Contacts of the helix formed by residues 210 - 215 (chain H) 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 PRO 210 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208H ALA 3.7 2.5 - - - +
209H PHE* 1.3 98.9 - - + +
211H ASP* 1.3 67.2 + - - +
212H ALA* 4.5 6.7 - - + +
213H ALA* 3.0 20.0 + - + +
214H ASP* 3.4 3.6 + - - -
242H ILE* 6.2 2.0 - - + -
244H ASN* 4.0 10.3 - - - +
245H ASP* 3.9 38.4 - - + +
246H ASP* 3.9 5.6 - - - +
247H ILE* 3.8 27.6 - - + -
261H ASP* 4.8 0.7 - - + +
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Residues in contact with ASP 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H PHE 4.2 0.7 - - - +
210H PRO* 1.3 72.5 - - - +
212H ALA* 1.3 56.0 + - - +
214H ASP* 2.7 31.5 + - - +
215H LYS* 3.0 22.9 + - + +
230H TYR* 3.3 29.2 - - + +
231H PHE* 4.1 10.2 - - - -
232H GLY* 3.1 25.9 + - - -
233H GLU* 3.0 28.8 + - - +
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Residues in contact with ALA 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H PRO* 3.2 6.9 - - + +
211H ASP* 1.3 77.2 - - - +
213H ALA* 1.3 62.0 + - - +
215H LYS* 3.3 25.1 + - - +
216H GLN* 3.8 21.6 + - - +
245H ASP* 5.4 5.2 - - + +
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Residues in contact with ALA 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209H PHE* 3.4 19.5 - - + -
210H PRO* 3.0 16.5 + - + +
212H ALA* 1.3 79.3 - - - +
214H ASP* 1.3 61.3 + - - +
216H GLN* 3.3 12.9 + - - +
217H THR* 3.4 19.2 + - + +
247H ILE* 3.6 23.3 - - + -
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Residues in contact with ASP 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155H HIS* 3.1 25.7 + - - -
186H HIS* 2.5 28.3 + - - -
209H PHE* 3.4 20.3 - - - -
210H PRO 3.4 2.3 + - - +
211H ASP* 2.7 16.6 + - - +
213H ALA* 1.3 70.7 - - - +
215H LYS* 1.3 60.8 + - - +
216H GLN 3.1 4.9 - - - -
217H THR* 3.1 20.8 + - - +
218H PRO* 3.9 2.1 - - - +
223H MET* 3.8 11.8 - - - +
226H HIS* 4.8 1.0 + - - -
227H LEU* 3.9 20.7 + - + +
230H TYR* 3.9 11.7 + - + -
231H PHE* 4.4 7.4 - - - -
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Residues in contact with LYS 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211H ASP* 3.0 23.7 + - - +
212H ALA* 3.6 16.8 - - - +
213H ALA 3.2 0.8 - - - -
214H ASP* 1.3 76.6 - - - +
216H GLN* 1.3 65.6 + - + +
217H THR 3.8 0.2 - - - -
226H HIS* 3.4 25.3 + - - +
230H TYR* 3.6 47.0 - - + +
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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