Contacts of the helix formed by residues 154 - 159 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C GLY 3.4 11.0 - - - -
74C HIS* 3.8 5.5 - - - +
77C GLU* 3.6 6.1 + - - -
105C GLU* 3.7 15.3 - - - -
153C GLY* 1.3 76.3 - - - -
155C HIS* 1.3 63.2 + - - -
156C GLY 2.8 12.2 + - - -
157C ALA* 3.1 14.7 + - - +
185C CYS* 3.9 11.5 - - - -
186C HIS* 3.7 7.5 - - - +
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Residues in contact with HIS 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 4.0 11.0 - - + +
69C PHE* 3.7 17.5 - + + -
71C THR* 3.2 25.9 + - + +
105C GLU* 3.7 3.5 + - - -
154C GLY* 1.3 71.7 - - - -
156C GLY* 1.3 61.3 + - - +
157C ALA 3.1 0.9 - - - -
158C LEU* 3.2 39.6 + - + +
159C ILE* 4.2 3.1 + - - +
185C CYS* 5.9 0.9 - - - -
186C HIS* 3.2 28.3 - + - -
209C PHE* 5.2 1.4 - - - -
214C ASP* 3.0 28.8 + - - -
222C TYR* 4.1 19.6 - + - -
223C MET* 3.9 17.3 - - - -
227C LEU* 4.0 10.7 - - + +
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Residues in contact with GLY 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA* 3.7 19.0 - - - +
58C GLU 4.3 0.7 - - - -
71C THR* 3.1 5.5 + - - -
72C GLY* 3.3 27.7 + - - -
154C GLY 2.8 3.6 + - - -
155C HIS* 1.3 79.1 - - - +
157C ALA* 1.3 55.7 + - - +
158C LEU 3.1 0.7 - - - -
159C ILE* 3.1 38.7 + - - +
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA* 4.4 3.0 - - - +
73C ASN* 5.0 4.9 - - - +
152C PRO 3.9 19.3 - - - +
153C GLY* 4.9 1.1 - - - +
154C GLY 3.1 13.1 + - - +
156C GLY* 1.3 76.9 - - - +
158C LEU* 1.3 62.0 + - - +
159C ILE 3.2 0.6 + - - -
161C LEU* 3.6 29.6 - - + +
162C PRO* 3.5 17.8 - - - +
186C HIS 3.8 19.7 - - - +
187C GLY* 4.1 4.0 - - - +
189C ALA* 4.6 2.9 - - - +
190C ALA 5.1 0.3 + - - -
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LEU* 4.0 22.7 - - + +
155C HIS* 3.4 29.8 - - + +
156C GLY 3.1 0.6 - - - -
157C ALA* 1.3 78.9 - - - +
159C ILE* 1.3 57.5 + - - +
160C GLY 3.6 1.2 + - - -
162C PRO* 3.3 18.8 - - - +
163C GLU* 6.1 0.2 - - - +
186C HIS* 3.8 36.1 - - + -
189C ALA* 3.7 26.5 - - + -
227C LEU* 4.3 12.6 - - + -
229C TRP* 4.2 31.1 + - + +
231C PHE* 4.2 9.0 - - + -
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Residues in contact with ILE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA* 5.6 2.1 - - - +
57C ASP* 5.0 7.4 - - - +
58C GLU* 3.7 46.1 + - + +
59C ARG 4.3 1.6 - - - +
60C TYR 3.3 31.9 - - - +
61C LEU* 3.8 26.0 - - + +
62C PRO* 5.4 1.8 - - + -
71C THR* 4.7 0.2 - - + -
155C HIS 4.3 1.1 - - - +
156C GLY* 3.1 23.8 + - - +
158C LEU* 1.3 76.7 - - - +
160C GLY* 1.3 62.6 + - - +
161C LEU* 2.9 17.5 + - - +
100D LEU* 4.6 8.5 - - + -
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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