Contacts of the helix formed by residues 139 - 144 (chain B) in PDB entry 2DH3
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 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B LEU* 4.6 7.6 - - - +
133B GLN* 3.0 22.0 + - - +
137B ALA* 2.9 25.1 + - - +
138B GLY* 1.3 75.9 - - - +
140B LEU* 1.3 63.5 + - - +
141B ALA* 3.7 9.7 - - + +
142B GLY* 2.7 33.9 + - - -
143B LEU* 3.3 3.6 + - - +
182B ASN 5.0 2.7 - - - +
183B PHE* 3.5 16.4 - - - +
184B GLY* 5.0 3.4 - - - +
188B ASP* 6.0 0.9 - - - +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU* 4.1 19.5 - - + -
139B ASN* 1.3 73.8 - - - +
141B ALA* 1.3 62.4 + - - +
143B LEU* 3.3 20.0 + - - +
144B LYS* 3.9 5.6 + - - -
160B LEU* 4.2 17.5 - - + -
163B ILE* 4.4 9.0 - - + -
179B ILE* 4.4 13.0 - - + -
183B PHE* 3.0 29.6 + - + +
184B GLY* 4.2 4.0 - - - +
185B SER 3.9 21.1 - - - +
188B ASP* 4.2 12.6 - - + -
189B PHE* 4.0 35.4 - - + +
192B LEU* 4.1 18.8 - - + +
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ASN* 3.3 10.6 + - + +
140B LEU* 1.3 78.8 - - - +
142B GLY* 1.3 60.8 + - - +
143B LEU 3.6 0.2 + - - -
144B LYS* 3.1 42.4 + - - +
145B GLY 4.9 0.3 + - - -
188B ASP* 4.1 26.4 - - + +
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLN* 3.4 20.3 + - - +
137B ALA* 4.9 5.2 - - - -
139B ASN* 2.7 22.7 + - - -
141B ALA* 1.3 71.9 - - - +
143B LEU* 1.3 62.4 + - - +
144B LYS 3.3 1.7 + - - -
145B GLY* 3.6 11.6 + - - -
146B ARG* 4.5 6.9 + - - +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ILE* 4.4 6.5 - - + -
129B LEU* 3.7 14.8 - - + -
132B PHE* 3.6 37.7 - - + -
133B GLN* 3.3 13.2 - - + +
139B ASN 3.3 6.5 + - - +
140B LEU* 3.3 12.7 + - - +
142B GLY* 1.3 76.9 - - - +
144B LYS* 1.3 64.3 + - - +
145B GLY 3.2 0.2 - - - -
146B ARG* 3.3 14.1 + - + +
147B LEU* 3.8 11.9 + - + +
150B LEU* 6.0 2.2 - - + -
158B LEU* 4.6 13.5 - - + -
160B LEU* 3.7 29.6 - - + -
192B LEU* 4.0 23.3 - - + -
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU 3.9 3.6 + - - -
141B ALA* 3.1 44.0 + - - +
142B GLY 3.3 0.2 - - - -
143B LEU* 1.3 78.8 - - - +
145B GLY* 1.3 62.6 + - - +
146B ARG 3.2 1.4 + - - -
147B LEU* 3.2 25.9 + - - +
148B ASP* 4.8 1.4 + - - +
188B ASP* 5.0 1.6 - - - +
191B SER* 3.9 31.5 + - - +
192B LEU* 3.8 20.8 - - + +
195B SER* 3.9 24.5 - - - +
199B LYS* 5.3 3.5 - - - -
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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