Contacts of the helix formed by residues 170 - 173 (chain D) in PDB entry 3LSU
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 TRP 170 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C GLY* 3.5 28.9 - - - -
171C GLU* 3.7 17.7 - - + -
182C MLY 6.1 4.9 - - - -
34D TYR* 3.7 14.4 - - - -
73D PHE* 4.1 9.0 - + - -
131D SER* 3.5 21.5 - - - +
132D GLY 3.5 20.7 - - - +
133D TRP* 3.9 4.2 - - - +
153D ASN* 2.9 40.0 + - - -
154D GLN* 3.3 22.8 - - + +
168D ASP* 3.1 24.5 + - - +
169D ALA* 1.3 80.8 - - - +
171D GLU* 1.3 65.7 + - - +
172D HIS* 3.4 36.8 - + + +
173D ALA* 2.9 18.4 + - - +
174D TYR* 3.5 4.0 - - - -
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Residues in contact with GLU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C HIS* 3.9 9.9 - - - -
131C SER* 4.9 2.9 + - - +
170C TRP* 3.6 19.7 - - + -
171C GLU* 3.4 25.4 + - + +
172C HIS* 2.8 57.4 + - - +
175C TYR* 5.8 0.2 - - - -
130D GLY 6.0 1.6 - - - +
131D SER* 5.2 2.8 + - - +
169D ALA 3.5 1.7 + - - +
170D TRP* 1.3 71.0 - - - +
172D HIS* 1.3 59.0 + - - +
173D ALA 2.9 0.9 + - - -
174D TYR* 3.1 27.7 + - + +
175D TYR* 2.9 43.8 + - + +
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Residues in contact with HIS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C GLU* 2.8 40.8 + - - +
175C TYR* 3.6 38.9 + - + -
22D ILE* 4.1 12.3 - - - +
26D HIS* 3.3 20.6 + + - +
30D HIS* 3.4 26.7 + + + +
34D TYR* 4.3 8.7 - - - -
81D HIS* 4.0 0.4 + - - -
154D GLN* 4.9 0.2 - - - -
168D ASP* 3.7 0.2 + - - -
170D TRP* 3.4 30.0 - + + +
171D GLU* 1.3 72.2 - - - +
173D ALA* 1.3 64.8 + - - +
174D TYR 3.2 0.7 + - - -
175D TYR 4.5 2.1 + - - -
176D LEU* 5.7 0.3 + - - +
208D MN 2.2 35.9 + - - -
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Residues in contact with ALA 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 4.8 4.3 - - - +
22D ILE* 3.7 16.8 - - - +
26D HIS* 3.9 14.8 + - + -
84D PHE* 5.4 0.2 - - + -
168D ASP* 3.7 29.6 - - - +
170D TRP 2.9 15.6 + - - +
172D HIS* 1.3 81.7 - - - +
174D TYR* 1.3 60.6 + - + +
185D TYR* 3.6 30.4 + - + +
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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