Contacts of the helix formed by residues 182 - 187 (chain A) in PDB entry 1UWV
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ALA 3.3 12.0 + - - -
179A CYS* 2.6 24.0 + - - -
181A GLY* 1.3 78.0 - - - +
183A LEU* 1.3 61.8 + - - +
184A GLN 3.7 0.3 + - - -
218A LYS* 3.4 39.0 + - - +
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Residues in contact with LEU 183 (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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179A CYS* 3.6 13.9 - - - +
180A LEU* 3.2 39.4 + - + +
181A GLY 3.4 0.6 - - - +
182A SER* 1.3 78.4 - - - +
184A GLN* 1.3 64.4 + - - +
185A ALA* 3.9 6.7 - - + +
186A MSE 3.3 24.2 + - - +
189A LEU* 4.3 18.4 - - + -
205A LEU* 4.6 0.4 - - + -
211A LEU* 5.6 1.3 - - + -
215A ASP* 3.4 30.3 - - + +
218A LYS* 3.9 26.2 - - + -
219A LEU* 4.1 22.0 - - + -
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Residues in contact with GLN 184 (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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182A SER 3.7 2.0 + - - -
183A LEU* 1.3 72.5 - - - +
185A ALA* 1.3 57.0 + - - +
186A MSE 3.0 7.0 + - - +
187A ARG* 4.4 19.2 + - - -
188A HIS* 5.5 0.7 - - - -
212A SER* 2.9 29.3 + - - +
214A ALA* 3.8 15.5 - - - +
215A ASP* 2.8 16.7 + - - +
218A LYS* 4.5 9.2 - - - +
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Residues in contact with ALA 185 (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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183A LEU* 3.2 4.4 - - + -
184A GLN* 1.3 69.4 - - - +
186A MSE 1.3 63.4 + - - +
187A ARG 3.1 3.4 - - - -
188A HIS* 2.9 32.7 + - + -
189A LEU* 3.4 16.3 - - + +
209A ALA 5.9 0.2 - - - +
210A PRO 5.5 2.5 - - - +
211A LEU* 3.7 29.2 - - + -
212A SER 5.8 0.4 - - - +
215A ASP* 2.7 19.9 + - - +
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Residues in contact with MSE 186 (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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137A TYR* 3.2 45.6 - - + +
142A GLN* 4.0 10.3 - - + +
143A GLN 4.0 2.5 - - - -
144A LEU* 3.9 45.5 - - + +
180A LEU 3.4 20.6 - - - +
181A GLY* 3.5 26.9 - - - +
183A LEU* 3.3 13.4 + - - +
184A GLN 3.0 4.2 + - - +
185A ALA* 1.3 77.3 - - - +
187A ARG* 1.3 60.9 - - - +
188A HIS 3.2 1.5 + - - -
189A LEU* 3.8 19.8 + - + +
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Residues in contact with ARG 187 (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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137A TYR* 3.5 61.1 + - + +
184A GLN 4.4 16.1 + - - -
185A ALA 3.0 1.8 + - - -
186A MSE 1.3 79.6 - - - +
188A HIS* 1.3 95.5 + - + +
189A LEU 3.7 2.2 + - - +
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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