Contacts of the helix formed by residues 252 - 257 (chain P) in PDB entry 1PP9
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 ASP 252 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131P TYR* 3.6 20.0 + - - +
138P MET* 3.8 17.1 - - + +
251P GLY* 1.3 72.6 - - - +
253P PRO* 1.3 74.3 - - - +
254P ASP* 2.7 39.9 + - - +
255P ASN* 3.0 19.2 + - - +
256P TYR* 4.4 8.2 + - - -
267P HIS 5.5 0.3 - - - +
269P LYS* 3.7 32.2 + - - +
270P PRO 5.5 0.2 - - - +
3008P JZR 4.3 9.7 + - - +
3009P GOL 4.3 3.5 + - - +
121Q HIS* 4.8 1.8 + - - -
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Residues in contact with PRO 253 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248P ASP 6.0 0.2 - - - +
251P GLY 4.1 5.2 - - - +
252P ASP* 1.3 90.4 - - - +
254P ASP* 1.3 61.4 + - - +
256P TYR* 3.0 24.1 + - + +
3008P JZR 4.1 3.1 - - - +
118Q ARG 3.4 20.6 - - - +
119Q ALA* 3.4 23.5 - - - +
120Q ARG 4.1 4.0 - - - +
121Q HIS* 3.6 49.6 - - + +
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Residues in contact with ASP 254 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P GLN* 3.4 20.2 - - + +
138P MET* 3.7 24.8 - - + +
252P ASP* 2.7 24.1 + - - +
253P PRO* 1.3 73.3 - - - +
255P ASN* 1.3 58.0 + - - +
256P TYR 3.1 2.2 + - - -
257P THR* 3.3 18.6 + - - +
265P PRO* 3.8 25.1 - - - +
267P HIS* 5.0 5.0 + - - +
268P ILE* 5.0 6.1 + - - -
119Q ALA 4.8 6.1 - - - +
120Q ARG* 5.9 0.3 + - - -
121Q HIS* 5.3 7.5 + - - -
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Residues in contact with ASN 255 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63P PHE* 3.9 7.8 - - - -
80P ARG* 5.8 1.6 - - - +
131P TYR* 3.8 27.2 + - + +
134P PRO* 3.6 18.6 - - - +
136P GLY* 3.2 10.5 - - - +
137P GLN 4.2 0.4 - - - +
138P MET* 2.8 36.3 + - + +
139P SER* 2.9 25.5 + - - -
252P ASP 3.0 13.7 + - - +
254P ASP* 1.3 75.4 - - - +
256P TYR* 1.3 59.0 + - + +
257P THR 3.1 6.9 + - - -
501P HEM 5.2 2.0 + - - -
3014P AZI 3.1 20.0 + - - +
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Residues in contact with TYR 256 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63P PHE* 3.6 16.0 - - - -
80P ARG* 4.6 1.5 + - - -
81P TYR* 2.7 29.2 + - - -
248P ASP* 2.7 30.1 + - - -
252P ASP 4.4 6.3 - - - -
253P PRO* 3.0 18.1 + - + +
255P ASN* 1.3 79.0 - - + +
257P THR* 1.3 60.5 + - - +
258P PRO* 4.1 1.9 - - - +
3014P AZI 3.7 28.7 - - - -
115Q TYR* 3.7 38.0 - + + +
118Q ARG* 3.2 46.8 + - + -
119Q ALA* 3.8 17.2 - - + +
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Residues in contact with THR 257 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63P PHE* 4.0 2.2 - - - -
136P GLY* 3.1 3.3 - - - -
137P GLN* 2.7 42.3 + - + +
253P PRO 4.6 1.0 + - - -
254P ASP* 3.5 15.9 + - - -
255P ASN 3.1 0.4 - - - -
256P TYR* 1.3 80.5 - - - +
258P PRO* 1.3 77.0 - - + +
260P ASN* 6.1 0.7 - - + -
119Q ALA* 3.9 16.3 + - - +
120Q ARG* 4.3 9.2 + - - -
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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
------------------------------------------------------------
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