Contacts of the helix formed by residues 154 - 159 (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 154 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72E GLY 3.3 10.5 - - - -
74E HIS* 3.5 16.5 - - - +
77E GLU* 3.4 7.5 + - - -
105E GLU* 3.8 5.2 - - - -
153E GLY* 1.3 75.1 - - - -
155E HIS* 1.3 60.7 + - - -
156E GLY 2.8 12.4 + - - -
157E ALA* 3.0 17.2 + - - +
185E CYS* 4.1 10.5 - - - -
186E HIS* 3.9 7.5 - - - +
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Residues in contact with HIS 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E LEU* 4.3 4.0 - - + +
69E PHE* 3.7 18.4 - + + -
71E THR* 3.3 26.9 + - + +
105E GLU* 3.5 4.1 + - - -
154E GLY* 1.3 72.6 - - - -
156E GLY* 1.3 61.7 + - - +
157E ALA 3.1 0.9 - - - -
158E LEU* 3.1 42.3 + - + +
159E ILE* 3.9 7.3 - - - +
185E CYS* 5.8 1.3 - - - -
186E HIS* 3.3 27.7 - + - -
209E PHE* 5.3 2.2 - - - -
214E ASP* 3.0 29.6 + - - -
222E TYR* 4.1 20.7 - + - -
223E MET* 3.9 19.0 - - - -
227E LEU* 4.2 6.1 - - + +
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Residues in contact with GLY 156 (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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56E ALA* 3.7 18.2 - - - +
58E GLU 4.3 0.6 - - - +
71E THR* 3.1 1.8 + - - -
72E GLY* 2.8 33.7 + - - -
155E HIS* 1.3 79.3 - - - +
157E ALA* 1.3 60.1 + - - +
158E LEU 3.0 1.5 + - - -
159E ILE* 3.1 34.7 + - - +
161E LEU* 5.1 0.2 - - - +
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Residues in contact with ALA 157 (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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56E ALA* 4.4 4.1 - - - +
72E GLY 4.5 0.2 + - - -
73E ASN* 4.6 3.2 - - - +
152E PRO 3.9 20.4 - - - +
153E GLY 4.7 0.4 - - - -
154E GLY 3.0 13.8 + - - +
156E GLY* 1.3 76.7 - - - +
158E LEU* 1.3 61.7 + - - +
159E ILE 3.4 0.2 - - - -
161E LEU* 3.5 40.0 - - + +
162E PRO* 3.5 5.0 - - - +
186E HIS 3.6 20.4 - - - +
187E GLY* 4.1 4.3 - - - +
189E ALA* 4.4 4.0 - - - +
190E ALA 4.8 0.3 + - - -
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Residues in contact with LEU 158 (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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61E LEU* 3.9 20.4 - - + -
155E HIS* 3.3 41.7 - - + +
156E GLY 3.0 1.2 - - - -
157E ALA* 1.3 78.5 - - - +
159E ILE* 1.3 58.4 + - - +
160E GLY 3.3 1.2 + - - -
162E PRO* 3.1 23.8 - - - +
186E HIS* 3.9 26.7 - - + -
189E ALA* 3.7 24.7 - - + -
227E LEU* 4.2 14.8 - - + -
229E TRP* 3.9 28.3 - - + -
231E PHE* 4.2 7.9 - - + +
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Residues in contact with ILE 159 (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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56E ALA* 5.6 1.2 - - - +
57E ASP* 4.8 7.1 - - - +
58E GLU* 3.6 48.0 + - + +
59E ARG 4.1 2.0 - - - +
60E TYR 3.6 32.1 - - - +
61E LEU* 3.7 27.1 - - + -
62E PRO* 5.4 4.5 - - + -
71E THR* 4.7 0.2 - - + -
155E HIS 3.9 3.1 - - - +
156E GLY* 3.1 24.4 + - - +
158E LEU* 1.3 72.5 - - - +
160E GLY* 1.3 61.6 + - - +
161E LEU* 3.2 12.0 + - - +
100F LEU* 5.4 5.2 - - + -
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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