Contacts of the helix formed by residues 151 - 156 (chain B) in PDB entry 1DXO
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 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B GLY 3.9 0.2 + - - -
150B GLY* 1.3 76.5 - - - +
152B GLY* 1.3 65.9 + - - +
153B SER* 3.1 20.7 + - - -
154B MET* 3.0 35.8 + - - +
155B TYR* 3.3 10.7 - - - -
190B TYR* 3.9 0.7 - - - -
191B SER* 3.9 21.5 - - - -
235D GLY* 4.8 3.3 + - - -
236D PHE* 5.1 0.3 - - - -
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Residues in contact with GLY 152 (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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151B SER* 1.3 74.7 - - - +
153B SER* 1.3 57.0 + - - +
155B TYR* 2.9 20.3 + - - +
156B SER* 3.2 11.5 + - - -
190B TYR* 3.5 38.6 - - - +
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Residues in contact with SER 153 (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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151B SER* 3.1 17.0 + - - -
152B GLY* 1.3 77.1 - - - +
154B MET* 1.3 54.4 - - - +
156B SER* 2.8 25.3 + - - -
159B GLY* 2.9 14.2 - - - -
235D GLY* 3.1 27.4 + - - +
237D LEU* 3.3 21.5 - - - +
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Residues in contact with MET 154 (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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150B GLY* 3.4 12.1 - - - -
151B SER* 3.0 45.5 + - - +
152B GLY 3.1 1.0 - - - -
153B SER* 1.3 78.9 + - - +
155B TYR* 1.3 59.5 + - + +
156B SER 3.6 0.2 - - - -
159B GLY* 3.3 10.6 - - - -
160B ILE* 4.2 6.3 - - + +
161B HIS* 2.9 61.8 + - + +
162B GLY 3.4 0.3 + - - -
128D TYR* 6.3 0.2 - - + -
131D MET* 6.0 2.7 - - - +
232D PHE* 5.8 2.7 - - + -
235D GLY 4.3 1.8 - - - +
236D PHE* 4.0 43.7 - - + -
302D DQN 4.3 14.8 - - + -
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Residues in contact with TYR 155 (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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103B LEU* 4.0 8.0 - - + +
106B PHE* 3.9 5.5 - + - -
148B THR* 4.6 2.5 - - - -
150B GLY 3.9 11.2 - - - -
151B SER 3.3 14.6 - - - -
152B GLY 2.9 8.2 + - - +
154B MET* 1.3 78.8 - - - +
156B SER* 1.3 62.8 + - - +
161B HIS* 3.3 40.5 - + + -
162B GLY 3.2 8.3 - - - +
163B ASP* 3.4 3.5 - - - +
164B MET* 3.1 41.7 + - + +
167B ILE* 3.6 30.3 - - + -
190B TYR* 3.2 31.9 - + - +
301B FAD 2.6 36.5 + - - -
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Residues in contact with SER 156 (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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152B GLY 3.2 8.2 + - - -
153B SER* 2.8 22.7 + - - -
155B TYR* 1.3 83.2 - - - +
157B LEU* 1.3 65.6 + - - +
158B GLN* 4.0 8.1 + - - -
159B GLY* 2.9 11.4 + - - -
162B GLY 3.8 9.2 - - - -
163B ASP* 4.5 2.2 - - - -
237D LEU* 3.3 17.3 - - - +
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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