Contacts of the helix formed by residues 154 - 159 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLY 3.4 10.1 - - - -
74A HIS* 3.7 11.6 - - - +
77A GLU* 3.4 6.7 + - - -
105A GLU* 3.8 9.9 - - - -
153A GLY* 1.3 76.2 - - - -
155A HIS* 1.3 62.1 + - - -
156A GLY 3.0 11.1 + - - -
157A ALA* 3.1 14.7 + - - +
185A CYS* 3.7 14.0 - - - +
186A HIS* 3.8 8.9 - - - +
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Residues in contact with HIS 155 (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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61A LEU* 4.1 8.3 - - + +
69A PHE* 3.7 20.6 - + + -
71A THR* 3.3 24.1 + - + +
105A GLU* 3.6 5.4 + - - -
154A GLY* 1.3 71.2 - - - -
156A GLY* 1.3 63.6 + - - +
157A ALA 3.1 0.9 - - - -
158A LEU* 3.0 38.5 + - + +
159A ILE* 4.1 5.7 - - - +
185A CYS* 5.9 0.9 - - - -
186A HIS* 3.2 30.1 + + - -
209A PHE* 5.4 1.6 - - - -
214A ASP* 3.0 29.8 + - - -
217A THR* 6.2 0.2 - - - +
222A TYR* 3.9 23.6 - + - -
223A MET* 3.9 16.7 - - - -
227A LEU* 4.3 5.1 - - + +
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Residues in contact with GLY 156 (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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56A ALA* 3.6 15.7 - - - +
71A THR* 3.2 2.6 + - - -
72A GLY* 2.9 33.3 + - - -
155A HIS* 1.3 78.4 - - - +
157A ALA* 1.3 55.9 + - - +
158A LEU 3.0 0.2 - - - -
159A ILE* 2.9 43.5 + - - +
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Residues in contact with ALA 157 (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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56A ALA* 4.4 3.0 - - - +
72A GLY 4.6 0.4 + - - -
73A ASN* 4.7 4.2 - - - +
152A PRO 3.9 20.4 - - - +
153A GLY 4.7 0.2 - - - +
154A GLY 3.1 13.3 + - - +
155A HIS 3.1 0.6 - - - -
156A GLY* 1.3 76.2 - - - +
158A LEU* 1.3 58.0 + - - +
159A ILE 3.1 0.4 + - - -
161A LEU* 3.6 26.1 - - + +
162A PRO* 3.1 23.7 - - - +
186A HIS 3.9 19.5 - - - +
187A GLY* 4.0 7.4 - - - +
189A ALA* 4.6 2.1 - - - +
190A ALA 5.1 0.3 + - - -
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Residues in contact with LEU 158 (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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61A LEU* 4.3 22.2 - - + +
155A HIS* 3.0 36.9 + - - +
157A ALA* 1.3 79.4 - - - +
159A ILE* 1.3 57.8 + - - +
160A GLY 3.6 1.2 + - - -
162A PRO* 3.2 17.6 - - - +
186A HIS* 4.1 20.2 - - + -
189A ALA* 3.5 27.6 - - + -
227A LEU* 4.2 20.2 - - + -
229A TRP* 4.1 29.5 + - + +
231A PHE* 4.3 12.3 - - + +
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Residues in contact with ILE 159 (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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56A ALA* 5.1 2.8 - - + +
57A ASP* 4.8 7.9 - - - +
58A GLU* 3.5 48.7 - - + +
60A TYR 4.0 5.8 - - - +
61A LEU* 3.7 45.5 - - + +
62A PRO* 5.4 2.0 - - + -
71A THR* 4.2 4.3 - - + -
155A HIS 4.1 0.7 - - - +
156A GLY* 2.9 30.5 + - - +
158A LEU* 1.3 79.1 - - - +
160A GLY* 1.3 59.6 + - - +
161A LEU* 3.1 15.3 + - - +
100B LEU* 4.9 8.1 - - + -
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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