 64.4 + - - +
150A GLU* 3.3 12.7 + - - +
151A ILE* 3.7 9.8 + - - +
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Residues in contact with LEU 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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132A VAL* 3.7 31.9 - - + -
142A LEU* 3.9 23.3 - - + +
143A LEU 2.7 25.2 + - - +
144A LEU* 4.0 4.3 - - + -
147A GLY* 1.3 69.7 - - - -
149A ASN* 1.3 64.6 + - - +
151A ILE* 3.0 19.8 + - + +
152A MET* 3.0 16.7 + - - +
163A TRP* 4.4 2.9 - - + -
164A ALA* 4.1 20.4 - - + +
168A TRP* 3.5 34.1 - - + -
270A MET* 3.6 24.2 - - + -
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Residues in contact with ASN 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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144A LEU* 2.9 53.5 + - - +
145A GLU* 3.0 29.1 + - - +
146A PRO 4.1 2.9 - - - +
148A LEU* 1.3 73.7 - - - +
150A GLU* 1.3 61.6 + - - +
152A MET* 3.4 5.9 + - - +
153A ALA* 3.2 24.1 + - - +
269A ASP* 5.7 1.9 - - - +
270A MET* 4.2 16.0 - - - +
271A TRP* 4.7 7.3 - - - -
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Residues in contact with GLU 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 PRO* 3.1 22.5 + - + +
147A GLY 3.6 5.4 - - - +
148A LEU 3.1 0.4 + - - -
149A ASN* 1.3 72.9 - - - +
151A ILE* 1.3 74.8 + - + +
153A ALA* 3.2 4.6 + - - +
154A ASN* 3.0 46.2 + - - +
155A SER 5.5 0.5 + - - -
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Residues in contact with ILE 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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142A LEU* 4.2 15.7 - - + -
147A GLY 3.9 11.4 - - - +
148A LEU* 3.0 9.8 + - - +
150A GLU* 1.3 83.6 + - + +
152A MET* 1.3 62.4 + - - +
155A SER* 2.8 50.8 + - - +
160A GLU* 3.9 32.1 - - + +
161A ARG* 3.7 6.6 + - - -
163A TRP* 4.0 27.4 - - + -
164A ALA* 4.3 17.9 - - + -
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Residues in contact with MET 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 LEU 3.0 15.0 + - - +
149A ASN* 3.9 6.7 - - - +
150A GLU 3.3 0.4 - - - -
151A ILE* 1.3 74.4 - - - +
153A ALA* 1.3 57.5 + - - +
161A ARG* 3.2 45.7 + - - +
164A ALA* 4.1 12.1 - - + -
165A TRP* 3.8 31.2 - - + -
265A HIS* 3.8 21.8 - - + +
268A GLY* 2.9 22.4 - - - +
269A ASP* 3.4 35.0 - - - +
270A MET* 3.7 26.2 - - + +
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Residues in contact with ALA 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 ASN 3.2 15.8 + - - +
150A GLU* 3.7 2.9 - - - +
151A ILE 3.1 0.6 - - - -
152A MET* 1.3 81.0 - - - +
154A ASN* 1.3 73.9 + - - +
161A ARG* 4.7 2.5 + - - -
268A GLY* 3.3 8.6 - - - +
269A ASP* 5.7 0.7 - - + -
277A ASN* 2.9 42.7 - - - +
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Residues in contact with ASN 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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150A GLU* 3.0 34.3 + - - +
153A ALA* 1.3 94.0 + - - +
155A SER* 1.3 68.1 + - - +
156A LEU* 3.4 15.8 + - - +
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Residues in contact with SER 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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150A GLU* 4.3 0.4 + - - -
151A ILE* 2.8 31.7 + - - +
154A ASN* 1.3 73.7 - - - +
156A LEU* 1.3 61.6 + - - +
157A ASP 3.0 15.8 + - - -
160A GLU* 2.8 28.1 + - - -
161A ARG* 2.8 45.1 + - - +
252A TYR* 3.9 0.5 + - - -
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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