Contacts of the helix formed by residues 164 - 173 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ALA* 4.0 21.2 - - - +
163A VAL* 1.3 79.4 - - - +
165A GLU* 1.3 67.0 + - - +
166A GLU* 4.2 1.2 + - - +
167A VAL* 3.4 25.6 + - - +
168A CYS* 2.9 19.8 + - - +
96B ARG* 5.9 2.9 - - - -
97B PRO* 5.9 1.0 - - - +
165G GLU* 3.3 16.7 + - - -
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Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A VAL 3.6 1.6 + - - -
164A SER* 1.3 73.1 - - - +
166A GLU* 1.3 64.6 + - - +
168A CYS* 3.1 6.9 + - - +
169A SER* 2.8 26.6 + - - -
176A TYR* 3.8 24.9 + - + +
164G SER* 3.2 19.3 - - - -
165G GLU* 3.4 25.4 + - + +
166G GLU* 2.9 35.9 + - + +
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Residues in contact with GLU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A SER* 4.2 1.9 + - - +
165A GLU* 1.3 75.6 - - - +
167A VAL* 1.3 73.5 + - + +
169A SER* 3.2 6.3 + - - -
170A LYS* 3.0 49.7 + - + +
174B PRO* 5.3 3.8 - - + +
165G GLU* 2.7 27.1 + - + +
166G GLU* 5.1 0.9 - - - +
169G SER* 3.6 17.7 - - - +
176G TYR* 2.7 43.0 + - - +
178G PRO* 4.7 8.7 - - - +
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A VAL* 3.9 17.7 - - + -
164A SER* 3.1 19.5 + - - +
166A GLU* 1.3 86.1 - - + +
168A CYS* 1.4 55.8 + - - +
171A LEU* 2.7 56.6 + - + +
97B PRO* 5.1 12.3 - - + -
98B LEU* 4.6 8.7 - - + +
174B PRO* 3.9 23.8 - - + +
175B LEU* 4.0 20.6 - - + -
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Residues in contact with CYS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A VAL* 4.5 1.5 - - - +
164A SER 2.9 14.2 + - - +
165A GLU* 3.5 10.5 - - - +
167A VAL* 1.4 77.8 - - - +
169A SER* 1.3 67.1 + - - +
171A LEU* 3.0 6.1 + - - +
172A TYR* 2.8 29.3 + - - +
176A TYR* 3.6 26.7 - - + -
181A PHE* 4.0 2.9 - - - -
182A CYS* 2.0 63.3 - - + +
227A VAL* 5.3 2.9 - - - -
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLU 2.8 19.5 + - - -
166A GLU* 3.2 6.8 + - - -
168A CYS* 1.3 75.7 - - - +
170A LYS* 1.3 60.5 + - - +
173A ASP* 2.8 32.2 + - - +
176A TYR* 3.4 35.9 - - - +
166G GLU* 3.7 30.5 - - - +
169G SER* 5.2 0.3 + - - -
170G LYS* 4.0 8.4 + - - -
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Residues in contact with LYS 170 (chain A).
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* 3.0 37.8 + - + +
169A SER* 1.3 80.4 - - - +
171A LEU* 1.3 68.7 + - - +
172A TYR 3.0 1.0 + - - -
173A ASP* 3.4 14.7 + - - +
173B ASP* 4.4 7.7 + - - +
174B PRO* 3.5 37.7 - - + +
169G SER* 3.8 24.5 + - - -
170G LYS* 4.3 23.1 - - - +
173G ASP* 3.1 28.1 + - - +
176G TYR* 5.5 0.4 - - - +
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A VAL* 2.7 38.6 + - + +
168A CYS* 3.6 3.4 - - - +
170A LYS* 1.3 76.2 - - - +
172A TYR* 1.3 65.7 + - + +
173A ASP 3.6 1.6 - - - +
217A LYS* 3.1 33.1 + - - +
223A GLY 3.3 26.7 - - - +
224A VAL* 5.4 4.7 - - + -
225A PRO* 3.4 23.3 - - + -
98B LEU* 5.2 0.2 - - + -
173B ASP 5.6 0.2 - - - +
174B PRO* 4.1 19.7 - - + +
175B LEU* 4.5 9.2 - - + -
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Residues in contact with TYR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A CYS* 2.8 13.2 + - - +
169A SER 3.7 0.7 - - - -
171A LEU* 1.3 87.9 - - + +
173A ASP* 1.3 64.5 + - - +
175A LEU* 2.9 30.7 + - + +
176A TYR* 3.0 20.7 + - + +
180A MET* 6.3 0.2 - - - -
182A CYS* 3.8 23.8 - - - -
215A PHE* 3.8 23.1 - + + -
216A GLY* 3.6 4.9 - - - -
217A LYS* 3.4 44.9 + - + +
224A VAL* 4.3 5.5 - - + +
225A PRO* 2.7 37.3 + - + -
227A VAL* 3.6 21.4 - - + +
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Residues in contact with ASP 173 (chain A).
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 2.8 17.9 + - - +
170A LYS* 3.4 12.8 + - - +
171A LEU 4.8 1.4 - - - +
172A TYR* 1.3 79.5 - - - +
174A PRO* 1.3 78.9 - - - +
176A TYR* 4.4 2.7 - - - +
170D LYS* 4.7 6.9 - - - +
170G LYS* 2.9 28.2 + - - +
173H ASP* 5.0 7.8 - - - +
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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