Contacts of the helix formed by residues 164 - 173 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165L GLU* 3.4 15.2 + - - -
96M ARG* 5.2 6.8 - - - +
97M PRO* 5.7 2.1 - - - +
132P ALA* 3.9 21.8 - - - +
163P VAL* 1.3 77.3 - - - +
165P GLU* 1.3 66.9 + - - +
166P GLU* 4.2 1.9 + - - +
167P VAL* 3.2 26.3 + - - +
168P CYS* 2.8 22.3 + - - +
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Residues in contact with GLU 165 (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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164L SER* 3.6 11.2 - - - -
165L GLU* 3.5 28.1 + - - +
166L GLU* 3.0 36.5 + - + +
163P VAL 3.6 1.6 + - - -
164P SER* 1.3 74.2 - - - +
166P GLU* 1.3 59.9 + - - +
168P CYS* 2.8 6.2 + - - +
169P SER* 2.7 31.9 + - - -
176P TYR* 3.8 26.5 + - + +
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Residues in contact with GLU 166 (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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165L GLU* 3.0 22.3 + - + +
166L GLU* 5.4 1.3 - - - +
169L SER* 3.7 27.1 - - - +
176L TYR* 2.9 28.6 + - - +
178L PRO* 5.0 6.6 - - - +
174M PRO* 5.8 1.6 - - + +
164P SER* 4.2 2.6 + - - +
165P GLU* 1.3 77.9 - - - +
167P VAL* 1.3 72.2 + - + +
168P CYS 2.8 0.9 + - - -
169P SER* 3.1 6.1 + - - -
170P LYS* 3.0 51.9 + - + +
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Residues in contact with VAL 167 (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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97M PRO* 4.8 18.4 - - + -
98M LEU* 4.6 7.6 - - + +
174M PRO* 4.4 21.0 - - + +
175M LEU* 4.3 17.5 - - + -
163P VAL* 3.9 17.9 - - + -
164P SER* 3.2 20.3 + - - +
166P GLU* 1.3 85.9 - - + +
168P CYS* 1.3 57.8 + - - +
170P LYS* 3.9 0.5 - - - +
171P LEU* 2.8 53.1 + - + +
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Residues in contact with CYS 168 (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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163P VAL* 4.5 3.4 - - + +
164P SER 2.8 18.6 + - - +
165P GLU* 3.2 9.9 - - - +
166P GLU 2.8 2.0 + - - -
167P VAL* 1.3 77.7 - - - +
169P SER* 1.2 63.6 + - - +
172P TYR* 3.4 23.9 + - - +
176P TYR* 4.0 21.3 - - + -
181P PHE* 4.2 1.8 - - - -
182P CYS* 2.1 66.9 - - + -
227P VAL* 6.0 0.7 - - - -
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Residues in contact with SER 169 (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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166L GLU* 3.9 26.7 - - - +
169L SER* 5.4 0.9 + - - -
170L LYS* 4.3 5.8 + - - -
165P GLU 2.7 16.8 + - - -
166P GLU* 3.1 8.5 + - - -
168P CYS* 1.2 74.0 - - - +
170P LYS* 1.3 66.6 + - - +
172P TYR 3.6 0.2 - - - -
173P ASP* 2.8 32.1 + - - +
176P TYR* 3.3 37.7 - - - +
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Residues in contact with LYS 170 (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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169L SER* 4.1 16.7 + - - -
170L LYS* 4.3 23.6 - - - +
173L ASP* 2.9 30.0 + - - +
173M ASP* 4.9 4.4 + - - +
174M PRO* 3.8 35.0 - - + +
166P GLU* 3.0 48.4 + - + +
169P SER* 1.3 80.5 - - - +
171P LEU* 1.3 66.1 + - - +
172P TYR 3.1 0.9 + - - -
173P ASP* 3.5 14.9 + - - +
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Residues in contact with LEU 171 (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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98M LEU* 4.9 0.7 - - + -
174M PRO* 4.2 18.6 - - + +
175M LEU* 4.9 8.3 - - + -
167P VAL* 2.8 38.0 + - + +
168P CYS* 4.1 0.9 - - - +
170P LYS* 1.3 78.9 - - - +
172P TYR* 1.3 68.4 + - + +
173P ASP 4.9 0.9 - - - +
182P CYS* 5.6 0.2 - - - -
217P LYS* 3.1 32.6 + - - +
223P GLY 3.3 26.5 - - - +
224P VAL* 4.7 5.2 - - + -
225P PRO* 3.4 24.2 - - + -
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Residues in contact with TYR 172 (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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168P CYS 3.4 13.1 + - - +
169P SER 3.6 1.1 - - - -
170P LYS 3.1 0.4 - - - -
171P LEU* 1.3 86.9 - - + +
173P ASP* 1.3 64.3 + - - +
175P LEU* 2.9 30.4 + - + +
176P TYR* 3.0 19.1 + - + +
180P MET* 6.3 0.2 - - - -
182P CYS* 3.8 24.9 - - - -
215P PHE* 3.9 22.7 - + + -
216P GLY* 3.6 4.5 - - - -
217P LYS* 3.4 45.5 + - + +
224P VAL* 4.3 5.4 - - + +
225P PRO* 2.7 36.1 + - + -
227P VAL* 3.6 22.8 - - + +
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Residues in contact with ASP 173 (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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173I ASP* 5.0 6.6 - - - +
170L LYS* 3.1 26.6 + - - -
170O LYS* 4.2 9.8 + - - +
169P SER 2.8 17.7 + - - +
170P LYS* 3.5 12.9 + - - +
171P LEU 4.9 1.2 - - - +
172P TYR* 1.3 79.7 - - - +
174P PRO* 1.3 92.7 - - - +
176P TYR* 4.4 2.5 - - - +
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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