Contacts of the helix formed by residues 154 - 159 (chain G) in PDB entry 6PST
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 154 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152G TYR* 3.3 30.4 - - + +
153G VAL* 1.3 88.3 - - - +
155G ALA* 1.3 61.6 + - - +
156G SER* 3.1 4.7 + - - +
157G THR* 3.3 31.7 + - + +
158G ARG* 2.9 24.8 + - - +
174G ASP* 3.3 15.7 - - + +
1059I ARG* 3.1 32.8 - - - +
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Residues in contact with ALA 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G PRO* 1.3 73.1 - - - +
156G SER* 1.3 54.2 + - - +
158G ARG* 3.1 29.9 + - - +
159G ILE* 2.7 40.1 + - + +
172G LEU* 3.4 32.3 - - + +
173G VAL 4.4 0.9 - - - +
174G ASP* 3.3 12.9 + - - +
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Residues in contact with SER 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G PRO* 3.1 2.3 - - - +
155G ALA* 1.3 76.4 + - - +
157G THR* 1.3 65.7 + - - +
159G ILE* 2.9 34.6 + - - +
160G HIS* 4.7 0.2 - - - -
174G ASP* 5.2 1.0 + - - -
1059I ARG* 4.1 18.4 + - - -
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Residues in contact with THR 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153G VAL* 3.9 9.0 - - - +
154G PRO* 3.3 35.5 + - + +
156G SER* 1.3 77.7 - - - +
158G ARG* 1.3 65.4 + - - +
160G HIS* 3.7 16.6 + - - +
1059I ARG* 5.5 0.7 - - - +
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Residues in contact with ARG 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G THR* 3.8 25.9 + - - +
58G GLU* 5.3 2.9 - - - -
147G GLN* 5.0 3.1 - - - +
153G VAL* 3.0 38.0 + - + +
154G PRO 2.9 13.8 + - - +
155G ALA* 3.1 31.0 - - - +
156G SER 3.1 0.2 - - - -
157G THR* 1.3 79.1 + - - +
159G ILE* 1.3 58.2 + - - +
160G HIS* 2.9 28.2 + - - -
162G GLU* 5.9 0.2 - - - -
172G LEU* 3.3 25.7 - - + +
173G VAL 2.8 24.5 + - - -
175G ALA* 3.2 24.9 - - - +
177G TYR* 4.3 1.8 + - - -
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Residues in contact with ILE 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G ALA* 2.7 31.7 + - + +
156G SER* 2.9 20.1 - - - +
158G ARG* 1.3 71.7 - - - +
160G HIS* 1.3 60.7 + - - +
161G SER* 3.2 24.5 - - - +
162G GLU* 4.1 18.2 - - + +
166G ARG* 3.7 27.1 - - - +
172G LEU* 4.5 11.7 - - + -
876I GLU* 4.5 7.6 - - + +
878I THR* 6.0 6.1 - - + -
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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