Contacts of the helix formed by residues 160 - 163 (chain E) in PDB entry 1PV2
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 GLY 160 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57E ASP* 5.8 1.3 - - - -
97E ILE* 3.6 17.3 - - - +
158E LEU 3.3 4.6 + - - -
159E ILE* 1.3 73.1 - - - +
161E LEU* 1.3 62.8 + - - +
162E PRO* 3.3 3.5 - - - +
163E GLU* 3.0 22.4 + - - +
164E SER* 3.4 7.3 + - - -
100F LEU* 6.0 4.9 - - - -
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Residues in contact with LEU 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E ILE* 4.2 19.7 - - + +
55E ALA 4.2 18.4 - - - +
56E ALA* 5.1 3.4 - - - +
57E ASP* 5.3 2.2 - - - +
73E ASN* 6.3 0.4 - - - +
97E ILE* 3.6 27.1 - - + -
151E VAL* 3.9 27.6 - - + -
156E GLY 5.1 0.2 - - - +
157E ALA* 3.5 27.1 - - + +
159E ILE 3.2 6.4 + - - +
160E GLY* 1.3 72.4 - - - +
162E PRO* 1.3 66.2 - - + +
163E GLU 2.9 6.4 + - - -
164E SER* 3.0 15.1 + - - -
167E VAL* 3.9 13.7 - - + +
190E ALA* 4.1 16.8 - - + -
193E ALA* 3.7 9.7 - - - +
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Residues in contact with PRO 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E ALA 3.5 7.4 - - - +
158E LEU 3.1 26.5 - - - +
160E GLY 3.3 3.8 - - - +
161E LEU* 1.3 96.2 - - + +
163E GLU* 1.3 74.0 + - + +
164E SER 3.6 0.2 - - - -
189E ALA* 3.6 28.3 - - + +
190E ALA 4.2 3.6 - - - +
192E LEU* 3.6 14.1 - - + +
193E ALA* 3.5 19.6 + - - -
195E ARG* 4.1 6.0 + - - +
196E HIS* 5.8 0.2 - - - -
229E TRP* 4.0 21.1 - - + -
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Residues in contact with GLU 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E LEU 6.0 0.2 - - - +
160E GLY* 3.0 14.1 + - - +
161E LEU 2.9 1.4 + - - -
162E PRO* 1.3 90.9 - - + +
164E SER* 1.3 60.9 + - - +
165E GLN* 3.6 8.7 + - - +
193E ALA* 5.0 1.8 - - - +
195E ARG* 3.3 33.0 + - - +
196E HIS* 6.2 2.0 - - - -
229E TRP* 5.3 6.6 - - - -
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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