Contacts of the helix formed by residues 164 - 173 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ALA* 3.9 22.3 - - - +
163B VAL* 1.3 79.1 - - - +
165B GLU* 1.3 67.3 + - - +
166B GLU* 4.2 2.6 + - - +
167B VAL* 3.3 24.9 + - - +
168B CYS* 2.8 21.5 + - - +
96C ARG* 5.0 6.6 - - - +
97C PRO* 5.3 6.1 - - - +
98C LEU 5.7 1.1 + - - +
165F GLU* 3.4 15.0 + - - -
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL 3.5 1.6 + - - -
164B SER* 1.3 73.8 - - - +
166B GLU* 1.3 58.6 + - - +
168B CYS* 3.4 5.8 - - - +
169B SER* 2.8 32.1 + - - -
176B TYR* 3.8 23.9 + - + +
164F SER* 3.3 14.0 - - - -
165F GLU* 3.1 32.8 + - - +
166F GLU* 2.7 37.5 + - + +
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER* 4.2 3.2 + - - +
165B GLU* 1.3 70.4 - - - +
167B VAL* 1.3 76.2 + - + +
169B SER* 3.2 6.7 + - - -
170B LYS* 3.0 52.8 + - + +
174C PRO* 5.6 2.4 - - + +
165F GLU* 2.8 24.1 + - - +
166F GLU* 5.3 0.4 - - - +
169F SER* 3.7 20.6 - - - +
176F TYR* 2.8 41.8 + - - +
178F PRO* 4.7 10.0 - - - +
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 3.9 17.3 - - + -
164B SER* 3.1 20.7 + - - +
166B GLU* 1.3 83.0 - - + +
168B CYS* 1.4 55.4 + - - +
170B LYS* 4.0 0.5 - - - +
171B LEU* 2.8 56.9 + - + +
97C PRO* 4.7 16.8 - - + -
98C LEU* 4.4 5.8 - - + +
174C PRO* 4.3 21.5 - - + +
175C LEU* 3.9 21.3 - - + -
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Residues in contact with CYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 4.4 1.5 - - - +
164B SER 2.8 14.5 + - - +
165B GLU* 3.4 11.9 - - - +
167B VAL* 1.4 81.5 - - - +
169B SER* 1.3 63.1 + - - +
171B LEU* 3.3 4.3 + - - +
172B TYR* 3.1 25.2 + - - +
176B TYR* 3.7 25.8 - - + -
181B PHE* 3.9 2.5 - - - -
182B CYS* 2.1 63.7 - - + +
227B VAL* 5.6 2.2 - - - -
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Residues in contact with SER 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLU 2.8 19.8 + - - -
166B GLU* 3.2 8.3 + - - -
168B CYS* 1.3 73.9 - - - +
170B LYS* 1.3 59.8 + - - +
172B TYR 3.8 0.2 - - - -
173B ASP* 2.9 31.0 + - - +
176B TYR* 3.3 38.3 - - - +
166F GLU* 3.7 26.8 - - - +
169F SER* 4.9 0.9 + - - -
170F LYS* 3.8 8.3 + - - -
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Residues in contact with LYS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLU* 3.0 49.0 + - + +
169B SER* 1.3 79.8 - - - +
171B LEU* 1.3 68.4 + - - +
172B TYR 3.0 1.0 + - - -
173B ASP* 3.4 14.8 + - - +
173C ASP* 4.9 4.3 - - - +
174C PRO* 3.7 34.1 - - + +
169F SER* 3.9 19.9 + - - -
170F LYS* 4.4 18.4 - - - +
173F ASP* 2.9 32.3 + - - +
176F TYR* 5.5 0.4 - - - +
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B VAL* 2.8 36.3 + - + +
168B CYS 3.6 4.0 - - - +
170B LYS* 1.3 80.4 - - - +
172B TYR* 1.3 65.6 + - + +
173B ASP 4.9 1.3 - - - +
217B LYS* 3.1 33.2 + - - +
223B GLY 3.4 26.2 - - - +
224B VAL* 5.4 4.5 - - + -
225B PRO* 3.4 25.1 - - + -
98C LEU* 4.8 0.4 - - + -
174C PRO* 4.2 17.2 - - + +
175C LEU* 4.7 8.7 - - + -
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Residues in contact with TYR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B CYS 3.1 18.8 + - - +
169B SER 3.8 1.1 - - - -
170B LYS 3.1 0.2 - - - -
171B LEU* 1.3 85.6 - - + +
173B ASP* 1.3 69.3 + - - +
175B LEU* 2.9 24.4 + - + +
176B TYR* 3.1 20.0 + - + +
180B MET* 6.3 0.4 - - - -
182B CYS* 3.9 17.7 - - - -
215B PHE* 3.9 22.2 - + + -
216B GLY* 3.6 4.5 - - - -
217B LYS* 3.4 46.1 + - + +
224B VAL* 4.2 5.8 - - + +
225B PRO* 2.7 37.3 + - + -
227B VAL* 3.7 21.3 - - + +
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Residues in contact with ASP 173 (chain B).
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* 4.4 8.1 - - - +
171A LEU* 5.6 0.5 - - - +
169B SER 2.9 19.3 + - - +
170B LYS* 3.4 12.9 + - - +
171B LEU 4.9 1.4 - - - +
172B TYR* 1.3 80.1 - - - +
174B PRO* 1.3 78.4 - - - +
176B TYR* 4.3 2.9 - - - +
170F LYS* 2.9 27.9 + - - +
173G ASP* 4.8 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