Contacts of the helix formed by residues 164 - 173 (chain G) in PDB entry 2BDI
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 SER 164 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLU* 3.2 16.7 + - - -
132G ALA* 4.0 21.4 - - - +
163G VAL* 1.3 80.1 - - - +
165G GLU* 1.3 67.5 + - - +
166G GLU* 4.2 2.1 + - - +
167G VAL* 3.3 25.6 + - - +
168G CYS* 2.9 21.0 + - - +
96H ARG* 5.5 5.7 - - - +
97H PRO* 5.8 2.3 - - - +
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Residues in contact with GLU 165 (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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164A SER* 3.3 17.3 - - - -
165A GLU* 3.4 26.4 + - + +
166A GLU* 2.7 39.9 + - + +
163G VAL 3.6 1.4 + - - -
164G SER* 1.3 75.0 - - - +
166G GLU* 1.3 59.4 + - - +
168G CYS* 3.6 5.3 - - - +
169G SER* 2.8 32.4 + - - -
176G TYR* 3.7 23.9 + - + +
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Residues in contact with GLU 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU* 2.9 20.2 + - - +
166A GLU* 5.1 1.3 - - - +
169A SER* 3.7 21.8 - - - +
176A TYR* 2.9 38.2 + - - +
178A PRO* 4.8 7.6 - - - +
164G SER* 4.2 2.1 + - - +
165G GLU* 1.3 81.1 - - - +
167G VAL* 1.3 71.7 + - + +
169G SER* 3.1 6.1 + - - -
170G LYS* 3.0 51.4 + - + +
174H PRO* 5.5 2.6 - - + +
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Residues in contact with VAL 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163G VAL* 3.9 18.4 - - + -
164G SER* 3.2 20.0 + - - +
166G GLU* 1.3 87.9 - - + +
168G CYS* 1.3 57.6 + - - +
170G LYS* 4.0 0.3 - - - +
171G LEU* 2.7 52.9 + - + +
97H PRO* 4.8 17.3 - - + -
98H LEU* 4.5 6.5 - - + +
174H PRO* 4.3 19.9 - - + +
175H LEU* 4.1 18.6 - - + -
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Residues in contact with CYS 168 (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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163G VAL* 4.4 1.7 - - + +
164G SER 2.9 21.1 + - - +
165G GLU* 3.6 6.7 - - - +
167G VAL* 1.3 76.5 - - - +
169G SER* 1.3 62.8 + - - +
171G LEU* 4.5 3.4 - - - -
172G TYR* 3.2 23.1 + - - +
176G TYR* 3.8 24.4 - - + -
181G PHE* 4.1 2.5 - - - -
182G CYS* 2.1 62.8 - - + +
227G VAL* 5.6 1.1 - - - -
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Residues in contact with SER 169 (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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166A GLU* 3.6 28.5 - - - +
169A SER* 5.2 0.5 + - - -
170A LYS* 3.8 9.4 + - - -
165G GLU 2.8 21.9 + - - -
166G GLU* 3.1 7.8 + - - -
168G CYS* 1.3 71.7 - - - +
170G LYS* 1.4 61.1 + - - +
172G TYR 3.7 0.2 - - - -
173G ASP* 2.8 30.1 + - - +
176G TYR* 3.3 35.4 - - - +
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Residues in contact with LYS 170 (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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169A SER* 4.0 16.5 + - - -
170A LYS* 4.3 24.2 - - - +
173A ASP* 2.9 31.3 + - - +
176A TYR* 6.2 0.2 - - - +
166G GLU* 3.0 44.6 + - + +
169G SER* 1.4 74.3 - - - +
171G LEU* 1.3 68.7 + - - +
172G TYR 3.0 1.0 + - - -
173G ASP* 3.4 16.6 + - - +
173H ASP* 4.7 5.2 + - - +
174H PRO* 3.5 38.1 - - + +
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Residues in contact with LEU 171 (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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167G VAL* 2.7 36.3 + - + +
168G CYS 4.0 3.4 - - - +
170G LYS* 1.3 80.3 - - - +
172G TYR* 1.3 64.7 + - + +
173G ASP 4.8 1.6 - - - +
217G LYS* 3.1 32.8 + - - +
223G GLY 3.3 26.7 - - - +
224G VAL* 5.4 4.5 - - + -
225G PRO* 3.4 25.4 - - + -
98H LEU* 4.7 0.9 - - + -
174H PRO* 4.2 16.8 - - + +
175H LEU* 4.6 10.1 - - + -
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Residues in contact with TYR 172 (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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168G CYS* 3.2 12.6 + - - +
169G SER 3.7 1.6 - - - -
170G LYS 3.1 0.6 - - - -
171G LEU* 1.3 86.4 - - + +
173G ASP* 1.3 64.1 + - - +
175G LEU* 2.9 30.0 + - + +
176G TYR* 3.0 19.0 + - + +
180G MET* 6.3 0.2 - - - -
182G CYS* 3.8 24.2 - - - -
215G PHE* 3.8 22.9 - + + -
216G GLY* 3.6 5.2 - - - -
217G LYS* 3.5 45.1 + - + +
224G VAL* 4.3 5.1 - - + +
225G PRO* 2.6 37.6 + - + -
227G VAL* 3.6 21.3 - - + +
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Residues in contact with ASP 173 (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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170A LYS* 3.1 26.7 + - - +
173B ASP* 4.8 8.3 - - - +
170F LYS* 4.5 8.5 - - - +
169G SER 2.8 17.5 + - - +
170G LYS* 3.4 13.7 + - - +
171G LEU 4.8 1.4 - - - +
172G TYR* 1.3 80.5 - - - +
174G PRO* 1.3 80.6 - - - +
176G TYR* 4.4 2.2 - - - +
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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
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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