Contacts of the helix formed by residues 142 - 148 (chain B) in PDB entry 2DXU
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 SER 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ILE* 3.8 7.9 - - - -
131B ASN* 3.5 20.9 - - - -
132B VAL 3.4 15.9 + - - -
134B ASN 4.2 6.9 + - - -
136B VAL* 4.0 9.4 - - - -
141B THR* 1.3 79.4 + - - +
143B MET* 1.3 64.5 + - - +
144B LYS* 3.9 2.8 - - - +
145B LEU* 3.1 30.4 + - - +
146B GLU* 3.0 24.1 + - - +
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Residues in contact with MET 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B THR* 5.1 0.9 - - + -
90B LEU* 3.9 32.8 - - + -
93B PHE* 3.6 46.7 - - + -
95B ILE* 3.9 13.9 - - + -
112B ILE* 3.8 3.1 - - + +
130B LEU* 4.2 4.9 - - + -
131B ASN 3.1 13.0 + - - +
132B VAL* 3.4 18.1 + - - +
142B SER* 1.3 73.4 - - - +
144B LYS* 1.3 57.5 + - - +
146B GLU* 3.2 1.0 + - - -
147B LEU* 2.9 35.7 + - + +
151B VAL* 4.1 13.7 - - + -
156B VAL* 3.9 34.3 - - + -
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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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132B VAL 2.9 19.3 + - - +
133B ASN* 3.6 26.3 + - - +
135B LYS* 5.8 4.4 - - - +
142B SER* 3.9 3.4 - - - +
143B MET* 1.3 76.8 - - - +
145B LEU* 1.3 61.2 + - + +
148B GLY* 2.8 29.7 + - - -
149B SER* 3.6 24.9 + - - +
150B GLU* 3.1 30.9 + - - +
151B VAL* 4.3 1.9 - - - +
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Residues in contact with LEU 145 (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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134B ASN 5.6 1.1 - - - +
136B VAL* 4.1 22.2 - - + +
140B ALA 4.7 2.7 - - - +
141B THR* 3.8 12.3 - - - +
142B SER* 3.1 34.3 + - - +
144B LYS* 1.3 81.1 - - + +
146B GLU* 1.3 62.1 + - - +
148B GLY* 4.1 4.4 + - - -
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Residues in contact with GLU 146 (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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95B ILE* 4.0 22.2 - - + -
107B VAL* 3.6 32.4 - - + +
108B ASN* 4.5 11.1 + - - +
110B LYS* 5.1 3.8 - - - +
112B ILE* 4.6 2.7 - - + -
141B THR* 2.6 31.3 + - + +
142B SER 3.0 18.3 + - - +
143B MET 3.2 4.2 + - - +
145B LEU* 1.3 80.4 - - - +
147B LEU* 1.3 63.0 + - - +
148B GLY 3.6 0.2 - - - -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PHE* 3.4 37.5 - - + +
94B SER* 4.7 6.5 - - - +
95B ILE* 3.9 25.1 - - + -
143B MET* 2.9 16.0 + - + +
146B GLU* 1.3 79.4 - - - +
148B GLY* 1.3 62.4 + - - +
149B SER* 3.3 17.1 + - - +
151B VAL* 3.7 26.2 - - + -
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Residues in contact with GLY 148 (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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144B LYS* 2.8 19.8 + - - -
145B LEU 4.1 4.1 + - - -
146B GLU 3.6 1.8 - - - -
147B LEU* 1.3 73.6 - - - +
149B SER* 1.3 61.4 + - - +
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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